Starting phenix.real_space_refine on Fri Jul 19 23:23:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jir_36325/07_2024/8jir_36325.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jir_36325/07_2024/8jir_36325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jir_36325/07_2024/8jir_36325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jir_36325/07_2024/8jir_36325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jir_36325/07_2024/8jir_36325.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jir_36325/07_2024/8jir_36325.cif" } resolution = 2.57 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= 0.020 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 56 5.16 5 C 5731 2.51 5 N 1556 2.21 5 O 1671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R ARG 43": "NH1" <-> "NH2" Residue "R GLU 138": "OE1" <-> "OE2" Residue "R ARG 176": "NH1" <-> "NH2" Residue "R ARG 227": "NH1" <-> "NH2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "R ARG 380": "NH1" <-> "NH2" Residue "R GLU 408": "OE1" <-> "OE2" Residue "R GLU 412": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9014 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1884 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 226 Classifications: {'peptide': 29} Incomplete info: {'backbone_only': 1} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2581 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2886 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 13, 'TRANS': 369} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 401 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 4, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 206 Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.13, per 1000 atoms: 0.57 Number of scatterers: 9014 At special positions: 0 Unit cell: (80.325, 100.674, 175.644, 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 56 16.00 O 1671 8.00 N 1556 7.00 C 5731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.02 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.04 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.5 seconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 39.2% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 removed outlier: 4.288A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.549A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 removed outlier: 3.658A pdb=" N ASP A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 300 through 319 removed outlier: 3.682A pdb=" N TYR A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 358 removed outlier: 3.614A pdb=" N VAL A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A 345 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 357 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 358 " --> pdb=" O HIS A 354 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 24 Processing helix chain 'B' and resid 2 through 23 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.655A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'R' and resid 31 through 53 Processing helix chain 'R' and resid 89 through 94 removed outlier: 4.731A pdb=" N SER R 94 " --> pdb=" O PRO R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 169 removed outlier: 3.531A pdb=" N ALA R 158 " --> pdb=" O LEU R 154 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 200 Processing helix chain 'R' and resid 207 through 215 Processing helix chain 'R' and resid 223 through 257 removed outlier: 3.665A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU R 247 " --> pdb=" O TRP R 243 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU R 255 " --> pdb=" O LEU R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 276 removed outlier: 3.931A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 292 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 303 through 309 removed outlier: 3.758A pdb=" N ILE R 308 " --> pdb=" O TYR R 305 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE R 309 " --> pdb=" O TRP R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 310 through 338 Processing helix chain 'R' and resid 344 through 361 removed outlier: 3.733A pdb=" N ARG R 348 " --> pdb=" O ASP R 344 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 366 removed outlier: 3.765A pdb=" N ILE R 366 " --> pdb=" O HIS R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 404 removed outlier: 4.239A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 419 removed outlier: 3.569A pdb=" N PHE R 413 " --> pdb=" O VAL R 409 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.197A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.513A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.641A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.714A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.712A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B 158 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.189A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.049A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.425A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.937A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 80 through 82 432 hydrogen bonds defined for protein. 1239 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: 2.54 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1526 1.32 - 1.45: 2718 1.45 - 1.58: 4881 1.58 - 1.72: 0 1.72 - 1.85: 76 Bond restraints: 9201 Sorted by residual: bond pdb=" CA ARG B 150 " pdb=" C ARG B 150 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.04e-02 9.25e+03 3.20e+01 bond pdb=" CA GLY B 244 " pdb=" C GLY B 244 " ideal model delta sigma weight residual 1.520 1.480 0.041 7.30e-03 1.88e+04 3.09e+01 bond pdb=" CA TYR N 32 " pdb=" C TYR N 32 " ideal model delta sigma weight residual 1.523 1.464 0.059 1.21e-02 6.83e+03 2.40e+01 bond pdb=" C ARG B 150 " pdb=" O ARG B 150 " ideal model delta sigma weight residual 1.234 1.183 0.051 1.07e-02 8.73e+03 2.30e+01 bond pdb=" CA ILE B 58 " pdb=" C ILE B 58 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.19e-02 7.06e+03 1.33e+01 ... (remaining 9196 not shown) Histogram of bond angle deviations from ideal: 96.71 - 104.35: 109 104.35 - 111.98: 4490 111.98 - 119.61: 3220 119.61 - 127.25: 4560 127.25 - 134.88: 100 Bond angle restraints: 12479 Sorted by residual: angle pdb=" N GLY A 183 " pdb=" CA GLY A 183 " pdb=" C GLY A 183 " ideal model delta sigma weight residual 111.67 120.86 -9.19 9.20e-01 1.18e+00 9.97e+01 angle pdb=" N ASP R 122 " pdb=" CA ASP R 122 " pdb=" C ASP R 122 " ideal model delta sigma weight residual 113.19 101.88 11.31 1.19e+00 7.06e-01 9.04e+01 angle pdb=" N GLU R 125 " pdb=" CA GLU R 125 " pdb=" C GLU R 125 " ideal model delta sigma weight residual 109.62 96.71 12.91 1.50e+00 4.44e-01 7.40e+01 angle pdb=" N LEU R 32 " pdb=" CA LEU R 32 " pdb=" C LEU R 32 " ideal model delta sigma weight residual 111.14 103.47 7.67 1.08e+00 8.57e-01 5.04e+01 angle pdb=" N LEU B 152 " pdb=" CA LEU B 152 " pdb=" C LEU B 152 " ideal model delta sigma weight residual 111.14 104.00 7.14 1.08e+00 8.57e-01 4.38e+01 ... (remaining 12474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4875 17.97 - 35.94: 410 35.94 - 53.90: 127 53.90 - 71.87: 26 71.87 - 89.84: 17 Dihedral angle restraints: 5455 sinusoidal: 2055 harmonic: 3400 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual 93.00 -177.16 -89.84 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 154.60 -61.60 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 151.41 -58.41 1 1.00e+01 1.00e-02 4.57e+01 ... (remaining 5452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1272 0.099 - 0.197: 111 0.197 - 0.296: 19 0.296 - 0.395: 2 0.395 - 0.494: 2 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CA ASN B 155 " pdb=" N ASN B 155 " pdb=" C ASN B 155 " pdb=" CB ASN B 155 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.09e+00 chirality pdb=" CA HIS B 142 " pdb=" N HIS B 142 " pdb=" C HIS B 142 " pdb=" CB HIS B 142 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CA ILE B 37 " pdb=" N ILE B 37 " pdb=" C ILE B 37 " pdb=" CB ILE B 37 " both_signs ideal model delta sigma weight residual False 2.43 2.05 0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 1403 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 D6M P 101 " -0.045 2.00e-02 2.50e+03 7.63e-02 7.28e+01 pdb=" C04 D6M P 101 " 0.092 2.00e-02 2.50e+03 pdb=" C12 D6M P 101 " 0.075 2.00e-02 2.50e+03 pdb=" N03 D6M P 101 " -0.114 2.00e-02 2.50e+03 pdb=" O01 D6M P 101 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 205 " -0.023 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C TYR R 205 " 0.081 2.00e-02 2.50e+03 pdb=" O TYR R 205 " -0.031 2.00e-02 2.50e+03 pdb=" N SER R 206 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 57 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C LYS B 57 " -0.064 2.00e-02 2.50e+03 pdb=" O LYS B 57 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE B 58 " 0.021 2.00e-02 2.50e+03 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 72 2.56 - 3.14: 7542 3.14 - 3.73: 14011 3.73 - 4.31: 19759 4.31 - 4.90: 32539 Nonbonded interactions: 73923 Sorted by model distance: nonbonded pdb=" OE1 GLU P 15 " pdb=" OH TYR R 205 " model vdw 1.972 2.440 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.186 2.440 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.206 2.440 nonbonded pdb=" OG1 THR N 28 " pdb=" CE1 TYR N 32 " model vdw 2.221 3.340 nonbonded pdb=" NH2 ARG A 205 " pdb=" OD1 ASP B 186 " model vdw 2.221 2.520 ... (remaining 73918 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.310 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 0.059 9201 Z= 0.657 Angle : 1.023 12.907 12479 Z= 0.643 Chirality : 0.065 0.494 1406 Planarity : 0.006 0.083 1590 Dihedral : 15.934 87.516 3240 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.95 % Favored : 92.53 % Rotamer: Outliers : 6.61 % Allowed : 3.47 % Favored : 89.92 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % 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: -1.76 (0.24), residues: 1151 helix: 0.14 (0.25), residues: 434 sheet: -1.47 (0.32), residues: 236 loop : -2.20 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 248 HIS 0.012 0.002 HIS B 225 PHE 0.024 0.002 PHE B 151 TYR 0.033 0.003 TYR N 117 ARG 0.004 0.001 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 168 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 226 ASP cc_start: 0.8592 (t0) cc_final: 0.8311 (t0) REVERT: A 266 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8526 (mp0) REVERT: A 274 LYS cc_start: 0.8918 (pptt) cc_final: 0.8677 (pptt) REVERT: P 27 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.9005 (mmtt) REVERT: B 260 GLU cc_start: 0.8215 (pt0) cc_final: 0.7754 (pm20) REVERT: B 280 LYS cc_start: 0.8841 (tmtt) cc_final: 0.8537 (tmtt) REVERT: B 338 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8537 (mm) REVERT: G 36 ASP cc_start: 0.8284 (m-30) cc_final: 0.7992 (m-30) REVERT: N 117 TYR cc_start: 0.8664 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: N 123 GLN cc_start: 0.8262 (tp-100) cc_final: 0.8030 (tm-30) REVERT: N 124 VAL cc_start: 0.7635 (OUTLIER) cc_final: 0.7097 (p) REVERT: N 125 THR cc_start: 0.8974 (m) cc_final: 0.8413 (m) REVERT: R 222 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8321 (p0) outliers start: 61 outliers final: 13 residues processed: 205 average time/residue: 1.2525 time to fit residues: 272.8399 Evaluate side-chains 146 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 14 LYS Chi-restraints excluded: chain P residue 27 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 197 LYS Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 378 THR Chi-restraints excluded: chain R residue 409 VAL Chi-restraints excluded: chain R residue 411 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 88 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN R 140 GLN R 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9201 Z= 0.189 Angle : 0.603 8.870 12479 Z= 0.320 Chirality : 0.042 0.234 1406 Planarity : 0.005 0.061 1590 Dihedral : 8.828 89.493 1322 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.00 % Favored : 95.74 % Rotamer: Outliers : 3.36 % Allowed : 13.87 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.75 (0.25), residues: 1151 helix: 1.31 (0.25), residues: 441 sheet: -1.42 (0.32), residues: 236 loop : -1.74 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 214 HIS 0.006 0.001 HIS R 173 PHE 0.014 0.001 PHE B 151 TYR 0.025 0.002 TYR N 60 ARG 0.006 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 0.946 Fit side-chains REVERT: A 206 ASP cc_start: 0.8401 (t0) cc_final: 0.8110 (t0) REVERT: A 235 GLU cc_start: 0.8431 (tp30) cc_final: 0.7886 (tp30) REVERT: A 266 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8360 (mp0) REVERT: A 274 LYS cc_start: 0.8985 (pptt) cc_final: 0.8777 (pptt) REVERT: P 27 LYS cc_start: 0.9178 (mtmm) cc_final: 0.8801 (mmtt) REVERT: B 59 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: B 215 GLU cc_start: 0.8459 (pm20) cc_final: 0.7668 (pm20) REVERT: B 260 GLU cc_start: 0.8098 (pt0) cc_final: 0.7705 (pm20) REVERT: B 289 TYR cc_start: 0.8425 (m-80) cc_final: 0.7927 (m-80) REVERT: N 117 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.8028 (m-80) REVERT: N 123 GLN cc_start: 0.8127 (tp-100) cc_final: 0.7921 (tm-30) REVERT: N 124 VAL cc_start: 0.6878 (OUTLIER) cc_final: 0.6586 (p) REVERT: R 265 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7940 (tp) REVERT: R 408 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7954 (mp0) outliers start: 31 outliers final: 11 residues processed: 172 average time/residue: 1.1867 time to fit residues: 218.1053 Evaluate side-chains 160 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 378 THR Chi-restraints excluded: chain R residue 409 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 82 optimal weight: 50.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 32 GLN G 11 GLN ** R 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9201 Z= 0.211 Angle : 0.554 7.253 12479 Z= 0.294 Chirality : 0.042 0.149 1406 Planarity : 0.004 0.056 1590 Dihedral : 8.005 89.767 1295 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.31 % Rotamer: Outliers : 3.03 % Allowed : 18.20 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.25), residues: 1151 helix: 1.65 (0.25), residues: 439 sheet: -1.19 (0.33), residues: 224 loop : -1.63 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 120 HIS 0.004 0.001 HIS R 173 PHE 0.012 0.001 PHE B 151 TYR 0.021 0.001 TYR R 148 ARG 0.005 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.145 Fit side-chains REVERT: A 206 ASP cc_start: 0.8459 (t0) cc_final: 0.8142 (t0) REVERT: A 226 ASP cc_start: 0.8026 (t0) cc_final: 0.7759 (t0) REVERT: A 235 GLU cc_start: 0.8187 (tp30) cc_final: 0.7929 (tp30) REVERT: A 274 LYS cc_start: 0.9077 (pptt) cc_final: 0.8863 (pptt) REVERT: P 27 LYS cc_start: 0.9241 (mtmm) cc_final: 0.8797 (mmtt) REVERT: B 59 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8077 (m-80) REVERT: B 260 GLU cc_start: 0.8127 (pt0) cc_final: 0.7709 (pm20) REVERT: B 289 TYR cc_start: 0.8480 (m-80) cc_final: 0.8108 (m-80) REVERT: B 325 MET cc_start: 0.8264 (mmt) cc_final: 0.8041 (tpp) REVERT: N 106 ASP cc_start: 0.8320 (p0) cc_final: 0.7970 (p0) REVERT: N 123 GLN cc_start: 0.8094 (tp-100) cc_final: 0.7888 (tm-30) REVERT: N 124 VAL cc_start: 0.6785 (OUTLIER) cc_final: 0.6569 (p) REVERT: R 265 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7932 (tp) REVERT: R 338 ASN cc_start: 0.7416 (t0) cc_final: 0.6503 (t0) REVERT: R 409 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8330 (p) outliers start: 28 outliers final: 12 residues processed: 160 average time/residue: 1.1481 time to fit residues: 196.8105 Evaluate side-chains 151 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 378 THR Chi-restraints excluded: chain R residue 409 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 3.9990 chunk 77 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 97 optimal weight: 0.0040 chunk 29 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** R 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9201 Z= 0.172 Angle : 0.546 7.925 12479 Z= 0.289 Chirality : 0.041 0.191 1406 Planarity : 0.004 0.048 1590 Dihedral : 7.641 87.924 1293 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 3.25 % Allowed : 20.80 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.25), residues: 1151 helix: 1.87 (0.25), residues: 444 sheet: -1.12 (0.33), residues: 226 loop : -1.53 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 120 HIS 0.003 0.001 HIS A 324 PHE 0.010 0.001 PHE B 151 TYR 0.019 0.001 TYR R 148 ARG 0.005 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 1.006 Fit side-chains REVERT: A 190 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8713 (tt0) REVERT: A 200 ASP cc_start: 0.7708 (t0) cc_final: 0.7406 (t0) REVERT: A 206 ASP cc_start: 0.8461 (t0) cc_final: 0.8137 (t0) REVERT: A 226 ASP cc_start: 0.8012 (t0) cc_final: 0.7744 (t0) REVERT: A 235 GLU cc_start: 0.8353 (tp30) cc_final: 0.7848 (tp30) REVERT: B 260 GLU cc_start: 0.8113 (pt0) cc_final: 0.7686 (pm20) REVERT: B 289 TYR cc_start: 0.8484 (m-80) cc_final: 0.7976 (m-80) REVERT: N 38 ARG cc_start: 0.8783 (ptt180) cc_final: 0.8453 (ptm-80) REVERT: N 87 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7684 (ttmt) REVERT: N 106 ASP cc_start: 0.8325 (p0) cc_final: 0.7816 (p0) REVERT: N 123 GLN cc_start: 0.8025 (tp-100) cc_final: 0.7821 (tm-30) REVERT: R 265 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7927 (tp) outliers start: 30 outliers final: 10 residues processed: 163 average time/residue: 1.2114 time to fit residues: 211.1038 Evaluate side-chains 150 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9201 Z= 0.204 Angle : 0.546 6.518 12479 Z= 0.291 Chirality : 0.041 0.146 1406 Planarity : 0.004 0.043 1590 Dihedral : 7.261 85.965 1289 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.82 % Allowed : 22.43 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.25), residues: 1151 helix: 2.10 (0.25), residues: 440 sheet: -1.08 (0.32), residues: 233 loop : -1.38 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 214 HIS 0.003 0.001 HIS A 324 PHE 0.012 0.001 PHE A 189 TYR 0.019 0.001 TYR R 148 ARG 0.005 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 1.098 Fit side-chains REVERT: A 190 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8648 (tt0) REVERT: A 200 ASP cc_start: 0.7700 (t0) cc_final: 0.7415 (OUTLIER) REVERT: A 206 ASP cc_start: 0.8474 (t0) cc_final: 0.8153 (t0) REVERT: A 226 ASP cc_start: 0.8027 (t0) cc_final: 0.7802 (t0) REVERT: A 235 GLU cc_start: 0.8292 (tp30) cc_final: 0.7783 (tp30) REVERT: B 215 GLU cc_start: 0.8558 (pm20) cc_final: 0.8058 (pm20) REVERT: B 217 MET cc_start: 0.8388 (pmm) cc_final: 0.7949 (pmm) REVERT: B 260 GLU cc_start: 0.8135 (pt0) cc_final: 0.7693 (pm20) REVERT: B 289 TYR cc_start: 0.8563 (m-80) cc_final: 0.8101 (m-80) REVERT: N 38 ARG cc_start: 0.8806 (ptt180) cc_final: 0.8466 (ptm-80) REVERT: N 106 ASP cc_start: 0.8446 (p0) cc_final: 0.8149 (p0) REVERT: R 204 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.5392 (pmt) REVERT: R 221 GLN cc_start: 0.8092 (mt0) cc_final: 0.7722 (mm110) REVERT: R 265 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7931 (tp) outliers start: 26 outliers final: 15 residues processed: 151 average time/residue: 1.2013 time to fit residues: 193.7938 Evaluate side-chains 148 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN R 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9201 Z= 0.210 Angle : 0.541 7.516 12479 Z= 0.288 Chirality : 0.041 0.129 1406 Planarity : 0.004 0.040 1590 Dihedral : 7.145 84.214 1289 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.03 % Allowed : 22.97 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.25), residues: 1151 helix: 2.19 (0.25), residues: 441 sheet: -1.03 (0.32), residues: 233 loop : -1.29 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 243 HIS 0.003 0.001 HIS A 324 PHE 0.011 0.001 PHE R 324 TYR 0.019 0.001 TYR R 148 ARG 0.005 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.061 Fit side-chains REVERT: A 190 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8652 (tt0) REVERT: A 200 ASP cc_start: 0.7688 (t0) cc_final: 0.7414 (OUTLIER) REVERT: A 201 VAL cc_start: 0.9229 (OUTLIER) cc_final: 0.8965 (t) REVERT: A 206 ASP cc_start: 0.8485 (t0) cc_final: 0.8162 (t0) REVERT: A 226 ASP cc_start: 0.8045 (t0) cc_final: 0.7841 (t0) REVERT: A 235 GLU cc_start: 0.8259 (tp30) cc_final: 0.7712 (tp30) REVERT: B 215 GLU cc_start: 0.8537 (pm20) cc_final: 0.7947 (pm20) REVERT: B 217 MET cc_start: 0.8426 (pmm) cc_final: 0.8055 (pmm) REVERT: B 260 GLU cc_start: 0.8136 (pt0) cc_final: 0.7673 (pm20) REVERT: B 289 TYR cc_start: 0.8597 (m-80) cc_final: 0.8141 (m-80) REVERT: G 46 LYS cc_start: 0.8844 (ttpm) cc_final: 0.8638 (tppt) REVERT: N 38 ARG cc_start: 0.8775 (ptt180) cc_final: 0.8415 (ptm-80) REVERT: R 265 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7919 (tp) REVERT: R 408 GLU cc_start: 0.8228 (mp0) cc_final: 0.7972 (mp0) outliers start: 28 outliers final: 15 residues processed: 153 average time/residue: 1.1944 time to fit residues: 195.3382 Evaluate side-chains 159 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 79 optimal weight: 40.0000 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 68 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 0.0670 chunk 43 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9201 Z= 0.167 Angle : 0.537 8.504 12479 Z= 0.285 Chirality : 0.040 0.129 1406 Planarity : 0.004 0.039 1590 Dihedral : 6.971 81.600 1289 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.28 % Allowed : 24.05 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.25), residues: 1151 helix: 2.29 (0.25), residues: 441 sheet: -0.85 (0.32), residues: 226 loop : -1.34 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 214 HIS 0.003 0.001 HIS A 324 PHE 0.010 0.001 PHE A 189 TYR 0.018 0.001 TYR R 148 ARG 0.006 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 0.951 Fit side-chains REVERT: A 200 ASP cc_start: 0.7710 (t0) cc_final: 0.7418 (OUTLIER) REVERT: A 201 VAL cc_start: 0.9213 (OUTLIER) cc_final: 0.8968 (t) REVERT: A 206 ASP cc_start: 0.8471 (t0) cc_final: 0.8157 (t0) REVERT: A 235 GLU cc_start: 0.8254 (tp30) cc_final: 0.7715 (tp30) REVERT: B 215 GLU cc_start: 0.8517 (pm20) cc_final: 0.7933 (pm20) REVERT: B 217 MET cc_start: 0.8434 (pmm) cc_final: 0.8045 (pmm) REVERT: B 260 GLU cc_start: 0.8141 (pt0) cc_final: 0.7671 (pm20) REVERT: B 262 MET cc_start: 0.8042 (pmm) cc_final: 0.7771 (ppp) REVERT: B 289 TYR cc_start: 0.8577 (m-80) cc_final: 0.8044 (m-80) REVERT: G 46 LYS cc_start: 0.8851 (ttpm) cc_final: 0.8644 (tppt) REVERT: N 38 ARG cc_start: 0.8791 (ptt180) cc_final: 0.8466 (ptm-80) REVERT: R 204 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.5641 (pmt) REVERT: R 218 LEU cc_start: 0.8808 (mt) cc_final: 0.8577 (tp) REVERT: R 221 GLN cc_start: 0.8033 (mt0) cc_final: 0.7713 (mm110) REVERT: R 265 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7923 (tp) REVERT: R 292 GLU cc_start: 0.8394 (tt0) cc_final: 0.7801 (tt0) outliers start: 21 outliers final: 15 residues processed: 159 average time/residue: 1.2536 time to fit residues: 212.3711 Evaluate side-chains 157 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 7.9990 chunk 32 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 99 optimal weight: 0.0870 chunk 104 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 190 GLN R 180 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9201 Z= 0.159 Angle : 0.558 13.630 12479 Z= 0.291 Chirality : 0.040 0.129 1406 Planarity : 0.004 0.038 1590 Dihedral : 6.662 76.584 1289 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.06 % Allowed : 25.14 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.25), residues: 1151 helix: 2.44 (0.25), residues: 435 sheet: -0.77 (0.32), residues: 231 loop : -1.30 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 214 HIS 0.005 0.001 HIS R 180 PHE 0.009 0.001 PHE R 324 TYR 0.017 0.001 TYR N 60 ARG 0.007 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 1.086 Fit side-chains REVERT: A 190 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8647 (tt0) REVERT: A 200 ASP cc_start: 0.7631 (t0) cc_final: 0.7340 (OUTLIER) REVERT: A 201 VAL cc_start: 0.9179 (OUTLIER) cc_final: 0.8954 (t) REVERT: A 206 ASP cc_start: 0.8444 (t0) cc_final: 0.8121 (t0) REVERT: A 235 GLU cc_start: 0.8270 (tp30) cc_final: 0.7607 (tp30) REVERT: A 274 LYS cc_start: 0.9139 (pptt) cc_final: 0.8841 (pptt) REVERT: B 215 GLU cc_start: 0.8472 (pm20) cc_final: 0.7877 (pm20) REVERT: B 217 MET cc_start: 0.8442 (pmm) cc_final: 0.8070 (pmm) REVERT: B 228 ASP cc_start: 0.8330 (m-30) cc_final: 0.7982 (m-30) REVERT: B 260 GLU cc_start: 0.8138 (pt0) cc_final: 0.7662 (pm20) REVERT: B 289 TYR cc_start: 0.8565 (m-80) cc_final: 0.7979 (m-80) REVERT: G 42 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7962 (mp0) REVERT: G 46 LYS cc_start: 0.8836 (ttpm) cc_final: 0.8628 (tppt) REVERT: N 38 ARG cc_start: 0.8799 (ptt180) cc_final: 0.8319 (ptm-80) REVERT: N 90 ASP cc_start: 0.7604 (m-30) cc_final: 0.7029 (m-30) REVERT: R 122 ASP cc_start: 0.6585 (p0) cc_final: 0.6225 (p0) REVERT: R 182 ASN cc_start: 0.9012 (m-40) cc_final: 0.8800 (m-40) REVERT: R 204 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.5584 (pmt) REVERT: R 221 GLN cc_start: 0.7978 (mt0) cc_final: 0.7658 (mm110) REVERT: R 265 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7923 (tp) REVERT: R 292 GLU cc_start: 0.8222 (tt0) cc_final: 0.7792 (tt0) REVERT: R 408 GLU cc_start: 0.8298 (mp0) cc_final: 0.8096 (mp0) outliers start: 19 outliers final: 16 residues processed: 161 average time/residue: 1.3370 time to fit residues: 229.9929 Evaluate side-chains 160 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 222 ASP Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 338 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 79 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 107 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 190 GLN B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9201 Z= 0.246 Angle : 0.584 10.312 12479 Z= 0.310 Chirality : 0.042 0.151 1406 Planarity : 0.004 0.038 1590 Dihedral : 6.600 73.979 1289 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.60 % Allowed : 24.70 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.44 (0.25), residues: 1151 helix: 2.44 (0.25), residues: 435 sheet: -0.67 (0.33), residues: 224 loop : -1.25 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 214 HIS 0.003 0.001 HIS A 324 PHE 0.017 0.001 PHE A 189 TYR 0.019 0.001 TYR R 148 ARG 0.007 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 0.942 Fit side-chains REVERT: A 190 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8682 (tt0) REVERT: A 200 ASP cc_start: 0.7642 (t0) cc_final: 0.7382 (OUTLIER) REVERT: A 201 VAL cc_start: 0.9225 (OUTLIER) cc_final: 0.8976 (t) REVERT: A 206 ASP cc_start: 0.8477 (t0) cc_final: 0.8165 (t0) REVERT: A 235 GLU cc_start: 0.8141 (tp30) cc_final: 0.7539 (tp30) REVERT: A 274 LYS cc_start: 0.9158 (pptt) cc_final: 0.8838 (pptt) REVERT: B 215 GLU cc_start: 0.8448 (pm20) cc_final: 0.7858 (pm20) REVERT: B 217 MET cc_start: 0.8455 (pmm) cc_final: 0.8027 (pmm) REVERT: B 260 GLU cc_start: 0.8216 (pt0) cc_final: 0.7714 (pm20) REVERT: B 262 MET cc_start: 0.7896 (pmm) cc_final: 0.7385 (pmm) REVERT: B 289 TYR cc_start: 0.8637 (m-80) cc_final: 0.8183 (m-80) REVERT: G 42 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7964 (mp0) REVERT: G 62 ARG cc_start: 0.7340 (ppt170) cc_final: 0.6071 (mmt90) REVERT: R 182 ASN cc_start: 0.9012 (m-40) cc_final: 0.8734 (m110) REVERT: R 204 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.5730 (pmt) REVERT: R 221 GLN cc_start: 0.7815 (mt0) cc_final: 0.7479 (mm110) REVERT: R 265 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7930 (tp) REVERT: R 407 ASN cc_start: 0.8667 (m-40) cc_final: 0.8397 (t0) outliers start: 24 outliers final: 15 residues processed: 160 average time/residue: 1.2993 time to fit residues: 220.8662 Evaluate side-chains 160 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 190 GLN Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 265 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 0.0670 chunk 71 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 190 GLN P 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9201 Z= 0.178 Angle : 0.584 10.971 12479 Z= 0.306 Chirality : 0.041 0.170 1406 Planarity : 0.004 0.038 1590 Dihedral : 6.223 69.056 1287 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.73 % Allowed : 25.35 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.25), residues: 1151 helix: 2.51 (0.25), residues: 433 sheet: -0.65 (0.33), residues: 221 loop : -1.34 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 214 HIS 0.003 0.001 HIS A 324 PHE 0.010 0.001 PHE A 189 TYR 0.017 0.001 TYR R 148 ARG 0.006 0.000 ARG A 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 190 GLN cc_start: 0.9038 (tt0) cc_final: 0.8665 (tt0) REVERT: A 200 ASP cc_start: 0.7586 (t0) cc_final: 0.7334 (OUTLIER) REVERT: A 201 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8969 (t) REVERT: A 206 ASP cc_start: 0.8456 (t0) cc_final: 0.8129 (t0) REVERT: A 235 GLU cc_start: 0.8193 (tp30) cc_final: 0.7573 (tp30) REVERT: A 274 LYS cc_start: 0.9104 (pptt) cc_final: 0.8789 (pptt) REVERT: B 215 GLU cc_start: 0.8477 (pm20) cc_final: 0.7902 (pm20) REVERT: B 217 MET cc_start: 0.8466 (pmm) cc_final: 0.8076 (pmm) REVERT: B 260 GLU cc_start: 0.8222 (pt0) cc_final: 0.7677 (pm20) REVERT: B 262 MET cc_start: 0.7824 (pmm) cc_final: 0.7236 (pmm) REVERT: B 289 TYR cc_start: 0.8598 (m-80) cc_final: 0.8081 (m-80) REVERT: G 42 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7939 (mp0) REVERT: G 46 LYS cc_start: 0.8841 (ttpm) cc_final: 0.8619 (tppt) REVERT: R 182 ASN cc_start: 0.8999 (m-40) cc_final: 0.8712 (m110) REVERT: R 204 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.5850 (pmt) REVERT: R 221 GLN cc_start: 0.7770 (mt0) cc_final: 0.7460 (mm110) REVERT: R 265 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7909 (tp) REVERT: R 292 GLU cc_start: 0.8407 (tt0) cc_final: 0.7450 (tt0) REVERT: R 338 ASN cc_start: 0.6937 (t0) cc_final: 0.6648 (t0) REVERT: R 340 MET cc_start: 0.7692 (ppp) cc_final: 0.7250 (ppp) REVERT: R 407 ASN cc_start: 0.8717 (m-40) cc_final: 0.8492 (t0) REVERT: R 408 GLU cc_start: 0.8338 (mp0) cc_final: 0.8135 (mp0) outliers start: 16 outliers final: 15 residues processed: 156 average time/residue: 1.3165 time to fit residues: 217.7937 Evaluate side-chains 158 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 265 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 50.0000 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN P 13 GLN R 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.114167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.078709 restraints weight = 15903.326| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.22 r_work: 0.2947 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9201 Z= 0.274 Angle : 0.618 11.486 12479 Z= 0.325 Chirality : 0.043 0.159 1406 Planarity : 0.004 0.039 1590 Dihedral : 6.048 61.578 1287 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.06 % Allowed : 25.24 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.25), residues: 1151 helix: 2.45 (0.25), residues: 433 sheet: -0.67 (0.33), residues: 223 loop : -1.26 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 214 HIS 0.003 0.001 HIS A 324 PHE 0.011 0.001 PHE N 108 TYR 0.020 0.001 TYR R 148 ARG 0.008 0.000 ARG A 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4038.41 seconds wall clock time: 71 minutes 12.02 seconds (4272.02 seconds total)