Starting phenix.real_space_refine on Mon Mar 11 09:04:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm2_17756/03_2024/8pm2_17756.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm2_17756/03_2024/8pm2_17756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm2_17756/03_2024/8pm2_17756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm2_17756/03_2024/8pm2_17756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm2_17756/03_2024/8pm2_17756.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pm2_17756/03_2024/8pm2_17756.pdb" } resolution = 2.92 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= 0.013 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 52 5.16 5 C 4999 2.51 5 N 1345 2.21 5 O 1425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7821 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1773 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 93 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2587 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 420 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2036 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 2 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'8IA': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.60, per 1000 atoms: 0.59 Number of scatterers: 7821 At special positions: 0 Unit cell: (74.16, 98.056, 128.544, 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 52 16.00 O 1425 8.00 N 1345 7.00 C 4999 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 120 " - pdb=" SG CYS R 205 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.3 seconds 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1896 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 43.8% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 4.095A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.739A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.825A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.531A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.533A pdb=" N ASP A 310 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.013A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.573A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.758A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.875A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.665A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.600A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 50 through 75 removed outlier: 3.552A pdb=" N PHE R 54 " --> pdb=" O LEU R 50 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN R 65 " --> pdb=" O ALA R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 79 Processing helix chain 'R' and resid 80 through 100 removed outlier: 3.609A pdb=" N PHE R 84 " --> pdb=" O SER R 80 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU R 85 " --> pdb=" O PRO R 81 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL R 86 " --> pdb=" O ALA R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 109 removed outlier: 4.319A pdb=" N VAL R 106 " --> pdb=" O PRO R 102 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG R 107 " --> pdb=" O PHE R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 151 Processing helix chain 'R' and resid 154 through 159 Processing helix chain 'R' and resid 160 through 184 removed outlier: 3.984A pdb=" N ILE R 183 " --> pdb=" O GLY R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 250 Proline residue: R 224 - end of helix removed outlier: 4.266A pdb=" N VAL R 227 " --> pdb=" O ILE R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 298 removed outlier: 3.569A pdb=" N ARG R 267 " --> pdb=" O ARG R 263 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS R 270 " --> pdb=" O LYS R 266 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE R 282 " --> pdb=" O ALA R 278 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER R 285 " --> pdb=" O ALA R 281 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'R' and resid 317 through 327 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 335 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.775A pdb=" N VAL A 214 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.910A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.846A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.915A 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: 6.633A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.388A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.294A 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: 6.954A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.378A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.874A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.709A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.155A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1119 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: 2.27 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2525 1.34 - 1.46: 1867 1.46 - 1.58: 3530 1.58 - 1.70: 1 1.70 - 1.82: 73 Bond restraints: 7996 Sorted by residual: bond pdb=" C06 8IA R 401 " pdb=" N01 8IA R 401 " ideal model delta sigma weight residual 1.460 1.599 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" CAV Y01 R 402 " pdb=" CAZ Y01 R 402 " ideal model delta sigma weight residual 1.507 1.383 0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" CAI Y01 R 402 " pdb=" CAK Y01 R 402 " ideal model delta sigma weight residual 1.492 1.391 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" CBG Y01 R 402 " pdb=" CBI Y01 R 402 " ideal model delta sigma weight residual 1.537 1.442 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C07 8IA R 401 " pdb=" N01 8IA R 401 " ideal model delta sigma weight residual 1.446 1.529 -0.083 2.00e-02 2.50e+03 1.73e+01 ... (remaining 7991 not shown) Histogram of bond angle deviations from ideal: 98.33 - 105.52: 112 105.52 - 112.70: 4094 112.70 - 119.88: 2780 119.88 - 127.06: 3779 127.06 - 134.24: 95 Bond angle restraints: 10860 Sorted by residual: angle pdb=" CAM Y01 R 402 " pdb=" CAY Y01 R 402 " pdb=" OAW Y01 R 402 " ideal model delta sigma weight residual 111.19 125.69 -14.50 3.00e+00 1.11e-01 2.34e+01 angle pdb=" OAG Y01 R 402 " pdb=" CAY Y01 R 402 " pdb=" OAW Y01 R 402 " ideal model delta sigma weight residual 123.38 108.99 14.39 3.00e+00 1.11e-01 2.30e+01 angle pdb=" N TYR R 132 " pdb=" CA TYR R 132 " pdb=" C TYR R 132 " ideal model delta sigma weight residual 111.82 107.43 4.39 1.16e+00 7.43e-01 1.43e+01 angle pdb=" CA TYR R 132 " pdb=" C TYR R 132 " pdb=" O TYR R 132 " ideal model delta sigma weight residual 119.97 115.65 4.32 1.15e+00 7.56e-01 1.41e+01 angle pdb=" N TYR B 59 " pdb=" CA TYR B 59 " pdb=" CB TYR B 59 " ideal model delta sigma weight residual 110.88 105.89 4.99 1.38e+00 5.25e-01 1.31e+01 ... (remaining 10855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 4298 16.01 - 32.01: 376 32.01 - 48.02: 62 48.02 - 64.03: 16 64.03 - 80.03: 10 Dihedral angle restraints: 4762 sinusoidal: 1826 harmonic: 2936 Sorted by residual: dihedral pdb=" CB CYS R 120 " pdb=" SG CYS R 120 " pdb=" SG CYS R 205 " pdb=" CB CYS R 205 " ideal model delta sinusoidal sigma weight residual 93.00 168.84 -75.84 1 1.00e+01 1.00e-02 7.25e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -158.49 -21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ASP A 223 " pdb=" C ASP A 223 " pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta harmonic sigma weight residual 180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 4759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1165 0.099 - 0.198: 57 0.198 - 0.297: 1 0.297 - 0.395: 1 0.395 - 0.494: 1 Chirality restraints: 1225 Sorted by residual: chirality pdb=" C06 8IA R 401 " pdb=" C01 8IA R 401 " pdb=" C05 8IA R 401 " pdb=" N01 8IA R 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.79 0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CA ASN A 14 " pdb=" N ASN A 14 " pdb=" C ASN A 14 " pdb=" CB ASN A 14 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CBH Y01 R 402 " pdb=" CAT Y01 R 402 " pdb=" CAZ Y01 R 402 " pdb=" CBF Y01 R 402 " both_signs ideal model delta sigma weight residual False -2.85 -2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1222 not shown) Planarity restraints: 1380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 75 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" CD GLN B 75 " -0.040 2.00e-02 2.50e+03 pdb=" OE1 GLN B 75 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN B 75 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 378 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" CG ASP A 378 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP A 378 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP A 378 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO B 39 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.024 5.00e-02 4.00e+02 ... (remaining 1377 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 145 2.69 - 3.24: 7754 3.24 - 3.79: 12333 3.79 - 4.35: 16596 4.35 - 4.90: 27920 Nonbonded interactions: 64748 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.132 2.440 nonbonded pdb=" OG1 THR A 364 " pdb=" OD2 ASP A 368 " model vdw 2.159 2.440 nonbonded pdb=" NE2 GLN B 75 " pdb=" O VAL B 100 " model vdw 2.221 2.520 nonbonded pdb=" NH1 ARG A 228 " pdb=" O GLY B 162 " model vdw 2.234 2.520 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.248 2.440 ... (remaining 64743 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: 3.210 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: 0.000 Extract box with map and model: 10.870 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.100 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 7996 Z= 0.368 Angle : 0.776 14.501 10860 Z= 0.408 Chirality : 0.048 0.494 1225 Planarity : 0.005 0.060 1380 Dihedral : 13.034 80.034 2857 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: 0.56 (0.27), residues: 993 helix: 1.66 (0.27), residues: 383 sheet: -0.38 (0.34), residues: 212 loop : -0.37 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.010 0.002 HIS A 357 PHE 0.027 0.002 PHE B 234 TYR 0.018 0.002 TYR R 51 ARG 0.008 0.001 ARG R 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 SER cc_start: 0.8846 (p) cc_final: 0.8402 (t) REVERT: B 247 ASP cc_start: 0.7010 (m-30) cc_final: 0.6749 (m-30) REVERT: R 273 LYS cc_start: 0.7944 (ptmm) cc_final: 0.7742 (pttm) REVERT: R 277 ILE cc_start: 0.8425 (mt) cc_final: 0.8079 (mt) outliers start: 0 outliers final: 1 residues processed: 178 average time/residue: 1.2053 time to fit residues: 226.7804 Evaluate side-chains 127 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 292 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN N 82 GLN N 123 GLN R 217 ASN R 245 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7996 Z= 0.268 Angle : 0.575 6.699 10860 Z= 0.303 Chirality : 0.042 0.145 1225 Planarity : 0.004 0.038 1380 Dihedral : 6.248 55.949 1183 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.12 % Allowed : 9.73 % Favored : 87.16 % 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: 1.07 (0.27), residues: 993 helix: 2.18 (0.26), residues: 378 sheet: 0.01 (0.35), residues: 211 loop : -0.26 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 286 HIS 0.010 0.001 HIS A 357 PHE 0.017 0.002 PHE A 212 TYR 0.011 0.001 TYR R 132 ARG 0.007 0.001 ARG R 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 0.868 Fit side-chains REVERT: A 230 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: A 344 GLU cc_start: 0.7729 (tp30) cc_final: 0.7524 (tp30) REVERT: A 378 ASP cc_start: 0.7996 (m-30) cc_final: 0.7675 (m-30) REVERT: A 392 GLU cc_start: 0.8750 (tp30) cc_final: 0.8457 (mm-30) REVERT: B 59 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: B 247 ASP cc_start: 0.7397 (m-30) cc_final: 0.7128 (m-30) REVERT: G 42 GLU cc_start: 0.8364 (tp30) cc_final: 0.7882 (tp30) REVERT: N 5 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7244 (pt0) REVERT: R 217 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7964 (t0) outliers start: 25 outliers final: 8 residues processed: 140 average time/residue: 1.1863 time to fit residues: 176.1102 Evaluate side-chains 132 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 217 ASN Chi-restraints excluded: chain R residue 292 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN N 123 GLN R 217 ASN R 245 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7996 Z= 0.226 Angle : 0.528 6.467 10860 Z= 0.279 Chirality : 0.042 0.187 1225 Planarity : 0.003 0.037 1380 Dihedral : 6.049 56.672 1183 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.49 % Allowed : 13.59 % Favored : 83.92 % 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: 1.21 (0.27), residues: 993 helix: 2.34 (0.26), residues: 373 sheet: 0.23 (0.35), residues: 205 loop : -0.27 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.008 0.001 HIS A 357 PHE 0.017 0.001 PHE A 212 TYR 0.009 0.001 TYR R 132 ARG 0.007 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8045 (m-30) cc_final: 0.7648 (m-30) REVERT: A 392 GLU cc_start: 0.8730 (tp30) cc_final: 0.8494 (mm-30) REVERT: B 17 GLN cc_start: 0.9416 (tm-30) cc_final: 0.9157 (tm-30) REVERT: B 59 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.7599 (m-80) REVERT: B 247 ASP cc_start: 0.7451 (m-30) cc_final: 0.7208 (m-30) REVERT: G 42 GLU cc_start: 0.8363 (tp30) cc_final: 0.7845 (tp30) REVERT: R 108 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7593 (p) REVERT: R 113 TRP cc_start: 0.6641 (OUTLIER) cc_final: 0.6042 (m-90) REVERT: R 180 PHE cc_start: 0.7048 (m-80) cc_final: 0.6674 (t80) outliers start: 20 outliers final: 10 residues processed: 134 average time/residue: 1.2349 time to fit residues: 174.9189 Evaluate side-chains 132 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 113 TRP Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 270 LYS Chi-restraints excluded: chain R residue 282 PHE Chi-restraints excluded: chain R residue 285 SER Chi-restraints excluded: chain R residue 292 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 5 GLN N 31 ASN N 77 ASN N 123 GLN R 245 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7996 Z= 0.244 Angle : 0.534 6.658 10860 Z= 0.279 Chirality : 0.042 0.235 1225 Planarity : 0.004 0.036 1380 Dihedral : 5.922 58.661 1183 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.24 % Allowed : 15.46 % Favored : 81.30 % 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: 1.28 (0.27), residues: 993 helix: 2.37 (0.27), residues: 375 sheet: 0.27 (0.35), residues: 205 loop : -0.23 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.008 0.001 HIS A 357 PHE 0.016 0.001 PHE A 212 TYR 0.013 0.001 TYR R 132 ARG 0.005 0.000 ARG R 145 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: A 378 ASP cc_start: 0.8048 (m-30) cc_final: 0.7576 (m-30) REVERT: A 392 GLU cc_start: 0.8749 (tp30) cc_final: 0.8445 (mm-30) REVERT: B 17 GLN cc_start: 0.9414 (tm-30) cc_final: 0.9169 (tm-30) REVERT: B 59 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.7593 (m-80) REVERT: B 247 ASP cc_start: 0.7568 (m-30) cc_final: 0.7336 (m-30) REVERT: G 42 GLU cc_start: 0.8353 (tp30) cc_final: 0.7827 (tp30) REVERT: R 108 SER cc_start: 0.7905 (OUTLIER) cc_final: 0.7625 (p) REVERT: R 113 TRP cc_start: 0.6718 (OUTLIER) cc_final: 0.6071 (m-90) REVERT: R 180 PHE cc_start: 0.7022 (m-80) cc_final: 0.6671 (t80) outliers start: 26 outliers final: 13 residues processed: 137 average time/residue: 1.2750 time to fit residues: 184.5743 Evaluate side-chains 136 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 113 TRP Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 270 LYS Chi-restraints excluded: chain R residue 285 SER Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 292 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 5 GLN N 77 ASN R 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7996 Z= 0.264 Angle : 0.533 6.267 10860 Z= 0.281 Chirality : 0.042 0.170 1225 Planarity : 0.004 0.043 1380 Dihedral : 5.842 54.511 1183 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.62 % Allowed : 16.46 % Favored : 79.93 % 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: 1.38 (0.27), residues: 993 helix: 2.44 (0.27), residues: 379 sheet: 0.34 (0.35), residues: 205 loop : -0.20 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.009 0.001 HIS A 357 PHE 0.016 0.001 PHE A 212 TYR 0.012 0.001 TYR R 132 ARG 0.017 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7479 (pm20) cc_final: 0.7113 (pm20) REVERT: A 230 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: A 378 ASP cc_start: 0.8074 (m-30) cc_final: 0.7581 (m-30) REVERT: B 17 GLN cc_start: 0.9411 (tm-30) cc_final: 0.9158 (tm-30) REVERT: B 59 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: B 247 ASP cc_start: 0.7688 (m-30) cc_final: 0.7477 (m-30) REVERT: G 42 GLU cc_start: 0.8371 (tp30) cc_final: 0.7892 (tp30) REVERT: R 108 SER cc_start: 0.7885 (OUTLIER) cc_final: 0.7585 (p) REVERT: R 113 TRP cc_start: 0.6758 (OUTLIER) cc_final: 0.6096 (m-90) REVERT: R 180 PHE cc_start: 0.7047 (m-80) cc_final: 0.6693 (t80) REVERT: R 317 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.7276 (m-80) outliers start: 29 outliers final: 14 residues processed: 137 average time/residue: 1.2671 time to fit residues: 183.7508 Evaluate side-chains 135 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 113 TRP Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 285 SER Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 292 ASP Chi-restraints excluded: chain R residue 317 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN N 77 ASN N 123 GLN R 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7996 Z= 0.429 Angle : 0.608 6.631 10860 Z= 0.320 Chirality : 0.045 0.169 1225 Planarity : 0.004 0.040 1380 Dihedral : 6.067 54.505 1183 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.24 % Allowed : 16.83 % Favored : 78.93 % 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: 1.13 (0.27), residues: 993 helix: 2.21 (0.27), residues: 379 sheet: 0.17 (0.35), residues: 213 loop : -0.29 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.017 0.002 HIS A 220 PHE 0.020 0.002 PHE R 282 TYR 0.017 0.002 TYR N 80 ARG 0.010 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7217 (pm20) REVERT: A 378 ASP cc_start: 0.8109 (m-30) cc_final: 0.7632 (m-30) REVERT: B 59 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.7667 (m-80) REVERT: G 42 GLU cc_start: 0.8400 (tp30) cc_final: 0.7995 (tm-30) REVERT: R 113 TRP cc_start: 0.6884 (OUTLIER) cc_final: 0.6196 (m-90) REVERT: R 180 PHE cc_start: 0.7202 (m-80) cc_final: 0.6836 (t80) REVERT: R 317 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.7254 (m-80) outliers start: 34 outliers final: 23 residues processed: 146 average time/residue: 1.2060 time to fit residues: 186.5456 Evaluate side-chains 142 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 113 TRP Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 176 ILE Chi-restraints excluded: chain R residue 282 PHE Chi-restraints excluded: chain R residue 285 SER Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 292 ASP Chi-restraints excluded: chain R residue 317 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 0.0020 chunk 58 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN R 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7996 Z= 0.211 Angle : 0.556 9.454 10860 Z= 0.289 Chirality : 0.041 0.204 1225 Planarity : 0.004 0.035 1380 Dihedral : 5.821 48.640 1183 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.49 % Allowed : 19.33 % Favored : 77.18 % 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: 1.28 (0.27), residues: 993 helix: 2.35 (0.27), residues: 379 sheet: 0.26 (0.35), residues: 211 loop : -0.22 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 172 HIS 0.008 0.001 HIS A 220 PHE 0.017 0.001 PHE R 282 TYR 0.016 0.001 TYR N 60 ARG 0.009 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7111 (pm20) REVERT: A 230 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: A 378 ASP cc_start: 0.8080 (m-30) cc_final: 0.7600 (m-30) REVERT: B 59 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.7634 (m-80) REVERT: B 247 ASP cc_start: 0.7794 (m-30) cc_final: 0.7585 (m-30) REVERT: G 42 GLU cc_start: 0.8362 (tp30) cc_final: 0.7854 (tp30) REVERT: R 113 TRP cc_start: 0.6812 (OUTLIER) cc_final: 0.6200 (m-90) REVERT: R 180 PHE cc_start: 0.7008 (m-80) cc_final: 0.6700 (t80) REVERT: R 317 TYR cc_start: 0.7615 (OUTLIER) cc_final: 0.7170 (m-80) outliers start: 28 outliers final: 14 residues processed: 142 average time/residue: 1.2623 time to fit residues: 189.8517 Evaluate side-chains 139 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 113 TRP Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 282 PHE Chi-restraints excluded: chain R residue 285 SER Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 292 ASP Chi-restraints excluded: chain R residue 317 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 90 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN R 245 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7996 Z= 0.210 Angle : 0.550 8.724 10860 Z= 0.285 Chirality : 0.042 0.242 1225 Planarity : 0.004 0.038 1380 Dihedral : 5.689 45.619 1183 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.37 % Allowed : 19.95 % Favored : 76.68 % 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: 1.34 (0.27), residues: 993 helix: 2.42 (0.27), residues: 379 sheet: 0.23 (0.35), residues: 213 loop : -0.19 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 172 HIS 0.007 0.001 HIS A 220 PHE 0.016 0.001 PHE R 282 TYR 0.017 0.001 TYR N 60 ARG 0.008 0.001 ARG R 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7461 (pm20) cc_final: 0.7064 (pm20) REVERT: A 230 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: A 378 ASP cc_start: 0.8078 (m-30) cc_final: 0.7592 (m-30) REVERT: B 59 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.7554 (m-80) REVERT: G 42 GLU cc_start: 0.8347 (tp30) cc_final: 0.7838 (tp30) REVERT: R 113 TRP cc_start: 0.6855 (OUTLIER) cc_final: 0.6165 (m-90) REVERT: R 180 PHE cc_start: 0.7079 (m-80) cc_final: 0.6805 (t80) REVERT: R 317 TYR cc_start: 0.7630 (OUTLIER) cc_final: 0.7164 (m-80) outliers start: 27 outliers final: 15 residues processed: 141 average time/residue: 1.2457 time to fit residues: 185.6625 Evaluate side-chains 141 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 113 TRP Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 282 PHE Chi-restraints excluded: chain R residue 285 SER Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 292 ASP Chi-restraints excluded: chain R residue 317 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7996 Z= 0.245 Angle : 0.585 11.153 10860 Z= 0.300 Chirality : 0.042 0.259 1225 Planarity : 0.004 0.046 1380 Dihedral : 5.688 43.660 1183 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.24 % Allowed : 19.83 % Favored : 76.93 % 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: 1.31 (0.27), residues: 993 helix: 2.42 (0.27), residues: 378 sheet: 0.23 (0.35), residues: 213 loop : -0.22 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 172 HIS 0.007 0.001 HIS A 357 PHE 0.017 0.001 PHE A 212 TYR 0.017 0.001 TYR N 60 ARG 0.009 0.001 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7080 (pm20) REVERT: A 221 MET cc_start: 0.8149 (ttm) cc_final: 0.7895 (mtp) REVERT: A 230 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: A 378 ASP cc_start: 0.8090 (m-30) cc_final: 0.7600 (m-30) REVERT: B 59 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.7506 (m-80) REVERT: G 42 GLU cc_start: 0.8348 (tp30) cc_final: 0.7861 (tp30) REVERT: R 53 VAL cc_start: 0.7568 (p) cc_final: 0.7256 (m) REVERT: R 113 TRP cc_start: 0.6914 (OUTLIER) cc_final: 0.6236 (m-90) REVERT: R 180 PHE cc_start: 0.7076 (m-80) cc_final: 0.6813 (t80) REVERT: R 317 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.7206 (m-80) outliers start: 26 outliers final: 16 residues processed: 144 average time/residue: 1.2708 time to fit residues: 193.3008 Evaluate side-chains 143 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 113 TRP Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 282 PHE Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 292 ASP Chi-restraints excluded: chain R residue 317 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7996 Z= 0.265 Angle : 0.609 11.158 10860 Z= 0.312 Chirality : 0.043 0.249 1225 Planarity : 0.005 0.074 1380 Dihedral : 5.707 44.345 1183 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.24 % Allowed : 20.20 % Favored : 76.56 % 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: 1.28 (0.27), residues: 993 helix: 2.38 (0.27), residues: 378 sheet: 0.22 (0.35), residues: 213 loop : -0.23 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 172 HIS 0.007 0.001 HIS A 357 PHE 0.017 0.001 PHE A 212 TYR 0.017 0.001 TYR N 60 ARG 0.020 0.001 ARG A 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1986 Ramachandran restraints generated. 993 Oldfield, 0 Emsley, 993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7099 (pm20) REVERT: A 230 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: A 378 ASP cc_start: 0.8055 (m-30) cc_final: 0.7560 (m-30) REVERT: B 59 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: G 42 GLU cc_start: 0.8347 (tp30) cc_final: 0.7861 (tp30) REVERT: R 53 VAL cc_start: 0.7573 (p) cc_final: 0.7261 (m) REVERT: R 113 TRP cc_start: 0.6908 (OUTLIER) cc_final: 0.6206 (m-90) REVERT: R 180 PHE cc_start: 0.7102 (m-80) cc_final: 0.6831 (t80) REVERT: R 317 TYR cc_start: 0.7633 (OUTLIER) cc_final: 0.7213 (m-80) outliers start: 26 outliers final: 17 residues processed: 138 average time/residue: 1.2667 time to fit residues: 186.0945 Evaluate side-chains 142 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 113 TRP Chi-restraints excluded: chain R residue 127 ASP Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 282 PHE Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 292 ASP Chi-restraints excluded: chain R residue 317 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 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 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.109199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.086551 restraints weight = 14083.856| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.48 r_work: 0.3120 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7996 Z= 0.243 Angle : 0.601 9.774 10860 Z= 0.308 Chirality : 0.043 0.235 1225 Planarity : 0.004 0.046 1380 Dihedral : 5.673 45.720 1183 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.49 % Allowed : 20.32 % Favored : 76.18 % 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: 1.31 (0.27), residues: 993 helix: 2.42 (0.27), residues: 378 sheet: 0.23 (0.35), residues: 213 loop : -0.23 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 172 HIS 0.007 0.001 HIS A 220 PHE 0.027 0.002 PHE R 170 TYR 0.016 0.001 TYR N 60 ARG 0.009 0.001 ARG G 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3488.60 seconds wall clock time: 62 minutes 28.97 seconds (3748.97 seconds total)