Starting phenix.real_space_refine on Thu Nov 14 13:54:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geg_29969/11_2024/8geg_29969.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geg_29969/11_2024/8geg_29969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geg_29969/11_2024/8geg_29969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geg_29969/11_2024/8geg_29969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geg_29969/11_2024/8geg_29969.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8geg_29969/11_2024/8geg_29969.cif" } resolution = 3.8 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= -0.001 sd= 0.023 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 33 5.16 5 C 4150 2.51 5 N 1141 2.21 5 O 1157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6481 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 1925 Classifications: {'peptide': 307} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 174} Link IDs: {'PTRANS': 6, 'TRANS': 300} Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 645 Unresolved non-hydrogen angles: 802 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 4, 'GLU:plan': 24, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 398 Chain: "B" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2286 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 13, 'ASN:plan1': 8, 'ASP:plan': 21} Unresolved non-hydrogen planarities: 200 Chain: "G" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 318 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "R" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1937 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 119 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.63, per 1000 atoms: 0.71 Number of scatterers: 6481 At special positions: 0 Unit cell: (71.02, 96.46, 129.32, 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 33 16.00 O 1157 8.00 N 1141 7.00 C 4150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 1.0 seconds 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1848 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 8 sheets defined 52.3% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.651A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.530A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 113 Processing helix chain 'A' and resid 125 through 135 Processing helix chain 'A' and resid 146 through 153 Processing helix chain 'A' and resid 156 through 165 Processing helix chain 'A' and resid 172 through 181 removed outlier: 3.577A pdb=" N PHE A 178 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 238 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.913A pdb=" N ASN A 254 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.635A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.343A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 4.517A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'B' and resid 8 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.916A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 24 removed outlier: 4.093A 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 'R' and resid 32 through 61 removed outlier: 3.756A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 4.268A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.608A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.122A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 removed outlier: 4.388A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 181 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.509A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA R 202 " --> pdb=" O ALA R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 238 Processing helix chain 'R' and resid 270 through 299 removed outlier: 4.273A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.187A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 4.010A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 5.921A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.723A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.095A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.341A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.573A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.309A 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: 3.718A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.552A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.749A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1218 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: 2.07 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1317 1.33 - 1.45: 1647 1.45 - 1.57: 3605 1.57 - 1.69: 1 1.69 - 1.81: 44 Bond restraints: 6614 Sorted by residual: bond pdb=" CA ARG B 137 " pdb=" C ARG B 137 " ideal model delta sigma weight residual 1.521 1.465 0.056 1.28e-02 6.10e+03 1.88e+01 bond pdb=" CA GLU B 138 " pdb=" C GLU B 138 " ideal model delta sigma weight residual 1.522 1.487 0.036 1.20e-02 6.94e+03 8.80e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.451 -0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.574 -0.051 2.00e-02 2.50e+03 6.60e+00 bond pdb=" CA ALA B 140 " pdb=" C ALA B 140 " ideal model delta sigma weight residual 1.525 1.492 0.033 1.32e-02 5.74e+03 6.25e+00 ... (remaining 6609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 8966 1.96 - 3.91: 98 3.91 - 5.87: 20 5.87 - 7.83: 3 7.83 - 9.78: 2 Bond angle restraints: 9089 Sorted by residual: angle pdb=" N HIS B 142 " pdb=" CA HIS B 142 " pdb=" C HIS B 142 " ideal model delta sigma weight residual 108.52 100.36 8.16 1.63e+00 3.76e-01 2.51e+01 angle pdb=" N ARG B 137 " pdb=" CA ARG B 137 " pdb=" C ARG B 137 " ideal model delta sigma weight residual 108.76 101.07 7.69 1.58e+00 4.01e-01 2.37e+01 angle pdb=" N LEU A 132 " pdb=" CA LEU A 132 " pdb=" C LEU A 132 " ideal model delta sigma weight residual 111.28 106.18 5.10 1.09e+00 8.42e-01 2.19e+01 angle pdb=" C THR B 143 " pdb=" N GLY B 144 " pdb=" CA GLY B 144 " ideal model delta sigma weight residual 122.63 116.60 6.03 1.34e+00 5.57e-01 2.03e+01 angle pdb=" N GLY B 141 " pdb=" CA GLY B 141 " pdb=" C GLY B 141 " ideal model delta sigma weight residual 113.18 122.96 -9.78 2.37e+00 1.78e-01 1.70e+01 ... (remaining 9084 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 3500 16.03 - 32.06: 218 32.06 - 48.08: 39 48.08 - 64.11: 4 64.11 - 80.14: 7 Dihedral angle restraints: 3768 sinusoidal: 931 harmonic: 2837 Sorted by residual: dihedral pdb=" CA TYR B 59 " pdb=" C TYR B 59 " pdb=" N ALA B 60 " pdb=" CA ALA B 60 " ideal model delta harmonic sigma weight residual -180.00 -160.72 -19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA PHE R 208 " pdb=" C PHE R 208 " pdb=" N TYR R 209 " pdb=" CA TYR R 209 " ideal model delta harmonic sigma weight residual -180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ALA R 85 " pdb=" C ALA R 85 " pdb=" N VAL R 86 " pdb=" CA VAL R 86 " ideal model delta harmonic sigma weight residual 180.00 -163.24 -16.76 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 3765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 815 0.042 - 0.083: 217 0.083 - 0.125: 68 0.125 - 0.166: 2 0.166 - 0.208: 3 Chirality restraints: 1105 Sorted by residual: chirality pdb=" CA LEU B 139 " pdb=" N LEU B 139 " pdb=" C LEU B 139 " pdb=" CB LEU B 139 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 7.00e-01 ... (remaining 1102 not shown) Planarity restraints: 1169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 140 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.26e+00 pdb=" C ALA B 140 " 0.031 2.00e-02 2.50e+03 pdb=" O ALA B 140 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY B 141 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO R 323 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 357 " 0.012 2.00e-02 2.50e+03 1.23e-02 2.28e+00 pdb=" CG HIS A 357 " -0.027 2.00e-02 2.50e+03 pdb=" ND1 HIS A 357 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS A 357 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 357 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS A 357 " 0.003 2.00e-02 2.50e+03 ... (remaining 1166 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1001 2.76 - 3.29: 6506 3.29 - 3.83: 11005 3.83 - 4.36: 11133 4.36 - 4.90: 20225 Nonbonded interactions: 49870 Sorted by model distance: nonbonded pdb=" OG1 THR R 66 " pdb=" OD1 ASN R 69 " model vdw 2.221 3.040 nonbonded pdb=" O GLY B 77 " pdb=" N LEU B 95 " model vdw 2.302 3.120 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.330 3.040 nonbonded pdb=" O GLU A 327 " pdb=" N GLU A 330 " model vdw 2.377 3.120 nonbonded pdb=" OE1 GLN A 384 " pdb=" NE2 GLN R 229 " model vdw 2.385 3.120 ... (remaining 49865 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.090 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 19.460 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 0.056 6614 Z= 0.216 Angle : 0.582 9.782 9089 Z= 0.330 Chirality : 0.041 0.208 1105 Planarity : 0.003 0.040 1169 Dihedral : 12.032 80.140 1920 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.28), residues: 948 helix: 2.68 (0.25), residues: 433 sheet: 0.03 (0.38), residues: 180 loop : -0.76 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 281 HIS 0.013 0.001 HIS A 357 PHE 0.015 0.001 PHE R 289 TYR 0.015 0.001 TYR B 59 ARG 0.002 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.761 Fit side-chains REVERT: A 281 TRP cc_start: 0.7514 (m100) cc_final: 0.7237 (m100) REVERT: B 139 LEU cc_start: 0.7897 (mt) cc_final: 0.7693 (mt) REVERT: B 333 ASP cc_start: 0.8033 (p0) cc_final: 0.7706 (p0) REVERT: R 279 MET cc_start: 0.8616 (tpp) cc_final: 0.8286 (mmm) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1263 time to fit residues: 18.2168 Evaluate side-chains 70 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.0050 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 0.1980 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN B 75 GLN B 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6614 Z= 0.168 Angle : 0.506 5.546 9089 Z= 0.279 Chirality : 0.041 0.143 1105 Planarity : 0.003 0.036 1169 Dihedral : 4.359 27.986 1027 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.04 % Allowed : 10.63 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.28), residues: 948 helix: 2.83 (0.24), residues: 448 sheet: 0.02 (0.37), residues: 193 loop : -0.58 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 173 HIS 0.004 0.001 HIS B 54 PHE 0.018 0.001 PHE B 292 TYR 0.021 0.001 TYR B 59 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.715 Fit side-chains REVERT: B 333 ASP cc_start: 0.8197 (p0) cc_final: 0.7920 (p0) REVERT: G 48 ASP cc_start: 0.7516 (t0) cc_final: 0.7042 (t70) REVERT: R 169 ILE cc_start: 0.9059 (mm) cc_final: 0.8690 (mt) outliers start: 14 outliers final: 12 residues processed: 84 average time/residue: 0.1213 time to fit residues: 15.5959 Evaluate side-chains 81 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6614 Z= 0.212 Angle : 0.503 5.430 9089 Z= 0.276 Chirality : 0.041 0.151 1105 Planarity : 0.003 0.032 1169 Dihedral : 4.251 26.473 1027 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.12 % Allowed : 13.67 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.28), residues: 948 helix: 2.99 (0.24), residues: 447 sheet: -0.10 (0.36), residues: 193 loop : -0.56 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.004 0.001 HIS A 362 PHE 0.013 0.001 PHE B 235 TYR 0.020 0.001 TYR B 59 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.777 Fit side-chains REVERT: B 261 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8676 (mt) REVERT: B 333 ASP cc_start: 0.8284 (p0) cc_final: 0.7778 (p0) REVERT: G 48 ASP cc_start: 0.7522 (t0) cc_final: 0.6958 (t70) outliers start: 19 outliers final: 15 residues processed: 82 average time/residue: 0.1240 time to fit residues: 15.6624 Evaluate side-chains 85 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS ** R 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6614 Z= 0.169 Angle : 0.468 5.375 9089 Z= 0.257 Chirality : 0.040 0.149 1105 Planarity : 0.003 0.029 1169 Dihedral : 4.053 26.198 1027 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.34 % Allowed : 17.79 % Favored : 77.87 % 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: 1.86 (0.28), residues: 948 helix: 3.01 (0.24), residues: 454 sheet: -0.15 (0.36), residues: 189 loop : -0.62 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS B 54 PHE 0.021 0.001 PHE B 292 TYR 0.015 0.001 TYR R 141 ARG 0.002 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.773 Fit side-chains REVERT: B 333 ASP cc_start: 0.8310 (p0) cc_final: 0.7780 (p0) REVERT: R 174 TYR cc_start: 0.7251 (p90) cc_final: 0.7028 (p90) outliers start: 20 outliers final: 13 residues processed: 90 average time/residue: 0.1312 time to fit residues: 17.5315 Evaluate side-chains 82 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 0.0270 chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 HIS R 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6614 Z= 0.410 Angle : 0.622 6.146 9089 Z= 0.344 Chirality : 0.043 0.161 1105 Planarity : 0.004 0.028 1169 Dihedral : 4.693 27.698 1027 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 6.29 % Allowed : 18.44 % Favored : 75.27 % 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: 1.52 (0.27), residues: 948 helix: 2.67 (0.23), residues: 446 sheet: -0.11 (0.37), residues: 170 loop : -0.70 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 339 HIS 0.008 0.001 HIS A 362 PHE 0.031 0.002 PHE B 292 TYR 0.017 0.002 TYR B 59 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 67 time to evaluate : 0.747 Fit side-chains REVERT: A 255 MET cc_start: 0.7451 (mmm) cc_final: 0.6754 (tpp) REVERT: B 333 ASP cc_start: 0.8477 (p0) cc_final: 0.7939 (p0) REVERT: G 48 ASP cc_start: 0.7609 (t0) cc_final: 0.6765 (t70) outliers start: 29 outliers final: 18 residues processed: 87 average time/residue: 0.1253 time to fit residues: 16.3286 Evaluate side-chains 82 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 89 optimal weight: 0.0870 overall best weight: 0.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6614 Z= 0.200 Angle : 0.511 6.779 9089 Z= 0.278 Chirality : 0.040 0.152 1105 Planarity : 0.003 0.041 1169 Dihedral : 4.329 27.979 1027 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.21 % Allowed : 19.74 % Favored : 75.05 % 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: 1.67 (0.28), residues: 948 helix: 2.87 (0.24), residues: 451 sheet: -0.20 (0.37), residues: 179 loop : -0.73 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 339 HIS 0.006 0.001 HIS B 54 PHE 0.027 0.001 PHE B 292 TYR 0.017 0.001 TYR R 141 ARG 0.001 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.801 Fit side-chains REVERT: B 261 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8768 (mt) REVERT: B 333 ASP cc_start: 0.8428 (p0) cc_final: 0.7848 (p0) REVERT: G 48 ASP cc_start: 0.7443 (t0) cc_final: 0.6702 (t70) REVERT: R 174 TYR cc_start: 0.7262 (p90) cc_final: 0.6846 (p90) outliers start: 24 outliers final: 15 residues processed: 95 average time/residue: 0.1316 time to fit residues: 18.6327 Evaluate side-chains 80 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 165 SER Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6614 Z= 0.203 Angle : 0.513 6.890 9089 Z= 0.277 Chirality : 0.040 0.153 1105 Planarity : 0.003 0.028 1169 Dihedral : 4.265 28.447 1027 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.99 % Allowed : 21.26 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.28), residues: 948 helix: 2.95 (0.24), residues: 451 sheet: -0.21 (0.37), residues: 179 loop : -0.81 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 277 HIS 0.006 0.001 HIS B 54 PHE 0.016 0.001 PHE B 292 TYR 0.014 0.001 TYR R 141 ARG 0.002 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.767 Fit side-chains REVERT: B 261 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8777 (mt) REVERT: B 333 ASP cc_start: 0.8423 (p0) cc_final: 0.7840 (p0) REVERT: G 48 ASP cc_start: 0.7403 (t0) cc_final: 0.6632 (t70) REVERT: R 174 TYR cc_start: 0.7129 (p90) cc_final: 0.6731 (p90) outliers start: 23 outliers final: 15 residues processed: 84 average time/residue: 0.1142 time to fit residues: 15.2723 Evaluate side-chains 82 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6614 Z= 0.228 Angle : 0.525 6.760 9089 Z= 0.283 Chirality : 0.041 0.154 1105 Planarity : 0.003 0.028 1169 Dihedral : 4.314 29.286 1027 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.77 % Allowed : 20.82 % Favored : 74.40 % 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: 1.65 (0.28), residues: 948 helix: 2.95 (0.24), residues: 451 sheet: -0.32 (0.36), residues: 179 loop : -0.82 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.007 0.001 HIS A 220 PHE 0.013 0.001 PHE B 235 TYR 0.020 0.001 TYR R 141 ARG 0.002 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.778 Fit side-chains REVERT: B 261 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8747 (mt) REVERT: B 333 ASP cc_start: 0.8427 (p0) cc_final: 0.7817 (p0) REVERT: R 174 TYR cc_start: 0.7125 (p90) cc_final: 0.6574 (p90) outliers start: 22 outliers final: 16 residues processed: 84 average time/residue: 0.1185 time to fit residues: 15.2707 Evaluate side-chains 82 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 213 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 85 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6614 Z= 0.167 Angle : 0.515 8.108 9089 Z= 0.272 Chirality : 0.040 0.148 1105 Planarity : 0.003 0.029 1169 Dihedral : 4.159 29.702 1027 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.90 % Allowed : 22.34 % Favored : 73.75 % 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: 1.66 (0.28), residues: 948 helix: 3.04 (0.24), residues: 447 sheet: -0.41 (0.36), residues: 185 loop : -0.84 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 277 HIS 0.006 0.001 HIS B 54 PHE 0.015 0.001 PHE R 289 TYR 0.019 0.001 TYR R 141 ARG 0.001 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.695 Fit side-chains REVERT: B 261 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8721 (mt) REVERT: B 333 ASP cc_start: 0.8557 (p0) cc_final: 0.8033 (p0) REVERT: R 174 TYR cc_start: 0.6922 (p90) cc_final: 0.6597 (p90) outliers start: 18 outliers final: 15 residues processed: 84 average time/residue: 0.1262 time to fit residues: 16.3186 Evaluate side-chains 85 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 88 optimal weight: 0.4980 chunk 76 optimal weight: 0.7980 chunk 7 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6614 Z= 0.161 Angle : 0.519 7.931 9089 Z= 0.274 Chirality : 0.040 0.152 1105 Planarity : 0.003 0.029 1169 Dihedral : 4.094 30.746 1027 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.69 % Allowed : 22.99 % Favored : 73.32 % 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: 1.70 (0.28), residues: 948 helix: 3.09 (0.24), residues: 447 sheet: -0.41 (0.36), residues: 187 loop : -0.84 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 339 HIS 0.006 0.001 HIS B 54 PHE 0.012 0.001 PHE B 199 TYR 0.019 0.001 TYR R 141 ARG 0.002 0.000 ARG G 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: B 261 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8711 (mt) REVERT: B 333 ASP cc_start: 0.8546 (p0) cc_final: 0.7993 (p0) REVERT: R 174 TYR cc_start: 0.6882 (p90) cc_final: 0.6611 (p90) outliers start: 17 outliers final: 15 residues processed: 82 average time/residue: 0.1292 time to fit residues: 15.9882 Evaluate side-chains 84 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 129 VAL Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 66 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.112918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.096764 restraints weight = 15652.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.098750 restraints weight = 9843.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.099956 restraints weight = 7105.273| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 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 : 0.003 0.030 6614 Z= 0.176 Angle : 0.525 7.410 9089 Z= 0.278 Chirality : 0.040 0.151 1105 Planarity : 0.003 0.029 1169 Dihedral : 4.094 29.413 1027 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.90 % Allowed : 23.21 % Favored : 72.89 % 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: 1.74 (0.28), residues: 948 helix: 3.12 (0.24), residues: 447 sheet: -0.39 (0.36), residues: 187 loop : -0.81 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 63 HIS 0.006 0.001 HIS B 54 PHE 0.013 0.001 PHE R 289 TYR 0.019 0.001 TYR R 141 ARG 0.002 0.000 ARG G 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1409.25 seconds wall clock time: 26 minutes 32.80 seconds (1592.80 seconds total)