Starting phenix.real_space_refine on Sat Nov 16 01:07:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2a_28810/11_2024/8f2a_28810.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2a_28810/11_2024/8f2a_28810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2a_28810/11_2024/8f2a_28810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2a_28810/11_2024/8f2a_28810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2a_28810/11_2024/8f2a_28810.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2a_28810/11_2024/8f2a_28810.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 6392 2.51 5 N 1734 2.21 5 O 1843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10044 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 810 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 109} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "P" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 279 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2996 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 16, 'TRANS': 352} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1899 Classifications: {'peptide': 231} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 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: 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 Time building chain proxies: 6.02, per 1000 atoms: 0.60 Number of scatterers: 10044 At special positions: 0 Unit cell: (93.4375, 168.188, 92.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 1843 8.00 N 1734 7.00 C 6392 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied NAG-ASN " NAG E 201 " - " ASN E 29 " " NAG E 202 " - " ASN E 71 " " NAG R 501 " - " ASN R 73 " " NAG R 502 " - " ASN R 130 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.2 seconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 12 sheets defined 43.7% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'E' and resid 29 through 37 removed outlier: 3.707A pdb=" N MET E 33 " --> pdb=" O ASN E 29 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU E 34 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG E 36 " --> pdb=" O GLY E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 48 removed outlier: 3.555A pdb=" N GLY E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 63 removed outlier: 3.565A pdb=" N ILE E 63 " --> pdb=" O SER E 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 60 through 63' Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.848A pdb=" N THR E 70 " --> pdb=" O TYR E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 101 removed outlier: 3.605A pdb=" N GLN E 99 " --> pdb=" O GLY E 95 " (cutoff:3.500A) 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 removed outlier: 3.613A pdb=" N VAL E 138 " --> pdb=" O ALA E 134 " (cutoff:3.500A) 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 16 Processing helix chain 'R' and resid 42 through 62 removed outlier: 3.589A pdb=" N GLN R 60 " --> pdb=" O TYR R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 removed outlier: 4.332A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.612A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 204 removed outlier: 3.536A pdb=" N ASN R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.720A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG R 213 " --> pdb=" O GLY R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.812A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 removed outlier: 3.620A pdb=" N THR R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.644A pdb=" N TRP R 290 " --> pdb=" O ASP R 287 " (cutoff:3.500A) 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 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 removed outlier: 3.632A pdb=" N SER R 378 " --> pdb=" O TYR R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 405 Processing helix chain 'A' and resid 12 through 40 Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.831A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.232A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.833A 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: 3.793A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.544A 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 10 through 22 removed outlier: 3.975A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.553A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA2, first strand: chain 'R' and resid 89 through 94 removed outlier: 3.565A pdb=" N VAL R 117 " --> pdb=" O ASP R 113 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.319A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.537A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.530A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.824A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.502A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.859A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.579A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.800A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.075A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1380 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: 3.16 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3261 1.34 - 1.46: 2532 1.46 - 1.58: 4382 1.58 - 1.70: 0 1.70 - 1.82: 106 Bond restraints: 10281 Sorted by residual: bond pdb=" N VAL R 171 " pdb=" CA VAL R 171 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.98e+00 bond pdb=" N HIS B 311 " pdb=" CA HIS B 311 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.28e-02 6.10e+03 7.46e+00 bond pdb=" N ILE B 338 " pdb=" CA ILE B 338 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.27e-02 6.20e+03 7.18e+00 bond pdb=" N LYS A 24 " pdb=" CA LYS A 24 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.66e+00 bond pdb=" N LEU A 30 " pdb=" CA LEU A 30 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.63e+00 ... (remaining 10276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 13562 1.56 - 3.12: 340 3.12 - 4.68: 51 4.68 - 6.24: 8 6.24 - 7.80: 2 Bond angle restraints: 13963 Sorted by residual: angle pdb=" N VAL B 90 " pdb=" CA VAL B 90 " pdb=" C VAL B 90 " ideal model delta sigma weight residual 111.81 107.88 3.93 8.60e-01 1.35e+00 2.08e+01 angle pdb=" N HIS B 311 " pdb=" CA HIS B 311 " pdb=" C HIS B 311 " ideal model delta sigma weight residual 110.10 116.66 -6.56 1.49e+00 4.50e-01 1.94e+01 angle pdb=" N ARG R 174 " pdb=" CA ARG R 174 " pdb=" C ARG R 174 " ideal model delta sigma weight residual 112.54 107.20 5.34 1.22e+00 6.72e-01 1.91e+01 angle pdb=" CA GLY R 177 " pdb=" C GLY R 177 " pdb=" O GLY R 177 " ideal model delta sigma weight residual 121.41 118.14 3.27 8.80e-01 1.29e+00 1.38e+01 angle pdb=" N LEU R 176 " pdb=" CA LEU R 176 " pdb=" C LEU R 176 " ideal model delta sigma weight residual 112.54 108.15 4.39 1.22e+00 6.72e-01 1.29e+01 ... (remaining 13958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 5572 17.59 - 35.18: 438 35.18 - 52.77: 89 52.77 - 70.36: 23 70.36 - 87.96: 10 Dihedral angle restraints: 6132 sinusoidal: 2414 harmonic: 3718 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 161.90 -68.90 1 1.00e+01 1.00e-02 6.14e+01 dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual -86.00 -27.97 -58.03 1 1.00e+01 1.00e-02 4.52e+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 93.00 130.91 -37.91 1 1.00e+01 1.00e-02 2.03e+01 ... (remaining 6129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1348 0.061 - 0.122: 185 0.122 - 0.183: 20 0.183 - 0.243: 4 0.243 - 0.304: 3 Chirality restraints: 1560 Sorted by residual: chirality pdb=" CA HIS B 311 " pdb=" N HIS B 311 " pdb=" C HIS B 311 " pdb=" CB HIS B 311 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA LEU B 308 " pdb=" N LEU B 308 " pdb=" C LEU B 308 " pdb=" CB LEU B 308 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA LEU B 336 " pdb=" N LEU B 336 " pdb=" C LEU B 336 " pdb=" CB LEU B 336 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1557 not shown) Planarity restraints: 1787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 312 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.21e+00 pdb=" C ASP B 312 " -0.046 2.00e-02 2.50e+03 pdb=" O ASP B 312 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN B 313 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE R 269 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO R 270 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO R 270 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 270 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO B 236 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.023 5.00e-02 4.00e+02 ... (remaining 1784 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 484 2.73 - 3.27: 10204 3.27 - 3.82: 16920 3.82 - 4.36: 21980 4.36 - 4.90: 35913 Nonbonded interactions: 85501 Sorted by model distance: nonbonded pdb=" OE1 GLU A 330 " pdb=" OG1 THR A 335 " model vdw 2.188 3.040 nonbonded pdb=" OD1 ASN R 130 " pdb=" OG1 THR R 132 " model vdw 2.252 3.040 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.253 3.120 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.289 3.040 nonbonded pdb=" NH2 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.292 3.120 ... (remaining 85496 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.680 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.310 Find NCS groups from input model: 0.380 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:12.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.004 0.035 10281 Z= 0.236 Angle : 0.602 7.805 13963 Z= 0.383 Chirality : 0.046 0.304 1560 Planarity : 0.003 0.043 1783 Dihedral : 13.826 87.956 3702 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.76 % Allowed : 6.84 % Favored : 92.40 % 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: -2.70 (0.20), residues: 1258 helix: -2.68 (0.16), residues: 497 sheet: -0.61 (0.31), residues: 237 loop : -1.20 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.003 0.001 HIS A 41 PHE 0.012 0.001 PHE B 151 TYR 0.009 0.001 TYR R 391 ARG 0.003 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 170 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: P 10 GLN cc_start: 0.7464 (mp10) cc_final: 0.7243 (mp10) REVERT: R 94 PHE cc_start: 0.6972 (m-80) cc_final: 0.6592 (m-10) REVERT: R 260 ARG cc_start: 0.6683 (ptp-170) cc_final: 0.6350 (ptp-110) REVERT: R 314 PHE cc_start: 0.7770 (m-80) cc_final: 0.7160 (t80) REVERT: R 340 LYS cc_start: 0.7714 (mmmt) cc_final: 0.7114 (mttp) REVERT: R 399 GLN cc_start: 0.6784 (mt0) cc_final: 0.6565 (mt0) REVERT: R 405 GLN cc_start: 0.7592 (mt0) cc_final: 0.6841 (tp40) REVERT: A 55 THR cc_start: 0.8407 (m) cc_final: 0.8010 (m) REVERT: A 356 ARG cc_start: 0.7151 (mtm110) cc_final: 0.6534 (ptt-90) REVERT: B 46 ARG cc_start: 0.7491 (mtp85) cc_final: 0.7233 (mtm-85) REVERT: B 186 ASP cc_start: 0.8594 (m-30) cc_final: 0.8377 (m-30) REVERT: B 325 MET cc_start: 0.8463 (mmt) cc_final: 0.8198 (tpt) outliers start: 8 outliers final: 3 residues processed: 177 average time/residue: 1.4152 time to fit residues: 266.7995 Evaluate side-chains 148 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 145 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 97 HIS P 3 ASN P 18 HIS P 31 ASN R 121 HIS R 179 GLN R 186 ASN R 223 HIS R 227 GLN R 277 HIS R 383 GLN R 395 ASN A 19 GLN A 294 GLN B 6 GLN B 17 GLN B 88 ASN B 175 GLN B 268 ASN B 293 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10281 Z= 0.218 Angle : 0.578 7.583 13963 Z= 0.314 Chirality : 0.044 0.176 1560 Planarity : 0.005 0.051 1783 Dihedral : 5.493 54.365 1475 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.80 % Allowed : 11.11 % Favored : 87.08 % 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: -0.56 (0.22), residues: 1258 helix: 0.09 (0.22), residues: 500 sheet: -0.04 (0.31), residues: 233 loop : -0.86 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.006 0.001 HIS R 381 PHE 0.014 0.002 PHE R 161 TYR 0.011 0.001 TYR N 95 ARG 0.008 0.000 ARG R 321 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 PHE cc_start: 0.7040 (m-80) cc_final: 0.6735 (m-10) REVERT: R 215 ASP cc_start: 0.5397 (t0) cc_final: 0.5059 (m-30) REVERT: R 260 ARG cc_start: 0.6560 (ptp-170) cc_final: 0.6326 (ptp-110) REVERT: R 314 PHE cc_start: 0.7610 (m-10) cc_final: 0.7250 (t80) REVERT: R 340 LYS cc_start: 0.7753 (mmmt) cc_final: 0.7334 (mttp) REVERT: R 367 MET cc_start: 0.5313 (tpp) cc_final: 0.5022 (ptp) REVERT: R 370 LYS cc_start: 0.7212 (ttpp) cc_final: 0.6850 (ptmm) REVERT: R 374 TYR cc_start: 0.7400 (m-80) cc_final: 0.7149 (m-80) REVERT: R 399 GLN cc_start: 0.6947 (mt0) cc_final: 0.6485 (mt0) REVERT: R 405 GLN cc_start: 0.7492 (mt0) cc_final: 0.6795 (tp40) REVERT: A 55 THR cc_start: 0.8217 (m) cc_final: 0.7427 (m) REVERT: A 59 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.6574 (mp10) REVERT: A 265 ARG cc_start: 0.7603 (mtp85) cc_final: 0.7391 (mmp80) REVERT: A 356 ARG cc_start: 0.7189 (mtm110) cc_final: 0.6613 (ptt-90) REVERT: B 44 GLN cc_start: 0.7466 (mt0) cc_final: 0.7155 (mt0) outliers start: 19 outliers final: 5 residues processed: 164 average time/residue: 1.4249 time to fit residues: 249.2711 Evaluate side-chains 151 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain R residue 400 THR Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 110 optimal weight: 0.0370 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 383 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10281 Z= 0.174 Angle : 0.520 7.271 13963 Z= 0.281 Chirality : 0.042 0.148 1560 Planarity : 0.004 0.053 1783 Dihedral : 5.076 51.548 1473 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.80 % Allowed : 12.44 % Favored : 85.75 % 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: 0.22 (0.23), residues: 1258 helix: 1.06 (0.23), residues: 506 sheet: -0.02 (0.31), residues: 241 loop : -0.60 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.005 0.001 HIS R 381 PHE 0.012 0.001 PHE R 161 TYR 0.015 0.001 TYR R 146 ARG 0.007 0.000 ARG R 321 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 94 PHE cc_start: 0.7053 (m-80) cc_final: 0.6503 (m-10) REVERT: R 107 LYS cc_start: 0.6434 (mmtt) cc_final: 0.5999 (mmmt) REVERT: R 144 ASN cc_start: 0.7839 (m-40) cc_final: 0.7593 (m-40) REVERT: R 202 LEU cc_start: 0.7958 (mt) cc_final: 0.7727 (mm) REVERT: R 314 PHE cc_start: 0.7520 (m-10) cc_final: 0.7200 (t80) REVERT: R 340 LYS cc_start: 0.7668 (mmmt) cc_final: 0.7322 (mttp) REVERT: R 399 GLN cc_start: 0.7048 (mt0) cc_final: 0.6548 (mt0) REVERT: R 405 GLN cc_start: 0.7470 (mt0) cc_final: 0.7040 (mm-40) REVERT: A 55 THR cc_start: 0.8210 (m) cc_final: 0.7416 (m) REVERT: A 59 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.6584 (mp10) REVERT: A 356 ARG cc_start: 0.7157 (mtm110) cc_final: 0.6652 (ptt-90) REVERT: B 44 GLN cc_start: 0.7463 (mt0) cc_final: 0.7194 (mt0) REVERT: B 59 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8288 (t80) REVERT: B 186 ASP cc_start: 0.8647 (m-30) cc_final: 0.8434 (m-30) outliers start: 19 outliers final: 5 residues processed: 160 average time/residue: 1.4902 time to fit residues: 253.4248 Evaluate side-chains 151 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain B residue 12 GLU 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: 123 random chunks: chunk 110 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 383 GLN A 54 ASN A 292 ASN B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10281 Z= 0.176 Angle : 0.519 7.267 13963 Z= 0.278 Chirality : 0.042 0.148 1560 Planarity : 0.004 0.054 1783 Dihedral : 4.959 51.998 1472 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.80 % Allowed : 13.87 % Favored : 84.33 % 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: 0.54 (0.23), residues: 1258 helix: 1.45 (0.23), residues: 507 sheet: 0.06 (0.31), residues: 240 loop : -0.52 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.004 0.001 HIS R 381 PHE 0.012 0.001 PHE B 151 TYR 0.009 0.001 TYR N 95 ARG 0.007 0.000 ARG R 321 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: R 59 MET cc_start: 0.4604 (mmt) cc_final: 0.3973 (mtp) REVERT: R 94 PHE cc_start: 0.7009 (m-80) cc_final: 0.6707 (m-10) REVERT: R 144 ASN cc_start: 0.7812 (m-40) cc_final: 0.7583 (m-40) REVERT: R 202 LEU cc_start: 0.7943 (mt) cc_final: 0.7713 (mm) REVERT: R 258 ARG cc_start: 0.6970 (ptp-110) cc_final: 0.6615 (ptm160) REVERT: R 314 PHE cc_start: 0.7508 (m-10) cc_final: 0.7199 (t80) REVERT: R 340 LYS cc_start: 0.7630 (mmmt) cc_final: 0.7321 (mttt) REVERT: R 405 GLN cc_start: 0.7448 (mt0) cc_final: 0.7043 (mm-40) REVERT: A 55 THR cc_start: 0.8220 (m) cc_final: 0.7413 (m) REVERT: A 59 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.6602 (mp10) REVERT: A 356 ARG cc_start: 0.7159 (mtm110) cc_final: 0.6583 (ptt-90) REVERT: B 186 ASP cc_start: 0.8712 (m-30) cc_final: 0.8472 (m-30) outliers start: 19 outliers final: 8 residues processed: 164 average time/residue: 1.4633 time to fit residues: 256.4807 Evaluate side-chains 153 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 400 THR Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 60 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 286 ASN A 292 ASN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10281 Z= 0.255 Angle : 0.566 7.776 13963 Z= 0.305 Chirality : 0.044 0.193 1560 Planarity : 0.004 0.054 1783 Dihedral : 5.067 51.192 1469 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.37 % Allowed : 14.62 % Favored : 83.00 % 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: 0.54 (0.23), residues: 1258 helix: 1.41 (0.23), residues: 508 sheet: 0.22 (0.31), residues: 235 loop : -0.57 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.005 0.001 HIS B 311 PHE 0.014 0.002 PHE B 151 TYR 0.014 0.002 TYR R 146 ARG 0.008 0.001 ARG R 321 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 59 MET cc_start: 0.4536 (mmt) cc_final: 0.3878 (mtp) REVERT: R 94 PHE cc_start: 0.7018 (m-80) cc_final: 0.6668 (m-10) REVERT: R 202 LEU cc_start: 0.7949 (mt) cc_final: 0.7732 (mm) REVERT: R 314 PHE cc_start: 0.7543 (m-10) cc_final: 0.7201 (t80) REVERT: R 340 LYS cc_start: 0.7600 (mmmt) cc_final: 0.7295 (mttt) REVERT: R 405 GLN cc_start: 0.7529 (mt0) cc_final: 0.7208 (mm-40) REVERT: A 55 THR cc_start: 0.8228 (m) cc_final: 0.7392 (m) REVERT: A 59 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.6390 (mp10) REVERT: A 292 ASN cc_start: 0.9228 (OUTLIER) cc_final: 0.9027 (t0) REVERT: A 356 ARG cc_start: 0.7202 (mtm110) cc_final: 0.6592 (ptt-90) outliers start: 25 outliers final: 7 residues processed: 166 average time/residue: 1.3918 time to fit residues: 246.7430 Evaluate side-chains 153 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain R residue 400 THR Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 0.0470 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.0040 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.9894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 286 ASN A 292 ASN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10281 Z= 0.179 Angle : 0.520 8.376 13963 Z= 0.278 Chirality : 0.042 0.171 1560 Planarity : 0.004 0.055 1783 Dihedral : 4.870 50.773 1469 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.99 % Allowed : 15.00 % Favored : 83.00 % 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: 0.76 (0.23), residues: 1258 helix: 1.69 (0.23), residues: 507 sheet: 0.25 (0.31), residues: 242 loop : -0.53 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS B 311 PHE 0.012 0.001 PHE B 151 TYR 0.009 0.001 TYR N 94 ARG 0.008 0.000 ARG R 321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 59 MET cc_start: 0.4616 (mmt) cc_final: 0.4017 (mtp) REVERT: R 94 PHE cc_start: 0.7010 (m-80) cc_final: 0.6672 (m-10) REVERT: R 202 LEU cc_start: 0.7941 (mt) cc_final: 0.7725 (mm) REVERT: R 314 PHE cc_start: 0.7489 (m-10) cc_final: 0.7240 (t80) REVERT: R 340 LYS cc_start: 0.7551 (mmmt) cc_final: 0.7252 (mttp) REVERT: R 346 MET cc_start: 0.8122 (mmm) cc_final: 0.7917 (mmm) REVERT: R 405 GLN cc_start: 0.7530 (mt0) cc_final: 0.7212 (mm-40) REVERT: A 55 THR cc_start: 0.8224 (m) cc_final: 0.7363 (m) REVERT: A 59 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.6577 (mp10) REVERT: A 356 ARG cc_start: 0.7180 (mtm110) cc_final: 0.6582 (ptt-90) REVERT: B 59 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.8282 (t80) outliers start: 21 outliers final: 12 residues processed: 157 average time/residue: 1.3611 time to fit residues: 228.4170 Evaluate side-chains 154 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN P 22 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 383 GLN A 292 ASN B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10281 Z= 0.183 Angle : 0.528 8.272 13963 Z= 0.282 Chirality : 0.042 0.160 1560 Planarity : 0.004 0.055 1783 Dihedral : 4.865 50.748 1469 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.99 % Allowed : 15.10 % Favored : 82.91 % 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: 0.81 (0.23), residues: 1258 helix: 1.78 (0.24), residues: 507 sheet: 0.13 (0.31), residues: 242 loop : -0.48 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS B 311 PHE 0.012 0.001 PHE N 108 TYR 0.013 0.001 TYR R 146 ARG 0.009 0.000 ARG R 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 59 MET cc_start: 0.4636 (mmt) cc_final: 0.4072 (mtp) REVERT: R 94 PHE cc_start: 0.6899 (m-80) cc_final: 0.6579 (m-10) REVERT: R 202 LEU cc_start: 0.7949 (mt) cc_final: 0.7728 (mm) REVERT: R 314 PHE cc_start: 0.7495 (m-10) cc_final: 0.7247 (t80) REVERT: R 340 LYS cc_start: 0.7532 (mmmt) cc_final: 0.7241 (mttp) REVERT: R 346 MET cc_start: 0.8103 (mmm) cc_final: 0.7890 (mmm) REVERT: R 405 GLN cc_start: 0.7521 (mt0) cc_final: 0.7245 (mm-40) REVERT: A 55 THR cc_start: 0.8213 (m) cc_final: 0.7370 (m) REVERT: A 59 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.6493 (mp10) REVERT: A 292 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8834 (t0) REVERT: A 356 ARG cc_start: 0.7166 (mtm110) cc_final: 0.6580 (ptt-90) outliers start: 21 outliers final: 13 residues processed: 156 average time/residue: 1.3865 time to fit residues: 231.2430 Evaluate side-chains 153 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain R residue 400 THR Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 0.2980 chunk 58 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 383 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10281 Z= 0.148 Angle : 0.503 7.661 13963 Z= 0.268 Chirality : 0.041 0.161 1560 Planarity : 0.004 0.055 1783 Dihedral : 4.698 50.781 1469 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.33 % Allowed : 15.76 % Favored : 82.91 % 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: 1.05 (0.24), residues: 1258 helix: 2.02 (0.24), residues: 502 sheet: 0.38 (0.32), residues: 232 loop : -0.41 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.002 0.001 HIS R 381 PHE 0.011 0.001 PHE B 151 TYR 0.009 0.001 TYR N 60 ARG 0.009 0.000 ARG R 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 75 MET cc_start: 0.3408 (mpt) cc_final: 0.3079 (mtm) REVERT: R 59 MET cc_start: 0.4579 (mmt) cc_final: 0.4106 (mtp) REVERT: R 94 PHE cc_start: 0.6949 (m-80) cc_final: 0.6642 (m-10) REVERT: R 96 PRO cc_start: 0.7267 (Cg_endo) cc_final: 0.7012 (Cg_exo) REVERT: R 202 LEU cc_start: 0.7947 (mt) cc_final: 0.7724 (mm) REVERT: R 314 PHE cc_start: 0.7464 (m-10) cc_final: 0.7233 (t80) REVERT: R 339 LEU cc_start: 0.6956 (tm) cc_final: 0.5985 (mm) REVERT: R 340 LYS cc_start: 0.7514 (mmmt) cc_final: 0.7200 (mttp) REVERT: R 405 GLN cc_start: 0.7495 (mt0) cc_final: 0.7257 (mm-40) REVERT: A 55 THR cc_start: 0.8238 (m) cc_final: 0.7338 (m) REVERT: A 59 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.6522 (mp10) REVERT: A 356 ARG cc_start: 0.7114 (mtm110) cc_final: 0.6554 (ptt-90) outliers start: 14 outliers final: 9 residues processed: 152 average time/residue: 1.4711 time to fit residues: 237.8164 Evaluate side-chains 146 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN P 14 ASN P 31 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 383 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10281 Z= 0.171 Angle : 0.522 7.309 13963 Z= 0.277 Chirality : 0.042 0.210 1560 Planarity : 0.004 0.055 1783 Dihedral : 4.741 50.986 1469 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.14 % Allowed : 16.33 % Favored : 82.53 % 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: 0.98 (0.24), residues: 1258 helix: 1.94 (0.24), residues: 508 sheet: 0.20 (0.32), residues: 240 loop : -0.39 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS G 44 PHE 0.015 0.001 PHE A 212 TYR 0.009 0.001 TYR N 94 ARG 0.009 0.000 ARG R 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 75 MET cc_start: 0.3417 (mpt) cc_final: 0.2577 (mtp) REVERT: R 59 MET cc_start: 0.4576 (mmt) cc_final: 0.4093 (mtp) REVERT: R 94 PHE cc_start: 0.6932 (m-80) cc_final: 0.6624 (m-10) REVERT: R 96 PRO cc_start: 0.7199 (Cg_endo) cc_final: 0.6928 (Cg_exo) REVERT: R 202 LEU cc_start: 0.7945 (mt) cc_final: 0.7720 (mm) REVERT: R 314 PHE cc_start: 0.7480 (m-10) cc_final: 0.7242 (t80) REVERT: R 340 LYS cc_start: 0.7498 (mmmt) cc_final: 0.7209 (mttp) REVERT: R 405 GLN cc_start: 0.7510 (mt0) cc_final: 0.7276 (mm-40) REVERT: A 55 THR cc_start: 0.8228 (m) cc_final: 0.7299 (m) REVERT: A 59 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6315 (mp10) REVERT: A 356 ARG cc_start: 0.7132 (mtm110) cc_final: 0.6564 (ptt-90) outliers start: 12 outliers final: 8 residues processed: 152 average time/residue: 1.4519 time to fit residues: 235.9238 Evaluate side-chains 148 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.0980 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 97 HIS P 3 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 383 GLN A 294 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10281 Z= 0.151 Angle : 0.505 7.885 13963 Z= 0.268 Chirality : 0.041 0.206 1560 Planarity : 0.004 0.055 1783 Dihedral : 4.626 51.011 1469 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.14 % Allowed : 16.52 % Favored : 82.34 % 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: 1.11 (0.24), residues: 1258 helix: 2.13 (0.24), residues: 500 sheet: 0.24 (0.32), residues: 235 loop : -0.36 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.002 0.001 HIS R 381 PHE 0.011 0.001 PHE B 151 TYR 0.009 0.001 TYR A 339 ARG 0.010 0.000 ARG R 321 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 59 MET cc_start: 0.4552 (mmt) cc_final: 0.4075 (mtp) REVERT: R 94 PHE cc_start: 0.6961 (m-80) cc_final: 0.6664 (m-10) REVERT: R 96 PRO cc_start: 0.7196 (Cg_endo) cc_final: 0.6929 (Cg_exo) REVERT: R 202 LEU cc_start: 0.7934 (mt) cc_final: 0.7709 (mm) REVERT: R 314 PHE cc_start: 0.7469 (m-10) cc_final: 0.7236 (t80) REVERT: R 339 LEU cc_start: 0.6950 (tm) cc_final: 0.5995 (mm) REVERT: R 340 LYS cc_start: 0.7451 (mmmt) cc_final: 0.7177 (mttp) REVERT: R 405 GLN cc_start: 0.7485 (mt0) cc_final: 0.7273 (mm-40) REVERT: A 55 THR cc_start: 0.8242 (m) cc_final: 0.7316 (m) REVERT: A 59 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6288 (mp10) REVERT: A 356 ARG cc_start: 0.7101 (mtm110) cc_final: 0.6552 (ptt-90) outliers start: 12 outliers final: 8 residues processed: 148 average time/residue: 1.4062 time to fit residues: 222.0848 Evaluate side-chains 145 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 96 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 383 GLN B 268 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.197525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133052 restraints weight = 10685.280| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.75 r_work: 0.3499 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10281 Z= 0.179 Angle : 0.525 7.491 13963 Z= 0.280 Chirality : 0.042 0.197 1560 Planarity : 0.004 0.054 1783 Dihedral : 4.732 51.081 1469 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.14 % Allowed : 17.00 % Favored : 81.86 % 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: 1.05 (0.24), residues: 1258 helix: 2.00 (0.24), residues: 508 sheet: 0.23 (0.32), residues: 242 loop : -0.36 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.003 0.001 HIS G 44 PHE 0.011 0.001 PHE B 151 TYR 0.010 0.001 TYR R 146 ARG 0.009 0.000 ARG R 321 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4774.93 seconds wall clock time: 86 minutes 9.78 seconds (5169.78 seconds total)