Starting phenix.real_space_refine on Fri Jan 19 06:15:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0k_28759/01_2024/8f0k_28759.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0k_28759/01_2024/8f0k_28759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0k_28759/01_2024/8f0k_28759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0k_28759/01_2024/8f0k_28759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0k_28759/01_2024/8f0k_28759.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0k_28759/01_2024/8f0k_28759.pdb" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 78 5.16 5 C 6760 2.51 5 N 1761 2.21 5 O 1952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 36": "NH1" <-> "NH2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E ARG 108": "NH1" <-> "NH2" Residue "P ARG 11": "NH1" <-> "NH2" Residue "P TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 106": "OE1" <-> "OE2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R ARG 258": "NH1" <-> "NH2" Residue "R ARG 321": "NH1" <-> "NH2" Residue "R GLU 332": "OE1" <-> "OE2" Residue "R GLU 334": "OE1" <-> "OE2" Residue "R ARG 362": "NH1" <-> "NH2" Residue "R GLU 397": "OE1" <-> "OE2" Residue "R ARG 404": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10553 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 108} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "P" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 280 Unusual residues: {'NH2': 1} Classifications: {'peptide': 37, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 3, 'TRANS': 33} Chain: "R" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 3046 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 352} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1888 Classifications: {'peptide': 228} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 358 Unusual residues: {'NAG': 3, 'P42': 1, 'PLM': 8, 'PTY': 1, 'Y01': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 6.23, per 1000 atoms: 0.59 Number of scatterers: 10553 At special positions: 0 Unit cell: (99.125, 168.188, 93.4375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 2 15.00 O 1952 8.00 N 1761 7.00 C 6760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS E 82 " distance=2.04 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG E 201 " - " ASN E 29 " " NAG E 202 " - " ASN E 71 " " NAG R 501 " - " ASN R 125 " " NAG R 502 " - " ASN R 130 " " NAG R 503 " - " ASN R 73 " Time building additional restraints: 4.23 Conformation dependent library (CDL) restraints added in 1.8 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2390 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 13 sheets defined 45.5% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'E' and resid 29 through 48 Proline residue: E 38 - end of helix Processing helix chain 'E' and resid 52 through 57 removed outlier: 4.249A pdb=" N CYS E 57 " --> pdb=" O TRP E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 80 removed outlier: 4.287A pdb=" N PHE E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 115 through 120 Processing helix chain 'E' and resid 120 through 141 Proline residue: E 126 - end of helix Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 19 removed outlier: 3.765A pdb=" N HIS P 18 " --> pdb=" O ASN P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 24 Processing helix chain 'R' and resid 42 through 62 Processing helix chain 'R' and resid 131 through 135 Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.539A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.565A pdb=" N ASN R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.944A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 268 Processing helix chain 'R' and resid 270 through 284 Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 353 removed outlier: 3.512A pdb=" N LYS R 340 " --> pdb=" O HIS R 336 " (cutoff:3.500A) Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 406 Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.537A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.624A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.893A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.653A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AA2, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA3, first strand: chain 'R' and resid 90 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.434A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.973A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.560A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.800A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.276A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.583A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.507A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.748A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.172A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1488 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: 3.03 Time building geometry restraints manager: 4.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1724 1.32 - 1.45: 2934 1.45 - 1.57: 5975 1.57 - 1.70: 4 1.70 - 1.82: 112 Bond restraints: 10749 Sorted by residual: bond pdb=" C TYR P 37 " pdb=" N NH2 P 38 " ideal model delta sigma weight residual 2.329 1.326 1.003 1.40e-02 5.10e+03 5.13e+03 bond pdb=" N VAL R 250 " pdb=" CA VAL R 250 " ideal model delta sigma weight residual 1.461 1.498 -0.036 1.17e-02 7.31e+03 9.72e+00 bond pdb=" N THR R 254 " pdb=" CA THR R 254 " ideal model delta sigma weight residual 1.459 1.494 -0.034 1.19e-02 7.06e+03 8.34e+00 bond pdb=" N VAL E 79 " pdb=" CA VAL E 79 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.29e+00 bond pdb=" N GLU R 255 " pdb=" CA GLU R 255 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.15e-02 7.56e+03 8.25e+00 ... (remaining 10744 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.93: 217 105.93 - 113.00: 5680 113.00 - 120.06: 3856 120.06 - 127.13: 4633 127.13 - 134.19: 130 Bond angle restraints: 14516 Sorted by residual: angle pdb=" N VAL R 250 " pdb=" CA VAL R 250 " pdb=" C VAL R 250 " ideal model delta sigma weight residual 110.42 116.66 -6.24 9.60e-01 1.09e+00 4.22e+01 angle pdb=" N PHE R 253 " pdb=" CA PHE R 253 " pdb=" C PHE R 253 " ideal model delta sigma weight residual 111.36 116.89 -5.53 1.09e+00 8.42e-01 2.58e+01 angle pdb=" C PHE R 172 " pdb=" CA PHE R 172 " pdb=" CB PHE R 172 " ideal model delta sigma weight residual 110.90 103.34 7.56 1.58e+00 4.01e-01 2.29e+01 angle pdb=" C ASN E 86 " pdb=" CA ASN E 86 " pdb=" CB ASN E 86 " ideal model delta sigma weight residual 108.87 115.57 -6.70 1.55e+00 4.16e-01 1.87e+01 angle pdb=" CA VAL R 171 " pdb=" C VAL R 171 " pdb=" O VAL R 171 " ideal model delta sigma weight residual 121.05 116.38 4.67 1.11e+00 8.12e-01 1.77e+01 ... (remaining 14511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.31: 6282 25.31 - 50.63: 261 50.63 - 75.94: 47 75.94 - 101.25: 11 101.25 - 126.57: 6 Dihedral angle restraints: 6607 sinusoidal: 2904 harmonic: 3703 Sorted by residual: dihedral pdb=" CB CYS R 72 " pdb=" SG CYS R 72 " pdb=" SG CYS R 112 " pdb=" CB CYS R 112 " ideal model delta sinusoidal sigma weight residual -86.00 -145.39 59.39 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CB CYS R 95 " pdb=" SG CYS R 95 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual 93.00 129.21 -36.21 1 1.00e+01 1.00e-02 1.85e+01 dihedral pdb=" N1 PTY R 514 " pdb=" C2 PTY R 514 " pdb=" C3 PTY R 514 " pdb=" O11 PTY R 514 " ideal model delta sinusoidal sigma weight residual 65.33 -61.24 126.57 1 3.00e+01 1.11e-03 1.70e+01 ... (remaining 6604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1341 0.053 - 0.106: 193 0.106 - 0.159: 46 0.159 - 0.212: 10 0.212 - 0.265: 4 Chirality restraints: 1594 Sorted by residual: chirality pdb=" C6 PTY R 514 " pdb=" C1 PTY R 514 " pdb=" C5 PTY R 514 " pdb=" O7 PTY R 514 " both_signs ideal model delta sigma weight residual False 2.49 2.22 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA ARG R 258 " pdb=" N ARG R 258 " pdb=" C ARG R 258 " pdb=" CB ARG R 258 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA PHE R 172 " pdb=" N PHE R 172 " pdb=" C PHE R 172 " pdb=" CB PHE R 172 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 1591 not shown) Planarity restraints: 1821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 202 " -0.328 2.00e-02 2.50e+03 2.76e-01 9.50e+02 pdb=" C7 NAG E 202 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG E 202 " -0.196 2.00e-02 2.50e+03 pdb=" N2 NAG E 202 " 0.474 2.00e-02 2.50e+03 pdb=" O7 NAG E 202 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 170 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C PHE R 170 " -0.042 2.00e-02 2.50e+03 pdb=" O PHE R 170 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL R 171 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 175 " 0.011 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C SER R 175 " -0.041 2.00e-02 2.50e+03 pdb=" O SER R 175 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU R 176 " 0.014 2.00e-02 2.50e+03 ... (remaining 1818 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2322 2.78 - 3.31: 9812 3.31 - 3.84: 17739 3.84 - 4.37: 21830 4.37 - 4.90: 36870 Nonbonded interactions: 88573 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.252 2.440 nonbonded pdb=" CD GLU R 397 " pdb=" O HOH R 602 " model vdw 2.274 3.270 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.304 2.520 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.309 2.440 nonbonded pdb=" OG1 THR A 204 " pdb=" N SER A 205 " model vdw 2.319 2.520 ... (remaining 88568 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.750 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 30.820 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 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 : 0.010 1.003 10749 Z= 0.356 Angle : 0.594 9.660 14516 Z= 0.367 Chirality : 0.044 0.265 1594 Planarity : 0.007 0.276 1816 Dihedral : 14.281 126.565 4187 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.91 % Allowed : 9.83 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -1.70 (0.21), residues: 1254 helix: -1.82 (0.16), residues: 509 sheet: -0.24 (0.32), residues: 232 loop : -0.54 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 234 HIS 0.002 0.000 HIS R 381 PHE 0.007 0.001 PHE B 199 TYR 0.019 0.001 TYR E 83 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 211 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 131 VAL cc_start: 0.6974 (m) cc_final: 0.6758 (t) REVERT: E 133 MET cc_start: 0.5509 (mmm) cc_final: 0.5080 (mpm) REVERT: R 195 SER cc_start: 0.6745 (m) cc_final: 0.6315 (p) REVERT: R 225 PHE cc_start: 0.6191 (m-80) cc_final: 0.5886 (m-80) REVERT: R 314 PHE cc_start: 0.6289 (m-10) cc_final: 0.5874 (t80) REVERT: R 395 ASN cc_start: 0.6176 (t0) cc_final: 0.5832 (t0) REVERT: A 20 ARG cc_start: 0.6216 (mtm110) cc_final: 0.5755 (ttm110) REVERT: A 28 LYS cc_start: 0.7034 (ttpp) cc_final: 0.6807 (ttpp) REVERT: A 296 LEU cc_start: 0.6834 (mp) cc_final: 0.6507 (mt) REVERT: A 299 GLU cc_start: 0.5464 (mt-10) cc_final: 0.5250 (mt-10) REVERT: A 344 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7296 (mm-30) REVERT: B 45 MET cc_start: 0.7865 (mtt) cc_final: 0.7589 (mtm) REVERT: B 188 MET cc_start: 0.8426 (mmm) cc_final: 0.8151 (mmm) REVERT: G 21 MET cc_start: 0.5616 (mmm) cc_final: 0.5138 (mpm) REVERT: G 25 ILE cc_start: 0.6224 (pt) cc_final: 0.5892 (pt) REVERT: N 1 GLN cc_start: 0.6078 (tp-100) cc_final: 0.5826 (mm-40) REVERT: N 73 ASP cc_start: 0.7681 (t0) cc_final: 0.7410 (t0) outliers start: 10 outliers final: 2 residues processed: 218 average time/residue: 1.5282 time to fit residues: 352.7170 Evaluate side-chains 156 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain B residue 59 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 ASN E 103 ASN P 22 ASN P 31 ASN P 35 ASN R 184 HIS R 201 HIS R 223 HIS R 399 GLN A 14 ASN A 54 ASN A 59 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 387 HIS A 390 GLN B 9 GLN B 17 GLN B 88 ASN B 175 GLN B 293 ASN N 84 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10749 Z= 0.331 Angle : 0.750 9.745 14516 Z= 0.401 Chirality : 0.049 0.184 1594 Planarity : 0.006 0.054 1816 Dihedral : 12.028 134.629 1838 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.55 % Allowed : 10.83 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.23), residues: 1254 helix: 0.79 (0.21), residues: 521 sheet: -0.06 (0.32), residues: 244 loop : 0.05 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 234 HIS 0.011 0.003 HIS R 336 PHE 0.021 0.003 PHE N 108 TYR 0.020 0.003 TYR R 391 ARG 0.009 0.001 ARG B 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 147 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 174 ARG cc_start: 0.4829 (OUTLIER) cc_final: 0.4437 (mtm180) REVERT: R 195 SER cc_start: 0.6964 (m) cc_final: 0.6617 (p) REVERT: R 314 PHE cc_start: 0.6348 (m-80) cc_final: 0.5761 (t80) REVERT: R 340 LYS cc_start: 0.5185 (OUTLIER) cc_final: 0.4827 (mtpt) REVERT: A 20 ARG cc_start: 0.6282 (mtm110) cc_final: 0.5816 (ttm110) REVERT: A 28 LYS cc_start: 0.7258 (ttpp) cc_final: 0.6926 (ttpp) REVERT: A 265 ARG cc_start: 0.6847 (ptt-90) cc_final: 0.6219 (ppt90) REVERT: A 296 LEU cc_start: 0.7092 (mp) cc_final: 0.6759 (mt) REVERT: A 310 ASP cc_start: 0.6037 (m-30) cc_final: 0.5607 (m-30) REVERT: B 217 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6152 (pmm) REVERT: G 21 MET cc_start: 0.5547 (mmm) cc_final: 0.5275 (mpt) REVERT: N 1 GLN cc_start: 0.6188 (tp-100) cc_final: 0.5904 (mm-40) REVERT: N 73 ASP cc_start: 0.7851 (t0) cc_final: 0.7641 (t0) outliers start: 28 outliers final: 8 residues processed: 168 average time/residue: 1.5379 time to fit residues: 275.1514 Evaluate side-chains 151 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 340 LYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 98 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 0.0770 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 395 ASN R 396 ASN A 12 GLN A 213 GLN A 357 HIS A 390 GLN B 17 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10749 Z= 0.149 Angle : 0.524 6.771 14516 Z= 0.281 Chirality : 0.041 0.144 1594 Planarity : 0.004 0.038 1816 Dihedral : 10.891 121.898 1837 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.82 % Allowed : 12.10 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.23 (0.24), residues: 1254 helix: 1.78 (0.22), residues: 521 sheet: 0.02 (0.32), residues: 235 loop : 0.33 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.004 0.001 HIS R 336 PHE 0.017 0.001 PHE E 44 TYR 0.010 0.001 TYR R 191 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 151 time to evaluate : 1.148 Fit side-chains REVERT: E 48 MET cc_start: 0.0442 (ptp) cc_final: -0.0024 (ttm) REVERT: R 169 ILE cc_start: 0.6534 (mt) cc_final: 0.6183 (mm) REVERT: R 174 ARG cc_start: 0.4814 (OUTLIER) cc_final: 0.4324 (mtm180) REVERT: R 195 SER cc_start: 0.6928 (m) cc_final: 0.6539 (p) REVERT: R 314 PHE cc_start: 0.6296 (m-80) cc_final: 0.5739 (t80) REVERT: R 340 LYS cc_start: 0.5123 (mtmm) cc_final: 0.4840 (mppt) REVERT: R 383 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6803 (tt0) REVERT: R 408 GLN cc_start: 0.3374 (OUTLIER) cc_final: 0.3004 (tt0) REVERT: A 17 LYS cc_start: 0.5741 (OUTLIER) cc_final: 0.5325 (mtpt) REVERT: A 20 ARG cc_start: 0.6304 (mtm110) cc_final: 0.5969 (ttm110) REVERT: A 28 LYS cc_start: 0.7159 (ttpp) cc_final: 0.6856 (ttpp) REVERT: A 265 ARG cc_start: 0.6792 (ptt-90) cc_final: 0.6221 (ppt90) REVERT: A 296 LEU cc_start: 0.7013 (mp) cc_final: 0.6674 (mt) REVERT: G 21 MET cc_start: 0.5401 (mmm) cc_final: 0.5122 (mpt) REVERT: N 1 GLN cc_start: 0.6169 (tp-100) cc_final: 0.5958 (mm-40) REVERT: N 73 ASP cc_start: 0.7836 (t0) cc_final: 0.7633 (t0) outliers start: 20 outliers final: 5 residues processed: 163 average time/residue: 1.5659 time to fit residues: 270.5790 Evaluate side-chains 150 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 141 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 383 GLN Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 357 HIS A 390 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10749 Z= 0.156 Angle : 0.537 6.676 14516 Z= 0.285 Chirality : 0.041 0.145 1594 Planarity : 0.004 0.039 1816 Dihedral : 10.524 117.169 1837 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.73 % Allowed : 12.28 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.49 (0.24), residues: 1254 helix: 2.03 (0.23), residues: 521 sheet: 0.09 (0.32), residues: 233 loop : 0.45 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.004 0.001 HIS R 336 PHE 0.015 0.001 PHE A 212 TYR 0.009 0.001 TYR N 117 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.166 Fit side-chains REVERT: E 48 MET cc_start: 0.0495 (OUTLIER) cc_final: 0.0131 (mtm) REVERT: R 169 ILE cc_start: 0.6485 (mt) cc_final: 0.6091 (mm) REVERT: R 174 ARG cc_start: 0.4745 (OUTLIER) cc_final: 0.4314 (mtm180) REVERT: R 195 SER cc_start: 0.6987 (m) cc_final: 0.6576 (p) REVERT: R 314 PHE cc_start: 0.6247 (m-80) cc_final: 0.5696 (t80) REVERT: R 383 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6793 (tt0) REVERT: R 408 GLN cc_start: 0.3388 (OUTLIER) cc_final: 0.3032 (tt0) REVERT: A 17 LYS cc_start: 0.5713 (OUTLIER) cc_final: 0.5299 (mtpt) REVERT: A 20 ARG cc_start: 0.6273 (mtm110) cc_final: 0.5757 (ttm110) REVERT: A 28 LYS cc_start: 0.7138 (ttpp) cc_final: 0.6863 (ttpp) REVERT: A 265 ARG cc_start: 0.6800 (ptt-90) cc_final: 0.6232 (ppt90) REVERT: A 296 LEU cc_start: 0.7002 (mp) cc_final: 0.6663 (mt) REVERT: G 21 MET cc_start: 0.5398 (mmm) cc_final: 0.5135 (mpt) REVERT: N 1 GLN cc_start: 0.6173 (tp-100) cc_final: 0.5914 (mm-40) REVERT: N 73 ASP cc_start: 0.7841 (t0) cc_final: 0.7621 (t0) outliers start: 19 outliers final: 6 residues processed: 157 average time/residue: 1.6117 time to fit residues: 267.9413 Evaluate side-chains 156 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 383 GLN Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 336 HIS ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10749 Z= 0.263 Angle : 0.668 7.484 14516 Z= 0.355 Chirality : 0.046 0.217 1594 Planarity : 0.005 0.036 1816 Dihedral : 11.835 138.873 1837 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.27 % Allowed : 12.37 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.21 (0.24), residues: 1254 helix: 1.76 (0.23), residues: 521 sheet: 0.03 (0.33), residues: 230 loop : 0.31 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 234 HIS 0.006 0.002 HIS B 183 PHE 0.018 0.002 PHE A 212 TYR 0.013 0.002 TYR A 339 ARG 0.005 0.001 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: E 48 MET cc_start: 0.0611 (ptp) cc_final: 0.0244 (mmm) REVERT: R 174 ARG cc_start: 0.4792 (OUTLIER) cc_final: 0.4378 (mtm180) REVERT: R 195 SER cc_start: 0.7026 (m) cc_final: 0.6570 (p) REVERT: R 314 PHE cc_start: 0.6311 (m-80) cc_final: 0.5767 (t80) REVERT: R 340 LYS cc_start: 0.5058 (mtmt) cc_final: 0.4832 (mppt) REVERT: R 347 ILE cc_start: 0.6970 (mm) cc_final: 0.6599 (tt) REVERT: R 408 GLN cc_start: 0.3090 (OUTLIER) cc_final: 0.2801 (tt0) REVERT: A 16 GLU cc_start: 0.5372 (tp30) cc_final: 0.4627 (tp30) REVERT: A 17 LYS cc_start: 0.5717 (OUTLIER) cc_final: 0.5280 (ttmt) REVERT: A 20 ARG cc_start: 0.6314 (mtm110) cc_final: 0.5835 (ttm110) REVERT: A 28 LYS cc_start: 0.7183 (ttpp) cc_final: 0.6884 (ttpp) REVERT: A 50 GLU cc_start: 0.5293 (OUTLIER) cc_final: 0.4987 (pm20) REVERT: A 265 ARG cc_start: 0.6818 (ptt-90) cc_final: 0.6160 (ppt90) REVERT: A 296 LEU cc_start: 0.7077 (mp) cc_final: 0.6722 (mt) REVERT: B 61 MET cc_start: 0.8582 (ppp) cc_final: 0.8217 (ppp) REVERT: B 217 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6334 (pmm) REVERT: G 21 MET cc_start: 0.5459 (mmm) cc_final: 0.5178 (mpt) REVERT: N 1 GLN cc_start: 0.6177 (tp-100) cc_final: 0.5883 (tp40) outliers start: 25 outliers final: 9 residues processed: 156 average time/residue: 1.6712 time to fit residues: 275.7684 Evaluate side-chains 146 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 336 HIS A 213 GLN A 357 HIS A 390 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10749 Z= 0.146 Angle : 0.529 8.764 14516 Z= 0.279 Chirality : 0.041 0.145 1594 Planarity : 0.004 0.040 1816 Dihedral : 10.794 123.105 1837 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.73 % Allowed : 13.10 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.58 (0.24), residues: 1254 helix: 2.12 (0.23), residues: 522 sheet: 0.04 (0.32), residues: 236 loop : 0.55 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 234 HIS 0.003 0.001 HIS R 277 PHE 0.014 0.001 PHE A 212 TYR 0.009 0.001 TYR A 339 ARG 0.008 0.000 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: R 48 MET cc_start: -0.0141 (mmt) cc_final: -0.0407 (tmt) REVERT: R 169 ILE cc_start: 0.6534 (mt) cc_final: 0.6126 (mm) REVERT: R 174 ARG cc_start: 0.4748 (OUTLIER) cc_final: 0.4283 (mtm180) REVERT: R 195 SER cc_start: 0.7037 (m) cc_final: 0.6583 (p) REVERT: R 260 ARG cc_start: 0.5410 (ptp-170) cc_final: 0.5052 (ptp-170) REVERT: R 314 PHE cc_start: 0.6295 (m-80) cc_final: 0.5740 (t80) REVERT: R 408 GLN cc_start: 0.3230 (OUTLIER) cc_final: 0.2915 (tt0) REVERT: A 16 GLU cc_start: 0.5360 (tp30) cc_final: 0.4610 (tp30) REVERT: A 17 LYS cc_start: 0.5697 (OUTLIER) cc_final: 0.5237 (mtpt) REVERT: A 20 ARG cc_start: 0.6279 (mtm110) cc_final: 0.5823 (ttm110) REVERT: A 28 LYS cc_start: 0.7101 (ttpp) cc_final: 0.6809 (ttpp) REVERT: A 265 ARG cc_start: 0.6769 (ptt-90) cc_final: 0.6170 (ppt90) REVERT: A 296 LEU cc_start: 0.7059 (mp) cc_final: 0.6711 (mt) REVERT: G 21 MET cc_start: 0.5391 (mmm) cc_final: 0.5123 (mpt) REVERT: N 1 GLN cc_start: 0.6167 (tp-100) cc_final: 0.5873 (mm-40) outliers start: 19 outliers final: 8 residues processed: 160 average time/residue: 1.6652 time to fit residues: 282.0875 Evaluate side-chains 149 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 194 ASN R 336 HIS ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10749 Z= 0.156 Angle : 0.547 9.992 14516 Z= 0.287 Chirality : 0.041 0.152 1594 Planarity : 0.004 0.038 1816 Dihedral : 10.493 112.005 1837 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.09 % Allowed : 13.38 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.64 (0.25), residues: 1254 helix: 2.20 (0.23), residues: 518 sheet: 0.07 (0.33), residues: 231 loop : 0.56 (0.30), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 234 HIS 0.003 0.001 HIS R 336 PHE 0.015 0.001 PHE A 212 TYR 0.009 0.001 TYR N 117 ARG 0.003 0.000 ARG P 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0407 (OUTLIER) cc_final: 0.0019 (mpp) REVERT: R 48 MET cc_start: 0.0186 (mmt) cc_final: -0.0272 (tmt) REVERT: R 169 ILE cc_start: 0.6532 (mt) cc_final: 0.6101 (mm) REVERT: R 174 ARG cc_start: 0.4772 (OUTLIER) cc_final: 0.4320 (mtm180) REVERT: R 195 SER cc_start: 0.7059 (m) cc_final: 0.6595 (p) REVERT: R 256 LYS cc_start: 0.4851 (tptt) cc_final: 0.4487 (tmtt) REVERT: R 314 PHE cc_start: 0.6299 (m-80) cc_final: 0.5737 (t80) REVERT: R 383 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6794 (tt0) REVERT: R 408 GLN cc_start: 0.3230 (OUTLIER) cc_final: 0.2913 (tt0) REVERT: A 17 LYS cc_start: 0.5684 (OUTLIER) cc_final: 0.5225 (mtpt) REVERT: A 20 ARG cc_start: 0.6253 (mtm110) cc_final: 0.5773 (ttm110) REVERT: A 28 LYS cc_start: 0.7110 (ttpp) cc_final: 0.6825 (ttpp) REVERT: A 265 ARG cc_start: 0.6773 (ptt-90) cc_final: 0.6163 (ppt90) REVERT: A 296 LEU cc_start: 0.7059 (mp) cc_final: 0.6721 (mt) REVERT: B 61 MET cc_start: 0.8522 (ppp) cc_final: 0.8304 (ppp) REVERT: G 21 MET cc_start: 0.5388 (mmm) cc_final: 0.5126 (mpt) REVERT: N 1 GLN cc_start: 0.6158 (tp-100) cc_final: 0.5850 (mm-40) outliers start: 23 outliers final: 12 residues processed: 155 average time/residue: 1.6597 time to fit residues: 272.2369 Evaluate side-chains 154 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 MET Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain P residue 3 ASN Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 336 HIS Chi-restraints excluded: chain R residue 347 ILE Chi-restraints excluded: chain R residue 383 GLN Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10749 Z= 0.208 Angle : 0.607 11.077 14516 Z= 0.321 Chirality : 0.043 0.188 1594 Planarity : 0.004 0.037 1816 Dihedral : 10.847 112.754 1837 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.00 % Allowed : 13.01 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.45 (0.25), residues: 1254 helix: 2.00 (0.23), residues: 517 sheet: -0.01 (0.33), residues: 238 loop : 0.49 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 234 HIS 0.012 0.001 HIS R 336 PHE 0.017 0.002 PHE A 212 TYR 0.011 0.002 TYR R 338 ARG 0.004 0.001 ARG P 11 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0509 (OUTLIER) cc_final: 0.0199 (mpp) REVERT: R 48 MET cc_start: 0.0307 (mmt) cc_final: -0.0168 (tmt) REVERT: R 174 ARG cc_start: 0.4780 (OUTLIER) cc_final: 0.4400 (mtm180) REVERT: R 195 SER cc_start: 0.7076 (m) cc_final: 0.6599 (p) REVERT: R 256 LYS cc_start: 0.5020 (tptt) cc_final: 0.4724 (tmtt) REVERT: R 314 PHE cc_start: 0.6259 (m-80) cc_final: 0.5688 (t80) REVERT: R 340 LYS cc_start: 0.5018 (mttt) cc_final: 0.4579 (mttp) REVERT: R 383 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6878 (tt0) REVERT: R 408 GLN cc_start: 0.3240 (OUTLIER) cc_final: 0.2919 (tt0) REVERT: A 16 GLU cc_start: 0.5412 (tp30) cc_final: 0.4653 (tp30) REVERT: A 17 LYS cc_start: 0.5722 (OUTLIER) cc_final: 0.5270 (ttmt) REVERT: A 20 ARG cc_start: 0.6255 (mtm110) cc_final: 0.5871 (ttm110) REVERT: A 28 LYS cc_start: 0.7180 (ttpp) cc_final: 0.6852 (ttpp) REVERT: A 265 ARG cc_start: 0.6799 (ptt-90) cc_final: 0.6160 (ppt90) REVERT: A 296 LEU cc_start: 0.7069 (mp) cc_final: 0.6717 (mt) REVERT: G 21 MET cc_start: 0.5425 (mmm) cc_final: 0.5154 (mpt) REVERT: N 1 GLN cc_start: 0.6163 (tp-100) cc_final: 0.5907 (tp40) outliers start: 22 outliers final: 8 residues processed: 150 average time/residue: 1.6930 time to fit residues: 268.4681 Evaluate side-chains 145 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 383 GLN Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 109 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 103 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 336 HIS ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10749 Z= 0.154 Angle : 0.543 11.829 14516 Z= 0.284 Chirality : 0.041 0.150 1594 Planarity : 0.004 0.037 1816 Dihedral : 10.487 99.639 1837 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.73 % Allowed : 13.28 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.66 (0.25), residues: 1254 helix: 2.19 (0.23), residues: 518 sheet: 0.10 (0.33), residues: 236 loop : 0.58 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 234 HIS 0.007 0.001 HIS R 336 PHE 0.014 0.001 PHE A 212 TYR 0.009 0.001 TYR N 117 ARG 0.004 0.000 ARG P 11 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 47 MET cc_start: 0.0362 (OUTLIER) cc_final: 0.0145 (mpp) REVERT: R 48 MET cc_start: 0.0243 (mmt) cc_final: -0.0195 (tmt) REVERT: R 169 ILE cc_start: 0.6533 (mt) cc_final: 0.6100 (mm) REVERT: R 174 ARG cc_start: 0.4790 (OUTLIER) cc_final: 0.4376 (mtm180) REVERT: R 195 SER cc_start: 0.7068 (m) cc_final: 0.6553 (p) REVERT: R 314 PHE cc_start: 0.6240 (m-80) cc_final: 0.5699 (t80) REVERT: R 376 MET cc_start: 0.6298 (mmm) cc_final: 0.6036 (tpp) REVERT: R 383 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.6790 (tt0) REVERT: R 408 GLN cc_start: 0.3284 (OUTLIER) cc_final: 0.2936 (tt0) REVERT: A 17 LYS cc_start: 0.5682 (OUTLIER) cc_final: 0.5214 (mtpt) REVERT: A 20 ARG cc_start: 0.6174 (mtm110) cc_final: 0.5822 (ttm110) REVERT: A 28 LYS cc_start: 0.7073 (ttpp) cc_final: 0.6812 (ttpp) REVERT: A 265 ARG cc_start: 0.6774 (ptt-90) cc_final: 0.6164 (ppt90) REVERT: A 296 LEU cc_start: 0.7070 (mp) cc_final: 0.6717 (mt) REVERT: G 21 MET cc_start: 0.5388 (mmm) cc_final: 0.5118 (mpt) REVERT: N 1 GLN cc_start: 0.6166 (tp-100) cc_final: 0.5865 (mm-40) outliers start: 19 outliers final: 9 residues processed: 152 average time/residue: 1.6161 time to fit residues: 260.0784 Evaluate side-chains 150 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 136 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 MET Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 383 GLN Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 396 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10749 Z= 0.219 Angle : 0.623 12.193 14516 Z= 0.329 Chirality : 0.044 0.154 1594 Planarity : 0.004 0.067 1816 Dihedral : 11.010 108.147 1837 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.73 % Allowed : 13.56 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.41 (0.25), residues: 1254 helix: 1.99 (0.23), residues: 517 sheet: -0.05 (0.33), residues: 240 loop : 0.47 (0.30), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 234 HIS 0.007 0.001 HIS R 336 PHE 0.016 0.002 PHE A 246 TYR 0.012 0.002 TYR R 299 ARG 0.007 0.001 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: E 47 MET cc_start: 0.0366 (OUTLIER) cc_final: -0.0043 (ptt) REVERT: R 48 MET cc_start: 0.0410 (mmt) cc_final: -0.0259 (tmt) REVERT: R 174 ARG cc_start: 0.4845 (OUTLIER) cc_final: 0.4462 (mtm180) REVERT: R 314 PHE cc_start: 0.6258 (m-80) cc_final: 0.5750 (t80) REVERT: R 338 TYR cc_start: 0.4897 (m-10) cc_final: 0.3598 (t80) REVERT: R 383 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6871 (tt0) REVERT: R 408 GLN cc_start: 0.3278 (OUTLIER) cc_final: 0.2912 (tt0) REVERT: A 16 GLU cc_start: 0.5432 (tp30) cc_final: 0.4656 (tp30) REVERT: A 17 LYS cc_start: 0.5698 (OUTLIER) cc_final: 0.5304 (mtpp) REVERT: A 20 ARG cc_start: 0.6241 (mtm110) cc_final: 0.5947 (ttm110) REVERT: A 28 LYS cc_start: 0.7194 (ttpp) cc_final: 0.6868 (ttpp) REVERT: A 265 ARG cc_start: 0.6801 (ptt-90) cc_final: 0.6158 (ppt90) REVERT: A 296 LEU cc_start: 0.7069 (mp) cc_final: 0.6720 (mt) REVERT: G 21 MET cc_start: 0.5438 (mmm) cc_final: 0.5160 (mpt) REVERT: N 1 GLN cc_start: 0.6162 (tp-100) cc_final: 0.5897 (tp40) outliers start: 19 outliers final: 9 residues processed: 143 average time/residue: 1.6268 time to fit residues: 246.5552 Evaluate side-chains 143 residues out of total 1105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 174 ARG Chi-restraints excluded: chain R residue 198 ILE Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 383 GLN Chi-restraints excluded: chain R residue 408 GLN Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 396 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 HIS A 390 GLN B 266 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.233456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.181095 restraints weight = 6942.249| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.05 r_work: 0.3564 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10749 Z= 0.189 Angle : 0.595 13.069 14516 Z= 0.310 Chirality : 0.042 0.148 1594 Planarity : 0.004 0.059 1816 Dihedral : 10.765 104.641 1837 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.82 % Allowed : 13.38 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.45 (0.24), residues: 1254 helix: 2.01 (0.23), residues: 517 sheet: 0.03 (0.33), residues: 238 loop : 0.47 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 234 HIS 0.005 0.001 HIS R 336 PHE 0.016 0.002 PHE A 212 TYR 0.010 0.001 TYR N 117 ARG 0.005 0.001 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5312.54 seconds wall clock time: 95 minutes 46.87 seconds (5746.87 seconds total)