Starting phenix.real_space_refine on Sat Apr 6 22:23:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4p_41890/04_2024/8u4p_41890_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4p_41890/04_2024/8u4p_41890.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4p_41890/04_2024/8u4p_41890_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4p_41890/04_2024/8u4p_41890_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4p_41890/04_2024/8u4p_41890_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4p_41890/04_2024/8u4p_41890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4p_41890/04_2024/8u4p_41890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4p_41890/04_2024/8u4p_41890_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4p_41890/04_2024/8u4p_41890_updated.pdb" } resolution = 3.15 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= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2008 atoms to isotropic. 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 48 5.16 5 C 4508 2.51 5 N 1179 2.21 5 O 1271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 193": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 97": "OD1" <-> "OD2" Residue "R PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 153": "OE1" <-> "OE2" Residue "R TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7006 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1777 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2516 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 345 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 2304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2304 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "R" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'CLR': 1, 'VH6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.22, per 1000 atoms: 0.60 Number of scatterers: 7006 At special positions: 0 Unit cell: (73.1, 102, 130.9, 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 48 16.00 O 1271 8.00 N 1179 7.00 C 4508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.3 seconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1690 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 9 sheets defined 41.4% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.894A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 removed outlier: 3.639A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.810A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'R' and resid 34 through 64 Proline residue: R 42 - end of helix Processing helix chain 'R' and resid 74 through 89 Processing helix chain 'R' and resid 91 through 99 Processing helix chain 'R' and resid 107 through 139 removed outlier: 3.789A pdb=" N VAL R 124 " --> pdb=" O LEU R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 174 removed outlier: 5.221A pdb=" N TYR R 157 " --> pdb=" O GLU R 153 " (cutoff:3.500A) Proline residue: R 163 - end of helix removed outlier: 4.043A pdb=" N THR R 168 " --> pdb=" O ALA R 164 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE R 169 " --> pdb=" O LEU R 165 " (cutoff:3.500A) Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 193 through 207 Processing helix chain 'R' and resid 209 through 226 removed outlier: 3.669A pdb=" N LYS R 225 " --> pdb=" O ILE R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 266 removed outlier: 3.863A pdb=" N ALA R 237 " --> pdb=" O GLN R 233 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU R 238 " --> pdb=" O LYS R 234 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE R 243 " --> pdb=" O LYS R 239 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU R 244 " --> pdb=" O THR R 240 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU R 246 " --> pdb=" O VAL R 242 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N CYS R 251 " --> pdb=" O ALA R 247 " (cutoff:3.500A) Proline residue: R 254 - end of helix Processing helix chain 'R' and resid 274 through 302 removed outlier: 4.458A pdb=" N PHE R 293 " --> pdb=" O ALA R 289 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N HIS R 294 " --> pdb=" O LEU R 290 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N CYS R 295 " --> pdb=" O ALA R 291 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N CYS R 296 " --> pdb=" O PHE R 292 " (cutoff:3.500A) Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 307 through 317 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.734A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.822A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.076A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.878A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 202 removed outlier: 3.824A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.866A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.518A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.843A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'R' and resid 175 through 180 removed outlier: 3.597A pdb=" N ASN R 176 " --> pdb=" O ASP R 187 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 975 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 2.79 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: 2220 1.34 - 1.46: 1251 1.46 - 1.57: 3618 1.57 - 1.69: 4 1.69 - 1.81: 65 Bond restraints: 7158 Sorted by residual: bond pdb=" C12 VH6 R 702 " pdb=" C13 VH6 R 702 " ideal model delta sigma weight residual 1.647 1.544 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C14 VH6 R 702 " pdb=" N01 VH6 R 702 " ideal model delta sigma weight residual 1.553 1.478 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C09 VH6 R 702 " pdb=" N08 VH6 R 702 " ideal model delta sigma weight residual 1.557 1.498 0.059 2.00e-02 2.50e+03 8.75e+00 bond pdb=" C09 VH6 R 702 " pdb=" C10 VH6 R 702 " ideal model delta sigma weight residual 1.602 1.548 0.054 2.00e-02 2.50e+03 7.16e+00 bond pdb=" C6 CLR R 701 " pdb=" C7 CLR R 701 " ideal model delta sigma weight residual 1.492 1.544 -0.052 2.00e-02 2.50e+03 6.64e+00 ... (remaining 7153 not shown) Histogram of bond angle deviations from ideal: 98.55 - 105.65: 89 105.65 - 112.74: 3868 112.74 - 119.84: 2335 119.84 - 126.93: 3330 126.93 - 134.03: 85 Bond angle restraints: 9707 Sorted by residual: angle pdb=" C20 VH6 R 702 " pdb=" C19 VH6 R 702 " pdb=" C22 VH6 R 702 " ideal model delta sigma weight residual 107.63 124.67 -17.04 3.00e+00 1.11e-01 3.23e+01 angle pdb=" C02 VH6 R 702 " pdb=" N01 VH6 R 702 " pdb=" C14 VH6 R 702 " ideal model delta sigma weight residual 131.91 115.47 16.44 3.00e+00 1.11e-01 3.00e+01 angle pdb=" C16 VH6 R 702 " pdb=" C15 VH6 R 702 " pdb=" N08 VH6 R 702 " ideal model delta sigma weight residual 109.49 118.59 -9.10 3.00e+00 1.11e-01 9.20e+00 angle pdb=" C18 VH6 R 702 " pdb=" C19 VH6 R 702 " pdb=" C20 VH6 R 702 " ideal model delta sigma weight residual 120.03 112.02 8.01 3.00e+00 1.11e-01 7.13e+00 angle pdb=" C22 CLR R 701 " pdb=" C23 CLR R 701 " pdb=" C24 CLR R 701 " ideal model delta sigma weight residual 111.95 104.11 7.84 3.00e+00 1.11e-01 6.84e+00 ... (remaining 9702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.15: 4179 34.15 - 68.30: 80 68.30 - 102.45: 20 102.45 - 136.60: 6 136.60 - 170.76: 3 Dihedral angle restraints: 4288 sinusoidal: 1682 harmonic: 2606 Sorted by residual: dihedral pdb=" C14 VH6 R 702 " pdb=" C12 VH6 R 702 " pdb=" C13 VH6 R 702 " pdb=" N11 VH6 R 702 " ideal model delta sinusoidal sigma weight residual 130.46 -58.78 -170.76 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N23 VH6 R 702 " pdb=" C35 VH6 R 702 " pdb=" C36 VH6 R 702 " pdb=" N34 VH6 R 702 " ideal model delta sinusoidal sigma weight residual 92.67 -101.57 -165.76 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" N27 VH6 R 702 " pdb=" C28 VH6 R 702 " pdb=" C29 VH6 R 702 " pdb=" N30 VH6 R 702 " ideal model delta sinusoidal sigma weight residual -96.91 40.97 -137.88 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 4285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1016 0.071 - 0.142: 99 0.142 - 0.212: 0 0.212 - 0.283: 1 0.283 - 0.354: 3 Chirality restraints: 1119 Sorted by residual: chirality pdb=" C17 CLR R 701 " pdb=" C13 CLR R 701 " pdb=" C16 CLR R 701 " pdb=" C20 CLR R 701 " both_signs ideal model delta sigma weight residual False 2.55 2.91 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C20 CLR R 701 " pdb=" C17 CLR R 701 " pdb=" C21 CLR R 701 " pdb=" C22 CLR R 701 " both_signs ideal model delta sigma weight residual False 2.59 2.90 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C13 CLR R 701 " pdb=" C12 CLR R 701 " pdb=" C14 CLR R 701 " pdb=" C17 CLR R 701 " both_signs ideal model delta sigma weight residual False -2.93 -3.23 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 1116 not shown) Planarity restraints: 1208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 152 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.28e+00 pdb=" C ALA R 152 " 0.047 2.00e-02 2.50e+03 pdb=" O ALA R 152 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU R 153 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 298 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO R 299 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO R 299 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 299 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 158 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.02e+00 pdb=" C VAL R 158 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL R 158 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY R 159 " 0.008 2.00e-02 2.50e+03 ... (remaining 1205 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1209 2.77 - 3.30: 6438 3.30 - 3.84: 11002 3.84 - 4.37: 12880 4.37 - 4.90: 23481 Nonbonded interactions: 55010 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.240 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.245 2.440 nonbonded pdb=" OG SER A 293 " pdb=" OE1 GLU A 298 " model vdw 2.281 2.440 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.313 2.520 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.315 2.520 ... (remaining 55005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 6.130 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.840 Find NCS groups from input model: 0.200 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.004 0.103 7158 Z= 0.257 Angle : 0.625 17.044 9707 Z= 0.287 Chirality : 0.044 0.354 1119 Planarity : 0.003 0.036 1208 Dihedral : 17.042 170.756 2595 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.52 (0.29), residues: 882 helix: 1.74 (0.28), residues: 381 sheet: -0.17 (0.38), residues: 180 loop : -1.02 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS R 79 PHE 0.012 0.001 PHE A 189 TYR 0.008 0.001 TYR R 116 ARG 0.004 0.000 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.825 Fit side-chains REVERT: A 53 MET cc_start: 0.3392 (ttt) cc_final: 0.3191 (ttp) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2295 time to fit residues: 28.0915 Evaluate side-chains 76 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 79 optimal weight: 0.3980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7158 Z= 0.218 Angle : 0.483 5.050 9707 Z= 0.254 Chirality : 0.041 0.132 1119 Planarity : 0.003 0.035 1208 Dihedral : 12.939 153.915 1049 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.35 % Allowed : 6.21 % Favored : 92.44 % 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: 0.83 (0.29), residues: 882 helix: 2.13 (0.28), residues: 374 sheet: -0.15 (0.37), residues: 184 loop : -0.90 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS R 79 PHE 0.014 0.001 PHE A 189 TYR 0.009 0.001 TYR R 116 ARG 0.003 0.000 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.743 Fit side-chains REVERT: A 10 LYS cc_start: 0.7615 (tptt) cc_final: 0.7264 (tppt) outliers start: 10 outliers final: 8 residues processed: 86 average time/residue: 0.2325 time to fit residues: 25.8759 Evaluate side-chains 82 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain R residue 131 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 80 optimal weight: 0.0970 chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7158 Z= 0.155 Angle : 0.435 5.031 9707 Z= 0.231 Chirality : 0.039 0.131 1119 Planarity : 0.003 0.034 1208 Dihedral : 11.196 160.582 1049 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.89 % Allowed : 6.75 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.29), residues: 882 helix: 2.32 (0.28), residues: 375 sheet: 0.03 (0.39), residues: 176 loop : -0.88 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS R 79 PHE 0.013 0.001 PHE A 189 TYR 0.008 0.001 TYR R 116 ARG 0.004 0.000 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.808 Fit side-chains REVERT: A 10 LYS cc_start: 0.7600 (tptt) cc_final: 0.7259 (tppt) outliers start: 14 outliers final: 9 residues processed: 92 average time/residue: 0.2351 time to fit residues: 28.1017 Evaluate side-chains 82 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 131 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 41 optimal weight: 0.0270 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 70 optimal weight: 0.4980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7158 Z= 0.152 Angle : 0.434 5.091 9707 Z= 0.229 Chirality : 0.039 0.132 1119 Planarity : 0.003 0.034 1208 Dihedral : 10.270 156.098 1049 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.29 % Allowed : 8.50 % Favored : 89.20 % 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: 1.08 (0.29), residues: 882 helix: 2.35 (0.28), residues: 376 sheet: -0.00 (0.39), residues: 179 loop : -0.82 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS R 79 PHE 0.013 0.001 PHE A 189 TYR 0.008 0.001 TYR R 116 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.821 Fit side-chains REVERT: A 10 LYS cc_start: 0.7605 (tptt) cc_final: 0.7257 (tppt) outliers start: 17 outliers final: 13 residues processed: 92 average time/residue: 0.2253 time to fit residues: 27.1745 Evaluate side-chains 88 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 131 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7158 Z= 0.322 Angle : 0.519 6.020 9707 Z= 0.273 Chirality : 0.042 0.135 1119 Planarity : 0.003 0.033 1208 Dihedral : 10.491 160.822 1049 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.16 % Allowed : 10.53 % Favored : 87.31 % 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: 0.85 (0.29), residues: 882 helix: 2.19 (0.28), residues: 375 sheet: -0.23 (0.38), residues: 182 loop : -0.88 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.006 0.001 HIS R 79 PHE 0.017 0.002 PHE A 189 TYR 0.009 0.001 TYR R 116 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 1.009 Fit side-chains REVERT: A 10 LYS cc_start: 0.7694 (tptt) cc_final: 0.7309 (tppt) outliers start: 16 outliers final: 15 residues processed: 90 average time/residue: 0.2308 time to fit residues: 27.1884 Evaluate side-chains 86 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 131 SER Chi-restraints excluded: chain R residue 186 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7158 Z= 0.153 Angle : 0.435 5.143 9707 Z= 0.231 Chirality : 0.039 0.131 1119 Planarity : 0.003 0.033 1208 Dihedral : 10.093 156.505 1049 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.70 % Allowed : 10.80 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.29), residues: 882 helix: 2.37 (0.28), residues: 375 sheet: -0.07 (0.38), residues: 179 loop : -0.91 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS R 79 PHE 0.013 0.001 PHE A 189 TYR 0.008 0.001 TYR R 116 ARG 0.003 0.000 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 0.736 Fit side-chains REVERT: A 10 LYS cc_start: 0.7618 (tptt) cc_final: 0.7251 (tppt) outliers start: 20 outliers final: 16 residues processed: 93 average time/residue: 0.2205 time to fit residues: 26.9304 Evaluate side-chains 88 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 131 SER Chi-restraints excluded: chain R residue 186 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 71 optimal weight: 0.0770 chunk 47 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7158 Z= 0.152 Angle : 0.433 5.195 9707 Z= 0.229 Chirality : 0.039 0.131 1119 Planarity : 0.003 0.033 1208 Dihedral : 9.874 152.396 1049 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.16 % Allowed : 11.74 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.29), residues: 882 helix: 2.41 (0.28), residues: 376 sheet: -0.07 (0.38), residues: 179 loop : -0.87 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS R 79 PHE 0.013 0.001 PHE A 189 TYR 0.007 0.001 TYR R 116 ARG 0.004 0.000 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.850 Fit side-chains REVERT: A 10 LYS cc_start: 0.7614 (tptt) cc_final: 0.7242 (tppt) outliers start: 16 outliers final: 15 residues processed: 89 average time/residue: 0.2190 time to fit residues: 25.7501 Evaluate side-chains 88 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 131 SER Chi-restraints excluded: chain R residue 186 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.0030 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7158 Z= 0.114 Angle : 0.413 5.162 9707 Z= 0.220 Chirality : 0.039 0.131 1119 Planarity : 0.003 0.033 1208 Dihedral : 9.606 148.690 1049 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.16 % Allowed : 11.74 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.29), residues: 882 helix: 2.53 (0.28), residues: 375 sheet: 0.02 (0.37), residues: 182 loop : -0.81 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.000 HIS R 281 PHE 0.012 0.001 PHE A 189 TYR 0.007 0.001 TYR R 116 ARG 0.004 0.000 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.837 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 91 average time/residue: 0.2446 time to fit residues: 28.9053 Evaluate side-chains 89 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 131 SER Chi-restraints excluded: chain R residue 186 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.0570 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7158 Z= 0.188 Angle : 0.452 5.234 9707 Z= 0.238 Chirality : 0.040 0.161 1119 Planarity : 0.003 0.034 1208 Dihedral : 9.666 149.542 1049 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.89 % Allowed : 12.15 % Favored : 85.96 % 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: 1.12 (0.29), residues: 882 helix: 2.41 (0.28), residues: 378 sheet: -0.05 (0.38), residues: 179 loop : -0.80 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS R 79 PHE 0.014 0.001 PHE A 189 TYR 0.008 0.001 TYR R 116 ARG 0.004 0.000 ARG R 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.703 Fit side-chains REVERT: A 10 LYS cc_start: 0.7624 (tptt) cc_final: 0.7240 (tppt) REVERT: B 154 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8461 (t0) outliers start: 14 outliers final: 13 residues processed: 87 average time/residue: 0.2254 time to fit residues: 25.4715 Evaluate side-chains 88 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 131 SER Chi-restraints excluded: chain R residue 186 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 80 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 7 optimal weight: 0.0060 chunk 53 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7158 Z= 0.141 Angle : 0.433 5.182 9707 Z= 0.229 Chirality : 0.039 0.155 1119 Planarity : 0.003 0.033 1208 Dihedral : 9.532 147.797 1049 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.02 % Allowed : 12.15 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.29), residues: 882 helix: 2.47 (0.28), residues: 377 sheet: -0.03 (0.38), residues: 179 loop : -0.81 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS R 79 PHE 0.013 0.001 PHE A 189 TYR 0.007 0.001 TYR R 116 ARG 0.004 0.000 ARG R 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 0.703 Fit side-chains REVERT: A 10 LYS cc_start: 0.7595 (tptt) cc_final: 0.7223 (tppt) outliers start: 15 outliers final: 15 residues processed: 90 average time/residue: 0.2290 time to fit residues: 26.6574 Evaluate side-chains 91 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 51 THR Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 131 SER Chi-restraints excluded: chain R residue 186 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.0370 chunk 61 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 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 = 0.3635 r_free = 0.3635 target = 0.147787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.106335 restraints weight = 7729.927| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.32 r_work: 0.2899 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7158 Z= 0.123 Angle : 0.419 5.163 9707 Z= 0.221 Chirality : 0.039 0.147 1119 Planarity : 0.003 0.033 1208 Dihedral : 9.277 144.202 1049 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.02 % Allowed : 12.15 % Favored : 85.83 % 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: 1.24 (0.29), residues: 882 helix: 2.54 (0.28), residues: 376 sheet: 0.01 (0.38), residues: 179 loop : -0.77 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.002 0.000 HIS R 281 PHE 0.012 0.001 PHE A 189 TYR 0.007 0.001 TYR R 116 ARG 0.004 0.000 ARG R 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1796.76 seconds wall clock time: 33 minutes 27.36 seconds (2007.36 seconds total)