Starting phenix.real_space_refine on Fri Jul 19 05:36:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkj_44642/07_2024/9bkj_44642.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkj_44642/07_2024/9bkj_44642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkj_44642/07_2024/9bkj_44642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkj_44642/07_2024/9bkj_44642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkj_44642/07_2024/9bkj_44642.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkj_44642/07_2024/9bkj_44642.cif" } resolution = 2.59 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= 0.005 sd= 0.103 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 57 5.16 5 C 4357 2.51 5 N 1150 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 138": "OE1" <-> "OE2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 390": "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: 6795 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2483 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 3, 'ASP:plan': 3, 'ASN%COO:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 106 Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 396 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "P" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 77 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2234 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1604 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 3, 'TRANS': 200} Chain breaks: 4 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 63 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.29, per 1000 atoms: 0.63 Number of scatterers: 6795 At special positions: 0 Unit cell: (88.4, 88.4, 127.5, 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 57 16.00 O 1231 8.00 N 1150 7.00 C 4357 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 196 " distance=2.07 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: 3.21 Conformation dependent library (CDL) restraints added in 1.2 seconds 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 47.8% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 39 through 69 Processing helix chain 'R' and resid 74 through 104 removed outlier: 3.528A pdb=" N PHE R 79 " --> pdb=" O VAL R 75 " (cutoff:3.500A) Proline residue: R 96 - end of helix removed outlier: 3.975A pdb=" N ILE R 100 " --> pdb=" O PRO R 96 " (cutoff:3.500A) Proline residue: R 101 - end of helix Processing helix chain 'R' and resid 110 through 145 Processing helix chain 'R' and resid 147 through 151 Processing helix chain 'R' and resid 154 through 173 Processing helix chain 'R' and resid 174 through 179 removed outlier: 3.940A pdb=" N ILE R 178 " --> pdb=" O THR R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 238 removed outlier: 3.578A pdb=" N PHE R 218 " --> pdb=" O LEU R 214 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILE R 220 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Proline residue: R 221 - end of helix Processing helix chain 'R' and resid 306 through 339 Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 339 through 348 Processing helix chain 'R' and resid 349 through 371 removed outlier: 4.214A pdb=" N SER R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER R 363 " --> pdb=" O SER R 359 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS R 364 " --> pdb=" O TYR R 360 " (cutoff:3.500A) Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 374 through 385 Processing helix chain 'A' and resid 19 through 38 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.652A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.172A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.540A 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 352 removed outlier: 3.818A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.533A pdb=" N ARG A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.406A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.746A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.915A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.670A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.720A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.457A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.419A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 180 through 181 Processing sheet with id=AA9, first strand: chain 'R' and resid 185 through 186 Processing sheet with id=AB1, first strand: chain 'A' and resid 208 through 214 removed outlier: 4.047A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1101 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: 1.95 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1442 1.33 - 1.45: 1594 1.45 - 1.58: 3809 1.58 - 1.70: 1 1.70 - 1.82: 84 Bond restraints: 6930 Sorted by residual: bond pdb=" OH TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.679 1.583 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" CA SER B 316 " pdb=" CB SER B 316 " ideal model delta sigma weight residual 1.531 1.477 0.054 1.56e-02 4.11e+03 1.20e+01 bond pdb=" CA ALA B 56 " pdb=" CB ALA B 56 " ideal model delta sigma weight residual 1.533 1.488 0.045 1.35e-02 5.49e+03 1.10e+01 bond pdb=" N HIS B 225 " pdb=" CA HIS B 225 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.34e-02 5.57e+03 9.88e+00 bond pdb=" N ASN R 98 " pdb=" CA ASN R 98 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.29e-02 6.01e+03 9.49e+00 ... (remaining 6925 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.46: 168 106.46 - 113.41: 3826 113.41 - 120.36: 2610 120.36 - 127.31: 2745 127.31 - 134.26: 71 Bond angle restraints: 9420 Sorted by residual: angle pdb=" N CYS R 196 " pdb=" CA CYS R 196 " pdb=" C CYS R 196 " ideal model delta sigma weight residual 110.42 103.21 7.21 1.46e+00 4.69e-01 2.44e+01 angle pdb=" N TRP B 332 " pdb=" CA TRP B 332 " pdb=" C TRP B 332 " ideal model delta sigma weight residual 113.18 107.51 5.67 1.21e+00 6.83e-01 2.20e+01 angle pdb=" C MET P 6 " pdb=" N ASP P 7 " pdb=" CA ASP P 7 " ideal model delta sigma weight residual 120.38 126.24 -5.86 1.37e+00 5.33e-01 1.83e+01 angle pdb=" CA PHE R 185 " pdb=" C PHE R 185 " pdb=" O PHE R 185 " ideal model delta sigma weight residual 121.33 116.84 4.49 1.08e+00 8.57e-01 1.73e+01 angle pdb=" C MET R 173 " pdb=" N THR R 174 " pdb=" CA THR R 174 " ideal model delta sigma weight residual 120.09 125.21 -5.12 1.25e+00 6.40e-01 1.68e+01 ... (remaining 9415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 3766 17.92 - 35.84: 281 35.84 - 53.75: 44 53.75 - 71.67: 6 71.67 - 89.59: 2 Dihedral angle restraints: 4099 sinusoidal: 1496 harmonic: 2603 Sorted by residual: dihedral pdb=" CA CYS R 94 " pdb=" C CYS R 94 " pdb=" N MET R 95 " pdb=" CA MET R 95 " ideal model delta harmonic sigma weight residual -180.00 -162.29 -17.71 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA PHE R 218 " pdb=" C PHE R 218 " pdb=" N LEU R 219 " pdb=" CA LEU R 219 " ideal model delta harmonic sigma weight residual -180.00 -162.89 -17.11 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA LEU R 215 " pdb=" C LEU R 215 " pdb=" N ILE R 216 " pdb=" CA ILE R 216 " ideal model delta harmonic sigma weight residual -180.00 -163.55 -16.45 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 4096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 787 0.042 - 0.084: 225 0.084 - 0.126: 88 0.126 - 0.168: 12 0.168 - 0.210: 2 Chirality restraints: 1114 Sorted by residual: chirality pdb=" CA TRP P 5 " pdb=" N TRP P 5 " pdb=" C TRP P 5 " pdb=" CB TRP P 5 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA LEU R 99 " pdb=" N LEU R 99 " pdb=" C LEU R 99 " pdb=" CB LEU R 99 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA MET R 72 " pdb=" N MET R 72 " pdb=" C MET R 72 " pdb=" CB MET R 72 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 1111 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 329 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C THR B 329 " -0.035 2.00e-02 2.50e+03 pdb=" O THR B 329 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY B 330 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 184 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C PRO R 184 " -0.034 2.00e-02 2.50e+03 pdb=" O PRO R 184 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE R 185 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 196 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C CYS R 196 " -0.033 2.00e-02 2.50e+03 pdb=" O CYS R 196 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG R 197 " 0.011 2.00e-02 2.50e+03 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1556 2.79 - 3.32: 6533 3.32 - 3.84: 11364 3.84 - 4.37: 13717 4.37 - 4.90: 23585 Nonbonded interactions: 56755 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.260 2.440 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.269 2.440 nonbonded pdb=" NZ LYS B 280 " pdb=" O ASP B 322 " model vdw 2.296 2.520 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.328 2.440 nonbonded pdb=" OH TYR B 289 " pdb=" NE1 TRP B 297 " model vdw 2.343 2.520 ... (remaining 56750 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: 0.950 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 22.080 Find NCS groups from input model: 0.060 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:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 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 : 0.005 0.096 6930 Z= 0.299 Angle : 0.754 7.797 9420 Z= 0.475 Chirality : 0.046 0.210 1114 Planarity : 0.004 0.032 1178 Dihedral : 12.935 89.589 2398 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.96 % Favored : 97.81 % Rotamer: Outliers : 0.71 % Allowed : 1.13 % Favored : 98.16 % 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: 1.02 (0.29), residues: 869 helix: 2.14 (0.26), residues: 383 sheet: 0.40 (0.39), residues: 171 loop : -1.03 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.006 0.001 HIS B 54 PHE 0.020 0.001 PHE R 185 TYR 0.007 0.001 TYR B 289 ARG 0.004 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 0.754 Fit side-chains REVERT: B 195 ASP cc_start: 0.6424 (p0) cc_final: 0.6090 (p0) outliers start: 5 outliers final: 1 residues processed: 117 average time/residue: 1.3676 time to fit residues: 167.4643 Evaluate side-chains 98 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN B 266 HIS B 268 ASN A 220 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6930 Z= 0.175 Angle : 0.532 7.605 9420 Z= 0.275 Chirality : 0.042 0.148 1114 Planarity : 0.004 0.036 1178 Dihedral : 5.022 56.126 950 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.25 % Allowed : 10.18 % Favored : 86.56 % 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: 1.45 (0.29), residues: 869 helix: 2.64 (0.27), residues: 383 sheet: 0.31 (0.39), residues: 173 loop : -0.82 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.006 0.002 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.009 0.001 TYR A 360 ARG 0.005 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: B 217 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.6250 (pmm) REVERT: A 223 ASP cc_start: 0.6253 (OUTLIER) cc_final: 0.5888 (p0) outliers start: 23 outliers final: 6 residues processed: 107 average time/residue: 1.4810 time to fit residues: 165.5586 Evaluate side-chains 94 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 21 optimal weight: 0.3980 chunk 78 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN R 131 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6930 Z= 0.155 Angle : 0.508 7.681 9420 Z= 0.259 Chirality : 0.041 0.148 1114 Planarity : 0.003 0.036 1178 Dihedral : 4.818 53.413 949 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.97 % Allowed : 13.58 % Favored : 83.45 % 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: 1.62 (0.29), residues: 869 helix: 2.82 (0.27), residues: 379 sheet: 0.32 (0.40), residues: 178 loop : -0.70 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 209 HIS 0.004 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.013 0.001 TYR R 48 ARG 0.006 0.000 ARG R 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6170 (mp0) REVERT: A 223 ASP cc_start: 0.6260 (OUTLIER) cc_final: 0.5861 (p0) outliers start: 21 outliers final: 8 residues processed: 103 average time/residue: 1.3861 time to fit residues: 149.4052 Evaluate side-chains 93 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 297 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 6.9990 chunk 58 optimal weight: 0.0670 chunk 40 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6930 Z= 0.174 Angle : 0.509 7.652 9420 Z= 0.263 Chirality : 0.041 0.157 1114 Planarity : 0.003 0.035 1178 Dihedral : 4.828 55.359 949 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.83 % Allowed : 15.13 % Favored : 82.04 % 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: 1.58 (0.29), residues: 869 helix: 2.75 (0.27), residues: 383 sheet: 0.27 (0.39), residues: 178 loop : -0.68 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 209 HIS 0.004 0.001 HIS A 220 PHE 0.013 0.001 PHE R 79 TYR 0.009 0.001 TYR R 48 ARG 0.004 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6192 (mp0) REVERT: A 223 ASP cc_start: 0.6249 (OUTLIER) cc_final: 0.5861 (p0) outliers start: 20 outliers final: 8 residues processed: 101 average time/residue: 1.4229 time to fit residues: 150.4641 Evaluate side-chains 95 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 297 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6930 Z= 0.328 Angle : 0.622 8.743 9420 Z= 0.323 Chirality : 0.045 0.165 1114 Planarity : 0.004 0.041 1178 Dihedral : 5.314 57.544 949 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.25 % Allowed : 15.42 % Favored : 81.33 % 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: 1.16 (0.29), residues: 869 helix: 2.38 (0.27), residues: 382 sheet: 0.06 (0.39), residues: 178 loop : -0.86 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.007 0.002 HIS G 44 PHE 0.015 0.002 PHE R 185 TYR 0.016 0.002 TYR R 48 ARG 0.006 0.001 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6002 (mp0) REVERT: G 28 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.7175 (pt) REVERT: A 223 ASP cc_start: 0.6497 (OUTLIER) cc_final: 0.6096 (p0) REVERT: A 343 LYS cc_start: 0.6294 (tttm) cc_final: 0.6093 (tttm) outliers start: 23 outliers final: 7 residues processed: 104 average time/residue: 1.3351 time to fit residues: 145.7245 Evaluate side-chains 97 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 0.0970 chunk 20 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN A 213 GLN A 220 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6930 Z= 0.144 Angle : 0.502 8.872 9420 Z= 0.259 Chirality : 0.041 0.172 1114 Planarity : 0.003 0.036 1178 Dihedral : 4.865 58.513 949 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.68 % Allowed : 15.70 % Favored : 80.62 % 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: 1.48 (0.29), residues: 869 helix: 2.68 (0.27), residues: 382 sheet: 0.21 (0.40), residues: 177 loop : -0.74 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 209 HIS 0.004 0.001 HIS A 220 PHE 0.014 0.001 PHE R 185 TYR 0.007 0.001 TYR R 48 ARG 0.007 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6250 (mp0) REVERT: A 223 ASP cc_start: 0.6263 (OUTLIER) cc_final: 0.5887 (p0) outliers start: 26 outliers final: 7 residues processed: 111 average time/residue: 1.5012 time to fit residues: 174.4327 Evaluate side-chains 100 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 358 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 0.0570 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN A 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6930 Z= 0.138 Angle : 0.495 8.624 9420 Z= 0.254 Chirality : 0.041 0.183 1114 Planarity : 0.003 0.037 1178 Dihedral : 4.766 59.771 949 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.83 % Allowed : 16.69 % Favored : 80.48 % 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: 1.64 (0.30), residues: 869 helix: 2.83 (0.27), residues: 382 sheet: 0.22 (0.40), residues: 178 loop : -0.65 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 209 HIS 0.005 0.001 HIS A 220 PHE 0.013 0.001 PHE R 185 TYR 0.010 0.001 TYR B 59 ARG 0.006 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6254 (mp0) REVERT: R 327 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.6049 (ttp) REVERT: A 223 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.5881 (p0) REVERT: A 272 ASP cc_start: 0.6225 (t0) cc_final: 0.5544 (t70) outliers start: 20 outliers final: 9 residues processed: 110 average time/residue: 1.2863 time to fit residues: 148.6266 Evaluate side-chains 99 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 378 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 52 optimal weight: 0.0670 chunk 56 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 0.0980 chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN A 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6930 Z= 0.133 Angle : 0.501 9.146 9420 Z= 0.255 Chirality : 0.041 0.178 1114 Planarity : 0.003 0.036 1178 Dihedral : 4.693 59.705 949 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.12 % Allowed : 17.96 % Favored : 79.92 % 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: 1.73 (0.30), residues: 869 helix: 2.93 (0.27), residues: 382 sheet: 0.22 (0.40), residues: 178 loop : -0.61 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 152 HIS 0.004 0.001 HIS A 220 PHE 0.012 0.001 PHE R 185 TYR 0.006 0.001 TYR A 360 ARG 0.006 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: R 327 MET cc_start: 0.6282 (OUTLIER) cc_final: 0.6044 (ttp) REVERT: A 223 ASP cc_start: 0.6184 (OUTLIER) cc_final: 0.5780 (p0) REVERT: A 272 ASP cc_start: 0.6154 (t0) cc_final: 0.5597 (t70) outliers start: 15 outliers final: 7 residues processed: 109 average time/residue: 1.4828 time to fit residues: 169.1330 Evaluate side-chains 97 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 358 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.0980 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6930 Z= 0.160 Angle : 0.541 10.825 9420 Z= 0.269 Chirality : 0.042 0.184 1114 Planarity : 0.003 0.035 1178 Dihedral : 4.757 59.671 949 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.40 % Allowed : 18.10 % Favored : 79.49 % 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: 1.69 (0.30), residues: 869 helix: 2.87 (0.26), residues: 382 sheet: 0.28 (0.40), residues: 178 loop : -0.65 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 209 HIS 0.004 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.012 0.001 TYR A 360 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6273 (mp0) REVERT: R 327 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.6048 (ttp) REVERT: A 223 ASP cc_start: 0.6210 (OUTLIER) cc_final: 0.5791 (p0) REVERT: A 272 ASP cc_start: 0.6213 (t0) cc_final: 0.5632 (t70) outliers start: 17 outliers final: 10 residues processed: 100 average time/residue: 1.3281 time to fit residues: 139.0829 Evaluate side-chains 99 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 358 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN A 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6930 Z= 0.167 Angle : 0.550 11.334 9420 Z= 0.274 Chirality : 0.042 0.184 1114 Planarity : 0.003 0.035 1178 Dihedral : 4.789 58.234 949 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.55 % Allowed : 17.96 % Favored : 79.49 % 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: 1.63 (0.29), residues: 869 helix: 2.80 (0.26), residues: 383 sheet: 0.24 (0.40), residues: 178 loop : -0.65 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 209 HIS 0.005 0.001 HIS A 220 PHE 0.011 0.001 PHE A 212 TYR 0.013 0.001 TYR A 360 ARG 0.006 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6295 (mp0) REVERT: R 327 MET cc_start: 0.6325 (OUTLIER) cc_final: 0.6073 (ttp) REVERT: A 223 ASP cc_start: 0.6234 (OUTLIER) cc_final: 0.5810 (p0) outliers start: 18 outliers final: 10 residues processed: 101 average time/residue: 1.3655 time to fit residues: 144.8910 Evaluate side-chains 100 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 358 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 202 ASN A 220 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.185450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.134650 restraints weight = 7060.595| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.08 r_work: 0.3579 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6930 Z= 0.188 Angle : 0.570 11.214 9420 Z= 0.283 Chirality : 0.043 0.187 1114 Planarity : 0.003 0.034 1178 Dihedral : 4.876 58.215 949 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.83 % Allowed : 17.96 % Favored : 79.21 % 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: 1.60 (0.29), residues: 869 helix: 2.73 (0.26), residues: 384 sheet: 0.24 (0.40), residues: 178 loop : -0.62 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 209 HIS 0.005 0.001 HIS A 220 PHE 0.011 0.001 PHE A 212 TYR 0.013 0.001 TYR A 360 ARG 0.006 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3253.67 seconds wall clock time: 57 minutes 36.33 seconds (3456.33 seconds total)