Starting phenix.real_space_refine on Wed Feb 14 03:42:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqc_34947/02_2024/8hqc_34947.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqc_34947/02_2024/8hqc_34947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqc_34947/02_2024/8hqc_34947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqc_34947/02_2024/8hqc_34947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqc_34947/02_2024/8hqc_34947.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqc_34947/02_2024/8hqc_34947.pdb" } resolution = 3.89 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= 0.019 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 58 5.16 5 C 5429 2.51 5 N 1471 2.21 5 O 1580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "H GLU 220": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8538 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1984 Classifications: {'peptide': 275} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 38} Link IDs: {'PTRANS': 13, 'TRANS': 261} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 113 Chain: "B" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1544 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 35} Link IDs: {'PTRANS': 4, 'TRANS': 206} Chain breaks: 2 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2488 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 85 Chain: "D" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 472 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 22} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 2, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "G" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 384 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1666 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 4.75, per 1000 atoms: 0.56 Number of scatterers: 8538 At special positions: 0 Unit cell: (87.1755, 126.025, 147.819, 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 58 16.00 O 1580 8.00 N 1471 7.00 C 5429 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 47 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 54 " distance=2.04 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 55 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 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: 3.09 Conformation dependent library (CDL) restraints added in 1.8 seconds 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2208 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 12 sheets defined 41.1% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 35 through 39 Processing helix chain 'A' and resid 40 through 62 Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 63 through 67 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 72 through 96 Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 111 through 140 removed outlier: 3.762A pdb=" N MET A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 149 through 175 Proline residue: A 170 - end of helix removed outlier: 3.694A pdb=" N ARG A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 234 removed outlier: 3.539A pdb=" N LEU A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) Proline residue: A 215 - end of helix removed outlier: 3.561A pdb=" N ARG A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 269 removed outlier: 4.803A pdb=" N ALA A 247 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 276 through 289 removed outlier: 4.756A pdb=" N SER A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 303 removed outlier: 3.901A pdb=" N ASN A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Proline residue: A 298 - end of helix removed outlier: 3.778A pdb=" N TYR A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 315 Processing helix chain 'B' and resid 9 through 31 Processing helix chain 'B' and resid 45 through 53 Processing helix chain 'B' and resid 208 through 213 removed outlier: 3.738A pdb=" N TRP B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 217 Processing helix chain 'B' and resid 246 through 256 Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.835A pdb=" N ILE B 261 " --> pdb=" O LYS B 258 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP B 262 " --> pdb=" O PHE B 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 262' Processing helix chain 'B' and resid 271 through 282 removed outlier: 3.848A pdb=" N GLY B 276 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.848A pdb=" N ILE B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 311 removed outlier: 3.968A pdb=" N LYS B 311 " --> pdb=" O GLN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 351 Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 33 through 38 removed outlier: 3.633A pdb=" N ARG D 37 " --> pdb=" O THR D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 41 No H-bonds generated for 'chain 'D' and resid 39 through 41' Processing helix chain 'D' and resid 44 through 63 removed outlier: 4.243A pdb=" N GLU D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N CYS D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.552A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.697A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'B' and resid 186 through 192 removed outlier: 7.260A pdb=" N LYS B 35 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE B 223 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU B 37 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N CYS B 225 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 39 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N ASP B 227 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE B 222 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE B 268 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE B 224 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ASN B 270 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B 226 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.739A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 327 " --> pdb=" O TRP C 339 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA C 328 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU C 318 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY C 330 " --> pdb=" O SER C 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.907A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 3.654A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.601A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.711A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.752A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.464A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.173A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.894A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 3.35 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: 2781 1.34 - 1.46: 2030 1.46 - 1.58: 3818 1.58 - 1.70: 1 1.70 - 1.82: 75 Bond restraints: 8705 Sorted by residual: bond pdb=" CB PRO B 294 " pdb=" CG PRO B 294 " ideal model delta sigma weight residual 1.492 1.588 -0.096 5.00e-02 4.00e+02 3.72e+00 bond pdb=" CG PRO B 294 " pdb=" CD PRO B 294 " ideal model delta sigma weight residual 1.503 1.562 -0.059 3.40e-02 8.65e+02 3.04e+00 bond pdb=" CA ILE B 335 " pdb=" CB ILE B 335 " ideal model delta sigma weight residual 1.540 1.522 0.018 1.39e-02 5.18e+03 1.75e+00 bond pdb=" CA GLU B 8 " pdb=" C GLU B 8 " ideal model delta sigma weight residual 1.523 1.544 -0.020 1.80e-02 3.09e+03 1.27e+00 bond pdb=" CA ILE A 169 " pdb=" C ILE A 169 " ideal model delta sigma weight residual 1.524 1.536 -0.011 1.05e-02 9.07e+03 1.19e+00 ... (remaining 8700 not shown) Histogram of bond angle deviations from ideal: 99.23 - 106.19: 185 106.19 - 113.16: 4784 113.16 - 120.13: 2957 120.13 - 127.09: 3853 127.09 - 134.06: 97 Bond angle restraints: 11876 Sorted by residual: angle pdb=" CA PRO B 294 " pdb=" N PRO B 294 " pdb=" CD PRO B 294 " ideal model delta sigma weight residual 112.00 105.88 6.12 1.40e+00 5.10e-01 1.91e+01 angle pdb=" C MET B 53 " pdb=" N LYS B 54 " pdb=" CA LYS B 54 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" N ASN C 119 " pdb=" CA ASN C 119 " pdb=" CB ASN C 119 " ideal model delta sigma weight residual 114.17 110.39 3.78 1.14e+00 7.69e-01 1.10e+01 angle pdb=" N VAL C 90 " pdb=" CA VAL C 90 " pdb=" C VAL C 90 " ideal model delta sigma weight residual 113.53 110.47 3.06 9.80e-01 1.04e+00 9.72e+00 angle pdb=" C ASP A 180 " pdb=" N PHE A 181 " pdb=" CA PHE A 181 " ideal model delta sigma weight residual 121.54 126.80 -5.26 1.91e+00 2.74e-01 7.59e+00 ... (remaining 11871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 4771 17.92 - 35.83: 275 35.83 - 53.75: 46 53.75 - 71.67: 5 71.67 - 89.58: 3 Dihedral angle restraints: 5100 sinusoidal: 1684 harmonic: 3416 Sorted by residual: dihedral pdb=" CA ALA C 56 " pdb=" C ALA C 56 " pdb=" N LYS C 57 " pdb=" CA LYS C 57 " ideal model delta harmonic sigma weight residual 180.00 154.48 25.52 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CB CYS H 159 " pdb=" SG CYS H 159 " pdb=" SG CYS H 229 " pdb=" CB CYS H 229 " ideal model delta sinusoidal sigma weight residual 93.00 55.70 37.30 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CB CYS D 34 " pdb=" SG CYS D 34 " pdb=" SG CYS D 55 " pdb=" CB CYS D 55 " ideal model delta sinusoidal sigma weight residual 93.00 58.21 34.79 1 1.00e+01 1.00e-02 1.72e+01 ... (remaining 5097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 857 0.033 - 0.066: 385 0.066 - 0.099: 131 0.099 - 0.132: 45 0.132 - 0.165: 5 Chirality restraints: 1423 Sorted by residual: chirality pdb=" CA LYS B 54 " pdb=" N LYS B 54 " pdb=" C LYS B 54 " pdb=" CB LYS B 54 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA PRO B 294 " pdb=" N PRO B 294 " pdb=" C PRO B 294 " pdb=" CB PRO B 294 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA PHE A 139 " pdb=" N PHE A 139 " pdb=" C PHE A 139 " pdb=" CB PHE A 139 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 1420 not shown) Planarity restraints: 1507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 293 " 0.065 5.00e-02 4.00e+02 9.57e-02 1.46e+01 pdb=" N PRO B 294 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO B 294 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 294 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 314 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO B 315 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 315 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 315 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 139 " 0.013 2.00e-02 2.50e+03 1.52e-02 4.02e+00 pdb=" CG PHE A 139 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 139 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 139 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 139 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 139 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 139 " -0.001 2.00e-02 2.50e+03 ... (remaining 1504 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1328 2.76 - 3.29: 8721 3.29 - 3.83: 13369 3.83 - 4.36: 15081 4.36 - 4.90: 26644 Nonbonded interactions: 65143 Sorted by model distance: nonbonded pdb=" OG SER C 147 " pdb=" O MET C 188 " model vdw 2.223 2.440 nonbonded pdb=" ND2 ASN A 55 " pdb=" OD2 ASP A 82 " model vdw 2.249 2.520 nonbonded pdb=" NE2 HIS C 225 " pdb=" OG1 THR C 243 " model vdw 2.294 2.520 nonbonded pdb=" NH1 ARG H 202 " pdb=" OD2 ASP H 223 " model vdw 2.305 2.520 nonbonded pdb=" OE2 GLU A 176 " pdb=" OG SER D 66 " model vdw 2.314 2.440 ... (remaining 65138 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 group one per residue 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: 2.910 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: 9.920 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 25.860 Find NCS groups from input model: 0.250 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 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 : 0.003 0.096 8705 Z= 0.207 Angle : 0.686 7.754 11876 Z= 0.369 Chirality : 0.043 0.165 1423 Planarity : 0.005 0.096 1507 Dihedral : 11.767 89.582 2877 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.12 % Allowed : 0.12 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.25), residues: 1162 helix: 0.58 (0.26), residues: 407 sheet: -0.16 (0.30), residues: 269 loop : -0.23 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 63 HIS 0.007 0.001 HIS A 309 PHE 0.035 0.002 PHE A 139 TYR 0.015 0.001 TYR A 44 ARG 0.009 0.001 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 CYS cc_start: 0.6874 (t) cc_final: 0.6539 (t) REVERT: B 207 SER cc_start: 0.7336 (t) cc_final: 0.6882 (m) REVERT: B 255 CYS cc_start: 0.8373 (t) cc_final: 0.7946 (t) REVERT: B 305 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7649 (tm-30) REVERT: C 223 THR cc_start: 0.7828 (p) cc_final: 0.7618 (p) REVERT: C 339 TRP cc_start: 0.8841 (m100) cc_final: 0.8543 (m100) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.1907 time to fit residues: 51.5744 Evaluate side-chains 146 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 0.0970 chunk 48 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 55 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 295 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN G 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8705 Z= 0.188 Angle : 0.629 7.793 11876 Z= 0.324 Chirality : 0.043 0.147 1423 Planarity : 0.004 0.041 1507 Dihedral : 4.591 22.767 1249 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.93 % Allowed : 9.89 % Favored : 88.18 % 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: 0.18 (0.25), residues: 1162 helix: 0.79 (0.27), residues: 416 sheet: -0.01 (0.31), residues: 272 loop : -0.25 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.004 0.001 HIS A 99 PHE 0.014 0.001 PHE H 212 TYR 0.014 0.001 TYR H 60 ARG 0.006 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 CYS cc_start: 0.6871 (t) cc_final: 0.6421 (t) REVERT: B 207 SER cc_start: 0.7395 (t) cc_final: 0.6804 (m) REVERT: B 255 CYS cc_start: 0.8166 (t) cc_final: 0.7908 (t) REVERT: C 223 THR cc_start: 0.7695 (p) cc_final: 0.7464 (p) REVERT: D 29 ASN cc_start: 0.8364 (t0) cc_final: 0.8150 (t0) REVERT: G 36 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.7040 (t0) outliers start: 16 outliers final: 11 residues processed: 170 average time/residue: 0.1801 time to fit residues: 43.5267 Evaluate side-chains 169 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 157 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 0.0020 chunk 87 optimal weight: 0.0570 chunk 71 optimal weight: 0.0980 chunk 29 optimal weight: 6.9990 chunk 105 optimal weight: 0.3980 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 overall best weight: 0.2706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8705 Z= 0.152 Angle : 0.574 7.924 11876 Z= 0.293 Chirality : 0.041 0.143 1423 Planarity : 0.004 0.042 1507 Dihedral : 4.139 21.483 1249 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.17 % Allowed : 12.06 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1162 helix: 0.96 (0.27), residues: 413 sheet: 0.06 (0.31), residues: 260 loop : -0.13 (0.30), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.004 0.001 HIS A 99 PHE 0.013 0.001 PHE B 190 TYR 0.013 0.001 TYR H 60 ARG 0.004 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 179 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 118 LEU cc_start: 0.8587 (tp) cc_final: 0.8256 (tt) REVERT: A 294 CYS cc_start: 0.6919 (t) cc_final: 0.6610 (t) REVERT: B 207 SER cc_start: 0.7342 (t) cc_final: 0.6794 (m) REVERT: B 255 CYS cc_start: 0.7993 (t) cc_final: 0.7719 (t) REVERT: B 305 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7528 (tm-30) REVERT: B 322 HIS cc_start: 0.7753 (t-90) cc_final: 0.7535 (t70) REVERT: C 163 ASP cc_start: 0.7971 (p0) cc_final: 0.7750 (p0) REVERT: H 192 MET cc_start: 0.7951 (tmm) cc_final: 0.7617 (tmm) REVERT: H 204 SER cc_start: 0.8502 (t) cc_final: 0.8215 (m) outliers start: 18 outliers final: 14 residues processed: 183 average time/residue: 0.1742 time to fit residues: 45.6132 Evaluate side-chains 166 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 152 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 54 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 0.0570 chunk 30 optimal weight: 0.4980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8705 Z= 0.183 Angle : 0.587 8.266 11876 Z= 0.298 Chirality : 0.042 0.134 1423 Planarity : 0.004 0.045 1507 Dihedral : 4.097 21.963 1249 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.77 % Allowed : 15.56 % Favored : 81.66 % 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: 0.32 (0.25), residues: 1162 helix: 1.09 (0.27), residues: 412 sheet: -0.02 (0.31), residues: 264 loop : -0.29 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 211 HIS 0.006 0.001 HIS C 225 PHE 0.020 0.002 PHE A 255 TYR 0.011 0.001 TYR H 60 ARG 0.005 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 159 time to evaluate : 0.899 Fit side-chains REVERT: A 118 LEU cc_start: 0.8507 (tp) cc_final: 0.8287 (tt) REVERT: A 294 CYS cc_start: 0.7133 (t) cc_final: 0.6868 (t) REVERT: B 14 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7418 (tm-30) REVERT: B 207 SER cc_start: 0.7499 (t) cc_final: 0.6863 (m) REVERT: B 255 CYS cc_start: 0.7976 (t) cc_final: 0.7685 (t) REVERT: B 305 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7637 (tm-30) REVERT: B 341 ASP cc_start: 0.8868 (t0) cc_final: 0.8497 (t70) REVERT: C 234 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8215 (m-80) REVERT: H 192 MET cc_start: 0.7950 (tmm) cc_final: 0.7644 (tmm) REVERT: H 204 SER cc_start: 0.8467 (t) cc_final: 0.8252 (m) outliers start: 23 outliers final: 17 residues processed: 167 average time/residue: 0.1768 time to fit residues: 42.2061 Evaluate side-chains 164 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 223 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 57 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8705 Z= 0.252 Angle : 0.605 8.384 11876 Z= 0.311 Chirality : 0.043 0.137 1423 Planarity : 0.004 0.047 1507 Dihedral : 4.212 22.859 1249 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.74 % Allowed : 15.80 % Favored : 80.46 % 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: 0.26 (0.25), residues: 1162 helix: 1.12 (0.27), residues: 412 sheet: -0.12 (0.31), residues: 264 loop : -0.36 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 211 HIS 0.007 0.001 HIS C 225 PHE 0.019 0.002 PHE C 199 TYR 0.014 0.002 TYR C 105 ARG 0.006 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 148 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: B 14 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7446 (tm-30) REVERT: B 207 SER cc_start: 0.7600 (t) cc_final: 0.6912 (m) REVERT: B 255 CYS cc_start: 0.8011 (t) cc_final: 0.7755 (t) REVERT: B 341 ASP cc_start: 0.8940 (t0) cc_final: 0.8627 (t70) REVERT: C 234 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: H 192 MET cc_start: 0.8000 (tmm) cc_final: 0.7659 (tmm) REVERT: H 204 SER cc_start: 0.8549 (t) cc_final: 0.8298 (m) outliers start: 31 outliers final: 23 residues processed: 160 average time/residue: 0.1990 time to fit residues: 45.7184 Evaluate side-chains 168 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 1.9990 chunk 100 optimal weight: 0.0020 chunk 22 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8705 Z= 0.242 Angle : 0.601 8.861 11876 Z= 0.309 Chirality : 0.043 0.138 1423 Planarity : 0.004 0.049 1507 Dihedral : 4.262 23.135 1249 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.70 % Allowed : 17.01 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1162 helix: 1.12 (0.27), residues: 411 sheet: -0.24 (0.31), residues: 264 loop : -0.43 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.007 0.001 HIS C 225 PHE 0.021 0.002 PHE H 212 TYR 0.014 0.002 TYR C 105 ARG 0.005 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 150 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 139 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7591 (t80) REVERT: B 14 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7483 (tm-30) REVERT: B 341 ASP cc_start: 0.8953 (t0) cc_final: 0.8664 (t70) REVERT: C 234 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8296 (m-80) REVERT: H 192 MET cc_start: 0.7983 (tmm) cc_final: 0.7672 (tmm) REVERT: H 204 SER cc_start: 0.8592 (t) cc_final: 0.8333 (m) outliers start: 39 outliers final: 30 residues processed: 166 average time/residue: 0.1678 time to fit residues: 40.1377 Evaluate side-chains 175 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 139 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 62 optimal weight: 0.0370 chunk 111 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8705 Z= 0.194 Angle : 0.586 9.195 11876 Z= 0.299 Chirality : 0.042 0.135 1423 Planarity : 0.004 0.049 1507 Dihedral : 4.159 22.930 1249 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.07 % Allowed : 18.70 % Favored : 76.24 % 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: 0.22 (0.25), residues: 1162 helix: 1.20 (0.27), residues: 411 sheet: -0.26 (0.31), residues: 264 loop : -0.42 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.007 0.001 HIS C 225 PHE 0.016 0.001 PHE H 212 TYR 0.011 0.001 TYR C 105 ARG 0.009 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 155 time to evaluate : 0.882 Fit side-chains REVERT: A 139 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7282 (t80) REVERT: B 14 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7418 (tm-30) REVERT: B 341 ASP cc_start: 0.8955 (t0) cc_final: 0.8643 (t70) REVERT: C 211 TRP cc_start: 0.9061 (OUTLIER) cc_final: 0.8734 (m100) REVERT: C 234 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8265 (m-80) REVERT: G 11 GLN cc_start: 0.7412 (pp30) cc_final: 0.6954 (pp30) REVERT: H 138 ILE cc_start: 0.6446 (pt) cc_final: 0.6145 (pt) REVERT: H 204 SER cc_start: 0.8528 (t) cc_final: 0.8298 (m) outliers start: 42 outliers final: 32 residues processed: 172 average time/residue: 0.1765 time to fit residues: 43.4813 Evaluate side-chains 181 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 300 LEU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 140 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 0.1980 chunk 10 optimal weight: 0.5980 chunk 87 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8705 Z= 0.193 Angle : 0.592 8.887 11876 Z= 0.301 Chirality : 0.042 0.132 1423 Planarity : 0.004 0.073 1507 Dihedral : 4.133 22.574 1249 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.58 % Allowed : 18.82 % Favored : 76.60 % 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: 0.24 (0.25), residues: 1162 helix: 1.24 (0.27), residues: 412 sheet: -0.28 (0.30), residues: 265 loop : -0.42 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 211 HIS 0.006 0.001 HIS C 225 PHE 0.015 0.001 PHE A 139 TYR 0.011 0.001 TYR C 105 ARG 0.016 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 0.971 Fit side-chains REVERT: A 139 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7541 (t80) REVERT: B 341 ASP cc_start: 0.8956 (t0) cc_final: 0.8646 (t70) REVERT: C 234 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8280 (m-80) REVERT: H 138 ILE cc_start: 0.6405 (pt) cc_final: 0.6117 (pt) REVERT: H 204 SER cc_start: 0.8465 (t) cc_final: 0.8246 (m) outliers start: 38 outliers final: 30 residues processed: 169 average time/residue: 0.1936 time to fit residues: 46.4738 Evaluate side-chains 177 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 145 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.0980 chunk 94 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 103 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 67 optimal weight: 0.1980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8705 Z= 0.170 Angle : 0.595 9.464 11876 Z= 0.301 Chirality : 0.041 0.143 1423 Planarity : 0.004 0.055 1507 Dihedral : 4.015 22.481 1249 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.62 % Allowed : 19.78 % Favored : 76.60 % 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: 0.25 (0.25), residues: 1162 helix: 1.23 (0.27), residues: 417 sheet: -0.35 (0.30), residues: 271 loop : -0.35 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 143 HIS 0.006 0.001 HIS C 225 PHE 0.020 0.001 PHE A 139 TYR 0.009 0.001 TYR H 190 ARG 0.014 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 0.951 Fit side-chains REVERT: A 139 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7382 (t80) REVERT: B 341 ASP cc_start: 0.8958 (t0) cc_final: 0.8644 (t70) REVERT: C 234 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8235 (m-80) REVERT: G 11 GLN cc_start: 0.7398 (pp30) cc_final: 0.6972 (pp30) REVERT: H 138 ILE cc_start: 0.6248 (pt) cc_final: 0.5995 (pt) outliers start: 30 outliers final: 27 residues processed: 164 average time/residue: 0.1706 time to fit residues: 40.3352 Evaluate side-chains 176 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 0.0570 chunk 115 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 chunk 92 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8705 Z= 0.169 Angle : 0.592 9.200 11876 Z= 0.299 Chirality : 0.041 0.131 1423 Planarity : 0.004 0.055 1507 Dihedral : 3.919 22.108 1249 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.38 % Allowed : 20.02 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 1162 helix: 1.16 (0.27), residues: 424 sheet: -0.30 (0.30), residues: 266 loop : -0.29 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.007 0.001 HIS C 225 PHE 0.017 0.001 PHE A 135 TYR 0.009 0.001 TYR H 60 ARG 0.012 0.000 ARG A 229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: A 139 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7347 (t80) REVERT: B 305 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7598 (tm-30) REVERT: B 341 ASP cc_start: 0.8962 (t0) cc_final: 0.8633 (t70) REVERT: C 234 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8243 (m-80) REVERT: G 11 GLN cc_start: 0.7406 (pp30) cc_final: 0.6980 (pp30) REVERT: H 138 ILE cc_start: 0.6112 (pt) cc_final: 0.5804 (pt) REVERT: H 192 MET cc_start: 0.7877 (tmm) cc_final: 0.7445 (tmm) outliers start: 28 outliers final: 25 residues processed: 160 average time/residue: 0.1760 time to fit residues: 40.4686 Evaluate side-chains 172 residues out of total 1005 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 148 CYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 225 HIS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.0870 chunk 92 optimal weight: 0.0010 chunk 38 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 11 optimal weight: 0.0470 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.147135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126259 restraints weight = 12664.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123550 restraints weight = 23196.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.124612 restraints weight = 23385.328| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8705 Z= 0.150 Angle : 0.583 9.137 11876 Z= 0.293 Chirality : 0.041 0.131 1423 Planarity : 0.004 0.055 1507 Dihedral : 3.825 21.839 1249 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.90 % Allowed : 21.11 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1162 helix: 1.30 (0.27), residues: 418 sheet: -0.17 (0.31), residues: 265 loop : -0.28 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.006 0.001 HIS C 225 PHE 0.018 0.001 PHE A 135 TYR 0.009 0.001 TYR H 60 ARG 0.012 0.000 ARG A 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1920.96 seconds wall clock time: 35 minutes 29.98 seconds (2129.98 seconds total)