Starting phenix.real_space_refine on Tue Feb 20 11:57:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yxu_10996/02_2024/6yxu_10996.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yxu_10996/02_2024/6yxu_10996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yxu_10996/02_2024/6yxu_10996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yxu_10996/02_2024/6yxu_10996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yxu_10996/02_2024/6yxu_10996.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yxu_10996/02_2024/6yxu_10996.pdb" } resolution = 3.08 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= 0.003 sd= 0.026 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 97 5.16 5 C 17396 2.51 5 N 4943 2.21 5 O 5352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 6": "NH1" <-> "NH2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 98": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 98": "NH1" <-> "NH2" Residue "B TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C GLU 112": "OE1" <-> "OE2" Residue "C ASP 117": "OD1" <-> "OD2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C ARG 199": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C ARG 389": "NH1" <-> "NH2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "C GLU 462": "OE1" <-> "OE2" Residue "C ARG 473": "NH1" <-> "NH2" Residue "C ARG 496": "NH1" <-> "NH2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C ARG 604": "NH1" <-> "NH2" Residue "C ARG 664": "NH1" <-> "NH2" Residue "C ARG 678": "NH1" <-> "NH2" Residue "C ARG 686": "NH1" <-> "NH2" Residue "C GLU 688": "OE1" <-> "OE2" Residue "C GLU 759": "OE1" <-> "OE2" Residue "C ARG 762": "NH1" <-> "NH2" Residue "C ARG 788": "NH1" <-> "NH2" Residue "C ARG 861": "NH1" <-> "NH2" Residue "C TYR 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 916": "NH1" <-> "NH2" Residue "C ASP 945": "OD1" <-> "OD2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ARG 1058": "NH1" <-> "NH2" Residue "D ASP 8": "OD1" <-> "OD2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 164": "OD1" <-> "OD2" Residue "D ASP 167": "OD1" <-> "OD2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "D ARG 427": "NH1" <-> "NH2" Residue "D ARG 459": "NH1" <-> "NH2" Residue "D GLU 477": "OE1" <-> "OE2" Residue "D ARG 478": "NH1" <-> "NH2" Residue "D GLU 513": "OE1" <-> "OE2" Residue "D ARG 578": "NH1" <-> "NH2" Residue "D TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 630": "NH1" <-> "NH2" Residue "D GLU 639": "OE1" <-> "OE2" Residue "D ARG 694": "NH1" <-> "NH2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "D ARG 725": "NH1" <-> "NH2" Residue "D GLU 751": "OE1" <-> "OE2" Residue "D ARG 833": "NH1" <-> "NH2" Residue "D ARG 840": "NH1" <-> "NH2" Residue "D ASP 861": "OD1" <-> "OD2" Residue "D ARG 865": "NH1" <-> "NH2" Residue "D ARG 939": "NH1" <-> "NH2" Residue "D GLU 1037": "OE1" <-> "OE2" Residue "D ARG 1039": "NH1" <-> "NH2" Residue "D ARG 1084": "NH1" <-> "NH2" Residue "D GLU 1097": "OE1" <-> "OE2" Residue "D ASP 1102": "OD1" <-> "OD2" Residue "D GLU 1107": "OE1" <-> "OE2" Residue "D ARG 1160": "NH1" <-> "NH2" Residue "D ARG 1164": "NH1" <-> "NH2" Residue "D ASP 1170": "OD1" <-> "OD2" Residue "D GLU 1186": "OE1" <-> "OE2" Residue "D PHE 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1192": "NH1" <-> "NH2" Residue "D ARG 1193": "NH1" <-> "NH2" Residue "D GLU 1200": "OE1" <-> "OE2" Residue "D ARG 1205": "NH1" <-> "NH2" Residue "D GLU 1278": "OE1" <-> "OE2" Residue "D ARG 1280": "NH1" <-> "NH2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E ASP 63": "OD1" <-> "OD2" Residue "E ARG 94": "NH1" <-> "NH2" Residue "H ARG 4": "NH1" <-> "NH2" Residue "H ARG 28": "NH1" <-> "NH2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H ARG 40": "NH1" <-> "NH2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "H ASP 80": "OD1" <-> "OD2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "H ARG 105": "NH1" <-> "NH2" Residue "H ARG 126": "NH1" <-> "NH2" Residue "H ARG 134": "NH1" <-> "NH2" Residue "H ARG 146": "NH1" <-> "NH2" Residue "H GLU 170": "OE1" <-> "OE2" Residue "H ARG 188": "NH1" <-> "NH2" Residue "H ARG 212": "NH1" <-> "NH2" Residue "H ARG 226": "NH1" <-> "NH2" Residue "H ARG 244": "NH1" <-> "NH2" Residue "H GLU 340": "OE1" <-> "OE2" Residue "H ARG 364": "NH1" <-> "NH2" Residue "H ARG 374": "NH1" <-> "NH2" Residue "H GLU 382": "OE1" <-> "OE2" Residue "H GLU 385": "OE1" <-> "OE2" Residue "H ASP 392": "OD1" <-> "OD2" Residue "H ARG 415": "NH1" <-> "NH2" Residue "H ARG 448": "NH1" <-> "NH2" Residue "H ARG 458": "NH1" <-> "NH2" Residue "H ARG 461": "NH1" <-> "NH2" Residue "H GLU 509": "OE1" <-> "OE2" Residue "H ARG 513": "NH1" <-> "NH2" Residue "H GLU 529": "OE1" <-> "OE2" Residue "H GLU 532": "OE1" <-> "OE2" Residue "H ARG 559": "NH1" <-> "NH2" Residue "H ARG 566": "NH1" <-> "NH2" Residue "H GLU 605": "OE1" <-> "OE2" Residue "H ARG 617": "NH1" <-> "NH2" Residue "H ASP 658": "OD1" <-> "OD2" Residue "H ARG 683": "NH1" <-> "NH2" Residue "H ARG 701": "NH1" <-> "NH2" Residue "H ARG 711": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27791 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1716 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1771 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 218} Chain: "C" Number of atoms: 8424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8424 Classifications: {'peptide': 1088} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1029} Chain breaks: 1 Chain: "D" Number of atoms: 9916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1269, 9916 Classifications: {'peptide': 1269} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1211} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 597 Classifications: {'peptide': 76} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Chain: "H" Number of atoms: 5364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 5364 Classifications: {'peptide': 691} Link IDs: {'PTRANS': 37, 'TRANS': 653} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18930 SG CYS D 890 33.456 60.993 73.228 1.00 32.00 S ATOM 19492 SG CYS D 967 36.092 63.495 74.347 1.00 28.17 S ATOM 19534 SG CYS D 974 34.356 61.442 76.692 1.00 27.00 S ATOM 19553 SG CYS D 977 36.549 59.645 74.829 1.00 27.54 S ATOM 12370 SG CYS D 60 30.262 122.681 90.178 1.00 86.44 S ATOM 12388 SG CYS D 62 30.566 126.995 89.395 1.00 90.65 S ATOM 12497 SG CYS D 75 27.720 124.667 87.668 1.00 85.19 S ATOM 12523 SG CYS D 78 31.209 123.643 86.501 1.00 86.40 S Time building chain proxies: 14.79, per 1000 atoms: 0.53 Number of scatterers: 27791 At special positions: 0 Unit cell: (137.963, 149.598, 168.713, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 97 16.00 Mg 1 11.99 O 5352 8.00 N 4943 7.00 C 17396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.94 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 974 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 977 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 890 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 967 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 62 " Number of angles added : 12 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6606 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 42 sheets defined 37.8% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 203 through 225 removed outlier: 3.510A pdb=" N ALA A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.930A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.617A pdb=" N ILE B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 Processing helix chain 'C' and resid 45 through 55 removed outlier: 3.697A pdb=" N THR C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 67 Processing helix chain 'C' and resid 76 through 85 removed outlier: 3.759A pdb=" N VAL C 80 " --> pdb=" O GLY C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 117 Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.973A pdb=" N LEU C 228 " --> pdb=" O PRO C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 246 through 255 removed outlier: 3.507A pdb=" N MET C 250 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 279 through 292 removed outlier: 4.171A pdb=" N PHE C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 325 through 341 removed outlier: 3.616A pdb=" N VAL C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE C 333 " --> pdb=" O VAL C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 394 Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.671A pdb=" N LEU C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 422 Processing helix chain 'C' and resid 435 through 444 Processing helix chain 'C' and resid 523 through 529 removed outlier: 3.772A pdb=" N ARG C 529 " --> pdb=" O ASP C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 604 Processing helix chain 'C' and resid 621 through 630 removed outlier: 3.566A pdb=" N ALA C 625 " --> pdb=" O MET C 621 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 891 through 895 removed outlier: 3.595A pdb=" N MET C 895 " --> pdb=" O VAL C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 933 Processing helix chain 'C' and resid 972 through 983 removed outlier: 3.665A pdb=" N LEU C 976 " --> pdb=" O GLN C 972 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 982 " --> pdb=" O GLY C 978 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR C 983 " --> pdb=" O LEU C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1032 removed outlier: 3.839A pdb=" N ILE C1032 " --> pdb=" O ASP C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1060 through 1070 Processing helix chain 'C' and resid 1073 through 1081 Processing helix chain 'C' and resid 1087 through 1100 Processing helix chain 'C' and resid 1115 through 1120 Processing helix chain 'D' and resid 16 through 23 removed outlier: 3.750A pdb=" N ILE D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 89 removed outlier: 3.627A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 147 through 186 Processing helix chain 'D' and resid 190 through 227 removed outlier: 3.748A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 246 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 270 through 284 Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.683A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL D 299 " --> pdb=" O ARG D 295 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.897A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 360 Processing helix chain 'D' and resid 363 through 384 removed outlier: 3.764A pdb=" N VAL D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 444 through 452 removed outlier: 3.553A pdb=" N ALA D 448 " --> pdb=" O PRO D 444 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 464 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 486 through 491 removed outlier: 3.531A pdb=" N ILE D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 578 through 589 Processing helix chain 'D' and resid 614 through 623 removed outlier: 3.674A pdb=" N MET D 620 " --> pdb=" O ALA D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 650 Processing helix chain 'D' and resid 666 through 674 Processing helix chain 'D' and resid 688 through 703 Processing helix chain 'D' and resid 704 through 722 removed outlier: 4.003A pdb=" N VAL D 708 " --> pdb=" O PRO D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 762 removed outlier: 3.697A pdb=" N GLU D 751 " --> pdb=" O ARG D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 778 Processing helix chain 'D' and resid 778 through 792 removed outlier: 3.730A pdb=" N GLU D 782 " --> pdb=" O GLN D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 804 removed outlier: 3.999A pdb=" N VAL D 802 " --> pdb=" O ILE D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 818 removed outlier: 3.546A pdb=" N THR D 813 " --> pdb=" O ASN D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 851 Processing helix chain 'D' and resid 851 through 880 removed outlier: 3.968A pdb=" N ALA D 855 " --> pdb=" O ASN D 851 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ALA D 863 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU D 864 " --> pdb=" O ALA D 860 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR D 866 " --> pdb=" O THR D 862 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER D 880 " --> pdb=" O LEU D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 916 removed outlier: 4.450A pdb=" N GLU D 916 " --> pdb=" O ALA D 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 913 through 916' Processing helix chain 'D' and resid 944 through 950 Processing helix chain 'D' and resid 963 through 967 Processing helix chain 'D' and resid 975 through 979 Processing helix chain 'D' and resid 993 through 1004 removed outlier: 3.968A pdb=" N VAL D 997 " --> pdb=" O ALA D 993 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1009 Processing helix chain 'D' and resid 1028 through 1037 Processing helix chain 'D' and resid 1118 through 1126 Processing helix chain 'D' and resid 1127 through 1145 Processing helix chain 'D' and resid 1151 through 1163 removed outlier: 4.311A pdb=" N ILE D1155 " --> pdb=" O HIS D1151 " (cutoff:3.500A) Processing helix chain 'D' and resid 1184 through 1194 Processing helix chain 'D' and resid 1221 through 1228 Processing helix chain 'D' and resid 1229 through 1240 Processing helix chain 'D' and resid 1249 through 1256 Processing helix chain 'D' and resid 1265 through 1270 removed outlier: 3.611A pdb=" N ASN D1270 " --> pdb=" O SER D1266 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.505A pdb=" N ARG E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA E 44 " --> pdb=" O LEU E 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 39 through 44' Processing helix chain 'E' and resid 46 through 67 removed outlier: 4.048A pdb=" N ARG E 57 " --> pdb=" O TYR E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 98 Processing helix chain 'H' and resid 4 through 41 Processing helix chain 'H' and resid 45 through 67 Processing helix chain 'H' and resid 156 through 163 Processing helix chain 'H' and resid 170 through 188 removed outlier: 3.738A pdb=" N ASP H 174 " --> pdb=" O GLU H 170 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE H 175 " --> pdb=" O GLY H 171 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL H 176 " --> pdb=" O MET H 172 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA H 177 " --> pdb=" O ARG H 173 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR H 178 " --> pdb=" O ASP H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 220 Processing helix chain 'H' and resid 235 through 245 Processing helix chain 'H' and resid 274 through 280 Processing helix chain 'H' and resid 284 through 293 removed outlier: 3.719A pdb=" N VAL H 288 " --> pdb=" O LYS H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 329 Processing helix chain 'H' and resid 337 through 358 removed outlier: 4.055A pdb=" N ARG H 352 " --> pdb=" O VAL H 348 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA H 353 " --> pdb=" O VAL H 349 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA H 355 " --> pdb=" O GLU H 351 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG H 356 " --> pdb=" O ARG H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 382 Processing helix chain 'H' and resid 386 through 395 Processing helix chain 'H' and resid 399 through 409 removed outlier: 3.779A pdb=" N LEU H 404 " --> pdb=" O PRO H 400 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA H 405 " --> pdb=" O GLU H 401 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR H 409 " --> pdb=" O ALA H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 418 removed outlier: 3.782A pdb=" N GLY H 418 " --> pdb=" O ARG H 415 " (cutoff:3.500A) Processing helix chain 'H' and resid 436 through 447 removed outlier: 3.521A pdb=" N VAL H 443 " --> pdb=" O LEU H 439 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP H 444 " --> pdb=" O ASP H 440 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU H 445 " --> pdb=" O GLU H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 450 through 465 Processing helix chain 'H' and resid 509 through 516 Processing helix chain 'H' and resid 529 through 533 removed outlier: 3.567A pdb=" N GLU H 532 " --> pdb=" O GLU H 529 " (cutoff:3.500A) Processing helix chain 'H' and resid 534 through 545 Processing helix chain 'H' and resid 555 through 559 Processing helix chain 'H' and resid 568 through 573 Processing helix chain 'H' and resid 593 through 604 removed outlier: 4.013A pdb=" N VAL H 598 " --> pdb=" O GLU H 594 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA H 599 " --> pdb=" O ILE H 595 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA H 601 " --> pdb=" O ALA H 597 " (cutoff:3.500A) Processing helix chain 'H' and resid 633 through 645 removed outlier: 4.274A pdb=" N GLU H 639 " --> pdb=" O SER H 635 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE H 640 " --> pdb=" O ALA H 636 " (cutoff:3.500A) Processing helix chain 'H' and resid 680 through 687 removed outlier: 3.750A pdb=" N ILE H 684 " --> pdb=" O GLU H 680 " (cutoff:3.500A) Processing helix chain 'H' and resid 691 through 699 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 10 Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.042A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 53 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU A 141 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL A 51 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY A 143 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ALA A 49 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA5, first strand: chain 'B' and resid 8 through 13 removed outlier: 5.906A pdb=" N ARG B 18 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N THR B 198 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ARG B 20 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL B 196 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL B 22 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE B 194 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 98 removed outlier: 7.768A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 105 through 106 removed outlier: 3.788A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AA9, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.615A pdb=" N VAL C 30 " --> pdb=" O ALA C 964 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 87 through 88 removed outlier: 5.928A pdb=" N LEU C 96 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE C 131 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N PHE C 98 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLU C 129 " --> pdb=" O PHE C 98 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASP C 100 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR C 127 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY C 146 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL C 126 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N PHE C 144 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ALA C 128 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR C 142 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AB3, first strand: chain 'C' and resid 367 through 370 removed outlier: 3.603A pdb=" N SER C 168 " --> pdb=" O ARG C 445 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 175 through 176 removed outlier: 3.642A pdb=" N SER C 192 " --> pdb=" O ASP C 179 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 175 through 176 removed outlier: 3.687A pdb=" N HIS C 191 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE C 205 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 203 " --> pdb=" O VAL C 195 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 346 through 347 Processing sheet with id=AB7, first strand: chain 'C' and resid 496 through 497 removed outlier: 6.719A pdb=" N ILE C 503 " --> pdb=" O LEU C 522 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU C 522 " --> pdb=" O ILE C 503 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR C 505 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP C 520 " --> pdb=" O THR C 505 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR C 507 " --> pdb=" O GLN C 518 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN C 518 " --> pdb=" O TYR C 507 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS C 509 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 496 through 497 Processing sheet with id=AB9, first strand: chain 'C' and resid 550 through 553 Processing sheet with id=AC1, first strand: chain 'C' and resid 633 through 634 removed outlier: 6.537A pdb=" N VAL C 633 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 658 through 662 removed outlier: 6.146A pdb=" N MET C 652 " --> pdb=" O ILE C 641 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE C 641 " --> pdb=" O MET C 652 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 998 through 999 removed outlier: 7.514A pdb=" N ILE C 726 " --> pdb=" O GLY C 887 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE C 889 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU C 728 " --> pdb=" O ILE C 889 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 727 " --> pdb=" O ILE C 907 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ILE C 906 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU C 711 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU C 908 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA C 713 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR C1015 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 740 through 751 removed outlier: 8.234A pdb=" N ASN C 857 " --> pdb=" O SER C 845 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N SER C 845 " --> pdb=" O ASN C 857 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU C 859 " --> pdb=" O VAL C 843 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL C 843 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG C 861 " --> pdb=" O ILE C 841 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE C 841 " --> pdb=" O ARG C 861 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR C 863 " --> pdb=" O ILE C 839 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY C 836 " --> pdb=" O VAL C 787 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 792 through 794 removed outlier: 3.745A pdb=" N VAL C 794 " --> pdb=" O LEU C 828 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 935 through 936 Processing sheet with id=AC7, first strand: chain 'C' and resid 1033 through 1035 removed outlier: 6.222A pdb=" N CYS D 441 " --> pdb=" O GLN D 515 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1127 through 1129 Processing sheet with id=AC9, first strand: chain 'D' and resid 24 through 27 removed outlier: 4.514A pdb=" N SER D 24 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N HIS D 94 " --> pdb=" O SER D 24 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLY D 26 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY D 93 " --> pdb=" O VAL D 319 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AD2, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.654A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 327 through 329 Processing sheet with id=AD4, first strand: chain 'D' and resid 633 through 637 Processing sheet with id=AD5, first strand: chain 'D' and resid 885 through 887 removed outlier: 3.511A pdb=" N ARG D 886 " --> pdb=" O VAL D 973 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 896 through 899 Processing sheet with id=AD7, first strand: chain 'D' and resid 901 through 902 Processing sheet with id=AD8, first strand: chain 'D' and resid 922 through 923 removed outlier: 4.268A pdb=" N ARG D 922 " --> pdb=" O LEU D 943 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1044 through 1045 Processing sheet with id=AE1, first strand: chain 'D' and resid 1076 through 1082 removed outlier: 4.153A pdb=" N LYS D1080 " --> pdb=" O PHE D1063 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE D1063 " --> pdb=" O LYS D1080 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1181 through 1183 removed outlier: 5.308A pdb=" N ILE D1168 " --> pdb=" O ARG D1205 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ARG D1205 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1272 through 1275 removed outlier: 3.524A pdb=" N THR E 104 " --> pdb=" O GLN D1272 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN D1274 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 90 through 92 removed outlier: 6.316A pdb=" N ILE H 90 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP H 92 " --> pdb=" O GLU H 98 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU H 98 " --> pdb=" O ASP H 92 " (cutoff:3.500A) removed outlier: 9.215A pdb=" N ARG H 82 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU H 102 " --> pdb=" O ARG H 82 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR H 84 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY H 73 " --> pdb=" O ILE H 85 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N PHE H 72 " --> pdb=" O GLN H 128 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLN H 128 " --> pdb=" O PHE H 72 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG H 74 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG H 126 " --> pdb=" O ARG H 74 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP H 76 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP H 138 " --> pdb=" O HIS H 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 254 through 257 removed outlier: 6.497A pdb=" N VAL H 229 " --> pdb=" O VAL H 255 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N MET H 257 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL H 231 " --> pdb=" O MET H 257 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU H 230 " --> pdb=" O VAL H 526 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VAL H 525 " --> pdb=" O THR H 551 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL H 194 " --> pdb=" O VAL H 581 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 653 through 654 1083 hydrogen bonds defined for protein. 3033 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: 10.89 Time building geometry restraints manager: 11.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9639 1.34 - 1.46: 5676 1.46 - 1.58: 12781 1.58 - 1.70: 0 1.70 - 1.82: 172 Bond restraints: 28268 Sorted by residual: bond pdb=" C HIS D 544 " pdb=" N LEU D 545 " ideal model delta sigma weight residual 1.332 1.294 0.038 1.44e-02 4.82e+03 7.06e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.59e+00 bond pdb=" CB VAL D1131 " pdb=" CG2 VAL D1131 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.45e+00 bond pdb=" CG1 ILE C 158 " pdb=" CD1 ILE C 158 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.09e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 2.04e+00 ... (remaining 28263 not shown) Histogram of bond angle deviations from ideal: 97.60 - 104.90: 590 104.90 - 112.21: 14014 112.21 - 119.51: 9615 119.51 - 126.82: 13780 126.82 - 134.12: 324 Bond angle restraints: 38323 Sorted by residual: angle pdb=" N VAL D1195 " pdb=" CA VAL D1195 " pdb=" C VAL D1195 " ideal model delta sigma weight residual 112.12 107.06 5.06 8.40e-01 1.42e+00 3.63e+01 angle pdb=" N ILE C1043 " pdb=" CA ILE C1043 " pdb=" C ILE C1043 " ideal model delta sigma weight residual 113.71 108.57 5.14 9.50e-01 1.11e+00 2.93e+01 angle pdb=" N ARG D 624 " pdb=" CA ARG D 624 " pdb=" C ARG D 624 " ideal model delta sigma weight residual 114.04 110.02 4.02 1.24e+00 6.50e-01 1.05e+01 angle pdb=" CA PHE C 422 " pdb=" C PHE C 422 " pdb=" N GLY C 423 " ideal model delta sigma weight residual 118.27 113.41 4.86 1.59e+00 3.96e-01 9.35e+00 angle pdb=" N ILE D1169 " pdb=" CA ILE D1169 " pdb=" C ILE D1169 " ideal model delta sigma weight residual 111.62 109.39 2.23 7.90e-01 1.60e+00 7.96e+00 ... (remaining 38318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 15644 17.97 - 35.93: 1385 35.93 - 53.90: 202 53.90 - 71.87: 45 71.87 - 89.83: 26 Dihedral angle restraints: 17302 sinusoidal: 7039 harmonic: 10263 Sorted by residual: dihedral pdb=" CA ALA H 563 " pdb=" C ALA H 563 " pdb=" N GLY H 564 " pdb=" CA GLY H 564 " ideal model delta harmonic sigma weight residual 180.00 152.96 27.04 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ASP H 174 " pdb=" C ASP H 174 " pdb=" N ILE H 175 " pdb=" CA ILE H 175 " ideal model delta harmonic sigma weight residual -180.00 -154.06 -25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA GLN D 600 " pdb=" C GLN D 600 " pdb=" N ALA D 601 " pdb=" CA ALA D 601 " ideal model delta harmonic sigma weight residual 180.00 156.89 23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 17299 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2524 0.032 - 0.064: 1255 0.064 - 0.095: 394 0.095 - 0.127: 167 0.127 - 0.159: 16 Chirality restraints: 4356 Sorted by residual: chirality pdb=" CA PRO H 333 " pdb=" N PRO H 333 " pdb=" C PRO H 333 " pdb=" CB PRO H 333 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA ILE C 319 " pdb=" N ILE C 319 " pdb=" C ILE C 319 " pdb=" CB ILE C 319 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE B 193 " pdb=" N ILE B 193 " pdb=" C ILE B 193 " pdb=" CB ILE B 193 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 ... (remaining 4353 not shown) Planarity restraints: 5073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 246 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO H 247 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO H 247 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO H 247 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 895 " -0.045 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO C 896 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 896 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 896 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 223 " -0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO C 224 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 224 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 224 " -0.035 5.00e-02 4.00e+02 ... (remaining 5070 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 160 2.47 - 3.08: 20622 3.08 - 3.68: 39577 3.68 - 4.29: 61267 4.29 - 4.90: 103683 Nonbonded interactions: 225309 Sorted by model distance: nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D2003 " model vdw 1.862 2.170 nonbonded pdb=" OH TYR C1070 " pdb=" O ILE D 509 " model vdw 1.976 2.440 nonbonded pdb=" OH TYR A 176 " pdb=" O GLY C1007 " model vdw 2.031 2.440 nonbonded pdb=" OD2 ASP H 253 " pdb=" OG SER H 511 " model vdw 2.062 2.440 nonbonded pdb=" O SER C 173 " pdb=" OH TYR C 177 " model vdw 2.075 2.440 ... (remaining 225304 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.910 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 77.810 Find NCS groups from input model: 1.000 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 28268 Z= 0.382 Angle : 0.673 6.214 38323 Z= 0.372 Chirality : 0.043 0.159 4356 Planarity : 0.006 0.069 5073 Dihedral : 13.999 89.832 10696 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.43 % Favored : 90.54 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -4.95 (0.11), residues: 3563 helix: -3.11 (0.10), residues: 1334 sheet: -2.16 (0.22), residues: 400 loop : -3.78 (0.11), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 61 HIS 0.007 0.001 HIS H 368 PHE 0.025 0.002 PHE C 364 TYR 0.037 0.002 TYR E 53 ARG 0.011 0.001 ARG H 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.4939 time to fit residues: 232.8247 Evaluate side-chains 180 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 299 optimal weight: 7.9990 chunk 269 optimal weight: 20.0000 chunk 149 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 322 optimal weight: 8.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 470 HIS D 213 GLN D 245 GLN D 515 GLN D 760 GLN H 130 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28268 Z= 0.274 Angle : 0.633 7.787 38323 Z= 0.329 Chirality : 0.045 0.175 4356 Planarity : 0.006 0.060 5073 Dihedral : 4.964 24.941 3932 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.97 % Allowed : 7.52 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.74 (0.13), residues: 3563 helix: -1.05 (0.13), residues: 1339 sheet: -1.38 (0.23), residues: 421 loop : -2.58 (0.13), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 361 HIS 0.006 0.001 HIS D 505 PHE 0.016 0.002 PHE C 364 TYR 0.030 0.002 TYR E 53 ARG 0.007 0.001 ARG C 662 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 191 time to evaluate : 3.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 462 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7607 (mp0) outliers start: 29 outliers final: 16 residues processed: 210 average time/residue: 0.4288 time to fit residues: 141.2993 Evaluate side-chains 177 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 160 time to evaluate : 3.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 774 ASP Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 956 ILE Chi-restraints excluded: chain D residue 1163 LEU Chi-restraints excluded: chain D residue 1241 CYS Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 462 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 179 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 268 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 322 optimal weight: 8.9990 chunk 348 optimal weight: 10.0000 chunk 287 optimal weight: 4.9990 chunk 320 optimal weight: 0.9990 chunk 110 optimal weight: 0.0870 chunk 259 optimal weight: 4.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 HIS D 22 ASN ** D 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 766 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 28268 Z= 0.333 Angle : 0.615 9.120 38323 Z= 0.318 Chirality : 0.045 0.187 4356 Planarity : 0.005 0.061 5073 Dihedral : 4.687 23.822 3932 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 1.61 % Allowed : 9.94 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.75 (0.14), residues: 3563 helix: -0.11 (0.14), residues: 1326 sheet: -0.89 (0.25), residues: 423 loop : -2.07 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 58 HIS 0.007 0.001 HIS D 505 PHE 0.018 0.002 PHE D1187 TYR 0.019 0.002 TYR C1070 ARG 0.005 0.000 ARG D 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 171 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 406 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8678 (pp) outliers start: 48 outliers final: 25 residues processed: 211 average time/residue: 0.4277 time to fit residues: 141.7918 Evaluate side-chains 179 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 153 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 774 ASP Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain D residue 58 TRP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain D residue 1131 VAL Chi-restraints excluded: chain D residue 1241 CYS Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain H residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 319 optimal weight: 10.0000 chunk 242 optimal weight: 0.9990 chunk 167 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 324 optimal weight: 10.0000 chunk 343 optimal weight: 0.0670 chunk 169 optimal weight: 6.9990 chunk 307 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 overall best weight: 2.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 HIS ** D 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28268 Z= 0.242 Angle : 0.557 7.980 38323 Z= 0.286 Chirality : 0.043 0.191 4356 Planarity : 0.005 0.059 5073 Dihedral : 4.438 24.549 3932 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.02 % Allowed : 11.69 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.18 (0.14), residues: 3563 helix: 0.35 (0.15), residues: 1336 sheet: -0.58 (0.25), residues: 416 loop : -1.74 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 58 HIS 0.004 0.001 HIS D 505 PHE 0.012 0.001 PHE D 651 TYR 0.012 0.001 TYR C1070 ARG 0.006 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 164 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8048 (pp) REVERT: C 717 TRP cc_start: 0.9037 (OUTLIER) cc_final: 0.8573 (t60) REVERT: D 148 LEU cc_start: 0.5058 (OUTLIER) cc_final: 0.4686 (pp) outliers start: 60 outliers final: 30 residues processed: 217 average time/residue: 0.4053 time to fit residues: 140.2890 Evaluate side-chains 187 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 3.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 774 ASP Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 1241 CYS Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain H residue 273 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 285 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 chunk 4 optimal weight: 0.0570 chunk 255 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 292 optimal weight: 10.0000 chunk 237 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 175 optimal weight: 8.9990 chunk 307 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 overall best weight: 3.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 926 HIS ** D 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 28268 Z= 0.339 Angle : 0.601 9.108 38323 Z= 0.308 Chirality : 0.044 0.218 4356 Planarity : 0.005 0.056 5073 Dihedral : 4.525 24.457 3932 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.15 % Allowed : 12.87 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.01 (0.14), residues: 3563 helix: 0.43 (0.15), residues: 1341 sheet: -0.60 (0.24), residues: 443 loop : -1.57 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 58 HIS 0.006 0.001 HIS D 505 PHE 0.017 0.002 PHE D1187 TYR 0.019 0.002 TYR D 134 ARG 0.006 0.000 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 161 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8134 (pp) REVERT: C 717 TRP cc_start: 0.9108 (OUTLIER) cc_final: 0.8623 (t60) REVERT: D 406 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8771 (pp) REVERT: D 451 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7865 (mp) outliers start: 64 outliers final: 39 residues processed: 218 average time/residue: 0.4120 time to fit residues: 144.0172 Evaluate side-chains 194 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 151 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 764 ILE Chi-restraints excluded: chain C residue 774 ASP Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 470 LYS Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 906 ASP Chi-restraints excluded: chain D residue 956 ILE Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 1131 VAL Chi-restraints excluded: chain D residue 1241 CYS Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 273 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 115 optimal weight: 1.9990 chunk 309 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 201 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 343 optimal weight: 0.9990 chunk 285 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 180 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 GLN C 926 HIS D 233 GLN ** D 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28268 Z= 0.214 Angle : 0.547 8.937 38323 Z= 0.279 Chirality : 0.043 0.204 4356 Planarity : 0.004 0.058 5073 Dihedral : 4.334 24.759 3932 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.02 % Allowed : 13.67 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.72 (0.14), residues: 3563 helix: 0.67 (0.15), residues: 1343 sheet: -0.43 (0.25), residues: 424 loop : -1.39 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 58 HIS 0.003 0.001 HIS D 505 PHE 0.011 0.001 PHE D1187 TYR 0.012 0.001 TYR D 248 ARG 0.006 0.000 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 162 time to evaluate : 3.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8046 (pp) REVERT: C 717 TRP cc_start: 0.9084 (OUTLIER) cc_final: 0.8637 (t60) REVERT: D 74 ILE cc_start: 0.7212 (mm) cc_final: 0.6909 (tp) REVERT: D 256 MET cc_start: 0.5268 (ttt) cc_final: 0.4983 (ttt) REVERT: D 406 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8738 (pp) REVERT: E 63 ASP cc_start: 0.6652 (t0) cc_final: 0.6012 (t0) outliers start: 60 outliers final: 34 residues processed: 218 average time/residue: 0.3908 time to fit residues: 137.1257 Evaluate side-chains 187 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 3.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 1131 VAL Chi-restraints excluded: chain D residue 1241 CYS Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 273 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 331 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 195 optimal weight: 7.9990 chunk 250 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 289 optimal weight: 8.9990 chunk 191 optimal weight: 7.9990 chunk 342 optimal weight: 0.1980 chunk 214 optimal weight: 0.8980 chunk 208 optimal weight: 0.3980 chunk 157 optimal weight: 8.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 HIS ** D 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 28268 Z= 0.306 Angle : 0.583 9.085 38323 Z= 0.297 Chirality : 0.044 0.186 4356 Planarity : 0.004 0.057 5073 Dihedral : 4.402 24.365 3932 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.22 % Allowed : 13.97 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.14), residues: 3563 helix: 0.66 (0.15), residues: 1348 sheet: -0.41 (0.25), residues: 427 loop : -1.35 (0.15), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 58 HIS 0.004 0.001 HIS D 505 PHE 0.015 0.002 PHE D1187 TYR 0.015 0.001 TYR D 251 ARG 0.006 0.000 ARG D 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 158 time to evaluate : 3.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8119 (pp) REVERT: C 717 TRP cc_start: 0.9105 (OUTLIER) cc_final: 0.8660 (t60) REVERT: D 74 ILE cc_start: 0.7225 (mm) cc_final: 0.6929 (tp) REVERT: D 406 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8789 (pp) outliers start: 66 outliers final: 46 residues processed: 218 average time/residue: 0.3974 time to fit residues: 141.8468 Evaluate side-chains 203 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 154 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 774 ASP Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain D residue 6 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 906 ASP Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 1131 VAL Chi-restraints excluded: chain D residue 1241 CYS Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain H residue 403 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 211 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 204 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 217 optimal weight: 0.9980 chunk 233 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 268 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28268 Z= 0.246 Angle : 0.562 9.046 38323 Z= 0.286 Chirality : 0.043 0.236 4356 Planarity : 0.004 0.057 5073 Dihedral : 4.328 23.717 3932 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.91 % Allowed : 14.51 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.54 (0.14), residues: 3563 helix: 0.78 (0.15), residues: 1347 sheet: -0.33 (0.25), residues: 425 loop : -1.25 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 58 HIS 0.003 0.001 HIS D 505 PHE 0.013 0.001 PHE D1187 TYR 0.019 0.001 TYR D 251 ARG 0.007 0.000 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 156 time to evaluate : 3.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8088 (pp) REVERT: C 717 TRP cc_start: 0.9102 (OUTLIER) cc_final: 0.8670 (t60) REVERT: D 74 ILE cc_start: 0.7124 (mm) cc_final: 0.6864 (tp) REVERT: D 84 ARG cc_start: 0.6633 (mtm110) cc_final: 0.6354 (ttp-110) REVERT: D 406 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8800 (pp) outliers start: 57 outliers final: 46 residues processed: 208 average time/residue: 0.3845 time to fit residues: 130.5923 Evaluate side-chains 200 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 151 time to evaluate : 3.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 1131 VAL Chi-restraints excluded: chain D residue 1241 CYS Chi-restraints excluded: chain D residue 1258 LEU Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain H residue 403 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 311 optimal weight: 2.9990 chunk 327 optimal weight: 7.9990 chunk 299 optimal weight: 2.9990 chunk 318 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 250 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 288 optimal weight: 8.9990 chunk 301 optimal weight: 3.9990 chunk 317 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 GLN ** D 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 28268 Z= 0.456 Angle : 0.662 8.805 38323 Z= 0.338 Chirality : 0.046 0.246 4356 Planarity : 0.005 0.065 5073 Dihedral : 4.688 24.604 3932 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.25 % Allowed : 14.48 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.14), residues: 3563 helix: 0.46 (0.14), residues: 1349 sheet: -0.57 (0.25), residues: 442 loop : -1.30 (0.15), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 58 HIS 0.007 0.001 HIS D 505 PHE 0.021 0.002 PHE D1187 TYR 0.018 0.002 TYR D 251 ARG 0.009 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 150 time to evaluate : 3.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 717 TRP cc_start: 0.9138 (OUTLIER) cc_final: 0.8739 (t60) REVERT: D 84 ARG cc_start: 0.6717 (mtm110) cc_final: 0.6434 (ttp-110) REVERT: D 256 MET cc_start: 0.6501 (OUTLIER) cc_final: 0.5759 (tpt) REVERT: D 406 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8877 (pp) REVERT: E 63 ASP cc_start: 0.7117 (p0) cc_final: 0.6814 (p0) outliers start: 67 outliers final: 53 residues processed: 209 average time/residue: 0.3925 time to fit residues: 135.1842 Evaluate side-chains 202 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 146 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 774 ASP Chi-restraints excluded: chain C residue 825 ASP Chi-restraints excluded: chain C residue 830 VAL Chi-restraints excluded: chain C residue 843 VAL Chi-restraints excluded: chain C residue 943 VAL Chi-restraints excluded: chain C residue 1088 VAL Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain D residue 6 PHE Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 906 ASP Chi-restraints excluded: chain D residue 932 ASN Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 1131 VAL Chi-restraints excluded: chain D residue 1241 CYS Chi-restraints excluded: chain D residue 1258 LEU Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 273 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 209 optimal weight: 0.0970 chunk 337 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 234 optimal weight: 0.7980 chunk 353 optimal weight: 0.9980 chunk 325 optimal weight: 0.3980 chunk 281 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 GLN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 28268 Z= 0.161 Angle : 0.551 8.681 38323 Z= 0.280 Chirality : 0.042 0.226 4356 Planarity : 0.004 0.071 5073 Dihedral : 4.292 23.794 3932 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.44 % Allowed : 15.28 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.39 (0.14), residues: 3563 helix: 0.87 (0.15), residues: 1355 sheet: -0.24 (0.25), residues: 424 loop : -1.15 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 61 HIS 0.003 0.001 HIS C1026 PHE 0.010 0.001 PHE D 536 TYR 0.013 0.001 TYR D 248 ARG 0.015 0.000 ARG D 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 160 time to evaluate : 3.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 249 MET cc_start: 0.7894 (mmm) cc_final: 0.7589 (mmm) REVERT: C 717 TRP cc_start: 0.9095 (OUTLIER) cc_final: 0.8636 (t60) REVERT: D 74 ILE cc_start: 0.7035 (mm) cc_final: 0.6786 (tp) REVERT: D 84 ARG cc_start: 0.6718 (mtm110) cc_final: 0.6443 (ttp-110) REVERT: D 406 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8770 (pp) REVERT: H 462 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7685 (mp0) outliers start: 43 outliers final: 33 residues processed: 198 average time/residue: 0.4307 time to fit residues: 140.0795 Evaluate side-chains 185 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 4.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 692 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 1093 VAL Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 1131 VAL Chi-restraints excluded: chain D residue 1241 CYS Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 273 THR Chi-restraints excluded: chain H residue 462 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 223 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 282 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 289 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.067338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.052004 restraints weight = 87377.842| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.90 r_work: 0.2881 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28268 Z= 0.238 Angle : 0.563 11.261 38323 Z= 0.285 Chirality : 0.043 0.236 4356 Planarity : 0.004 0.055 5073 Dihedral : 4.252 23.396 3932 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.38 % Allowed : 15.65 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.34 (0.14), residues: 3563 helix: 0.92 (0.15), residues: 1350 sheet: -0.19 (0.25), residues: 424 loop : -1.14 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 370 HIS 0.003 0.001 HIS D 505 PHE 0.011 0.001 PHE D1187 TYR 0.014 0.001 TYR D 248 ARG 0.008 0.000 ARG A 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5111.98 seconds wall clock time: 94 minutes 13.11 seconds (5653.11 seconds total)