Starting phenix.real_space_refine on Mon Mar 11 17:21:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijd_35485/03_2024/8ijd_35485_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijd_35485/03_2024/8ijd_35485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijd_35485/03_2024/8ijd_35485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijd_35485/03_2024/8ijd_35485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijd_35485/03_2024/8ijd_35485_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ijd_35485/03_2024/8ijd_35485_neut_updated.pdb" } resolution = 3.25 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= 0.015 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 64 5.16 5 C 5544 2.51 5 N 1489 2.21 5 O 1627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "S GLU 210": "OE1" <-> "OE2" Residue "S TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 222": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8724 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2183 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 8, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 136 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1695 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "S" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1792 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'FI7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.10, per 1000 atoms: 0.58 Number of scatterers: 8724 At special positions: 0 Unit cell: (88.81, 120.35, 126.16, 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 64 16.00 O 1627 8.00 N 1489 7.00 C 5544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.02 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.07 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=1.85 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 3.10 Conformation dependent library (CDL) restraints added in 1.6 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 13 sheets defined 33.9% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 24 through 54 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 61 through 89 removed outlier: 3.591A pdb=" N LEU A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Proline residue: A 81 - end of helix removed outlier: 3.594A pdb=" N ARG A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 130 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 141 through 163 removed outlier: 5.068A pdb=" N HIS A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 217 Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 224 through 260 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 268 through 295 removed outlier: 4.084A pdb=" N SER A 271 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL A 272 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASP A 273 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN A 286 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.688A pdb=" N TYR A 294 " --> pdb=" O PRO A 291 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N TYR A 295 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'C' and resid 7 through 31 Processing helix chain 'C' and resid 46 through 50 Processing helix chain 'C' and resid 208 through 215 removed outlier: 4.703A pdb=" N HIS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N CYS C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE C 215 " --> pdb=" O TRP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 231 removed outlier: 3.782A pdb=" N TYR C 230 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP C 231 " --> pdb=" O SER C 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 231' Processing helix chain 'C' and resid 242 through 254 Processing helix chain 'C' and resid 271 through 280 removed outlier: 3.675A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 296 through 310 Processing helix chain 'C' and resid 330 through 350 Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 47 removed outlier: 4.543A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 169 through 171 Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.833A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.835A 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: 7.018A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.120A 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: 6.766A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 203 removed outlier: 4.099A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.977A 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: 6.689A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.526A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.854A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 319 through 322 removed outlier: 6.518A pdb=" N ILE C 264 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N HIS C 322 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU C 266 " --> pdb=" O HIS C 322 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N HIS C 195 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU C 36 " --> pdb=" O HIS C 195 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS C 197 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU C 38 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE C 199 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.146A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.257A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 144 through 147 398 hydrogen bonds defined for protein. 1098 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: 2.56 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2810 1.34 - 1.47: 2251 1.47 - 1.60: 3757 1.60 - 1.73: 2 1.73 - 1.86: 91 Bond restraints: 8911 Sorted by residual: bond pdb=" C20 FI7 A 401 " pdb=" C21 FI7 A 401 " ideal model delta sigma weight residual 1.355 1.543 -0.188 2.00e-02 2.50e+03 8.86e+01 bond pdb=" N ASN A 17 " pdb=" CA ASN A 17 " ideal model delta sigma weight residual 1.463 1.377 0.086 1.47e-02 4.63e+03 3.39e+01 bond pdb=" CA LYS A 16 " pdb=" C LYS A 16 " ideal model delta sigma weight residual 1.523 1.421 0.103 1.80e-02 3.09e+03 3.25e+01 bond pdb=" CA CYS A 18 " pdb=" C CYS A 18 " ideal model delta sigma weight residual 1.522 1.586 -0.063 1.20e-02 6.94e+03 2.78e+01 bond pdb=" ND1 HIS B 91 " pdb=" CE1 HIS B 91 " ideal model delta sigma weight residual 1.321 1.374 -0.053 1.00e-02 1.00e+04 2.76e+01 ... (remaining 8906 not shown) Histogram of bond angle deviations from ideal: 85.34 - 95.17: 7 95.17 - 105.01: 130 105.01 - 114.84: 5299 114.84 - 124.67: 6484 124.67 - 134.51: 176 Bond angle restraints: 12096 Sorted by residual: angle pdb=" N SER A 181 " pdb=" CA SER A 181 " pdb=" C SER A 181 " ideal model delta sigma weight residual 109.24 85.34 23.90 1.63e+00 3.76e-01 2.15e+02 angle pdb=" N CYS A 18 " pdb=" CA CYS A 18 " pdb=" C CYS A 18 " ideal model delta sigma weight residual 108.14 129.66 -21.52 1.52e+00 4.33e-01 2.00e+02 angle pdb=" N ARG A 222 " pdb=" CA ARG A 222 " pdb=" C ARG A 222 " ideal model delta sigma weight residual 111.28 125.75 -14.47 1.09e+00 8.42e-01 1.76e+02 angle pdb=" C GLU A 12 " pdb=" CA GLU A 12 " pdb=" CB GLU A 12 " ideal model delta sigma weight residual 112.09 91.90 20.19 1.54e+00 4.22e-01 1.72e+02 angle pdb=" N GLN A 170 " pdb=" CA GLN A 170 " pdb=" C GLN A 170 " ideal model delta sigma weight residual 109.96 90.98 18.98 1.50e+00 4.44e-01 1.60e+02 ... (remaining 12091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4545 17.86 - 35.71: 560 35.71 - 53.57: 135 53.57 - 71.42: 21 71.42 - 89.28: 14 Dihedral angle restraints: 5275 sinusoidal: 1984 harmonic: 3291 Sorted by residual: dihedral pdb=" C GLU A 12 " pdb=" N GLU A 12 " pdb=" CA GLU A 12 " pdb=" CB GLU A 12 " ideal model delta harmonic sigma weight residual -122.60 -97.82 -24.78 0 2.50e+00 1.60e-01 9.83e+01 dihedral pdb=" C PHE A 180 " pdb=" N PHE A 180 " pdb=" CA PHE A 180 " pdb=" CB PHE A 180 " ideal model delta harmonic sigma weight residual -122.60 -97.85 -24.75 0 2.50e+00 1.60e-01 9.80e+01 dihedral pdb=" CB CYS A 100 " pdb=" SG CYS A 100 " pdb=" SG CYS A 177 " pdb=" CB CYS A 177 " ideal model delta sinusoidal sigma weight residual 93.00 176.96 -83.96 1 1.00e+01 1.00e-02 8.59e+01 ... (remaining 5272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 1350 0.165 - 0.329: 17 0.329 - 0.494: 3 0.494 - 0.658: 3 0.658 - 0.823: 1 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CA ASP A 221 " pdb=" N ASP A 221 " pdb=" C ASP A 221 " pdb=" CB ASP A 221 " both_signs ideal model delta sigma weight residual False 2.51 1.69 0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" CA CYS A 177 " pdb=" N CYS A 177 " pdb=" C CYS A 177 " pdb=" CB CYS A 177 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.02e+00 chirality pdb=" CA GLU A 12 " pdb=" N GLU A 12 " pdb=" C GLU A 12 " pdb=" CB GLU A 12 " both_signs ideal model delta sigma weight residual False 2.51 3.07 -0.56 2.00e-01 2.50e+01 7.86e+00 ... (remaining 1371 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 FI7 A 401 " -0.093 2.00e-02 2.50e+03 1.21e-01 1.83e+02 pdb=" C17 FI7 A 401 " 0.017 2.00e-02 2.50e+03 pdb=" C20 FI7 A 401 " -0.143 2.00e-02 2.50e+03 pdb=" N19 FI7 A 401 " 0.208 2.00e-02 2.50e+03 pdb=" O18 FI7 A 401 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 15 " 0.038 2.00e-02 2.50e+03 8.63e-02 7.45e+01 pdb=" C LYS A 15 " -0.149 2.00e-02 2.50e+03 pdb=" O LYS A 15 " 0.061 2.00e-02 2.50e+03 pdb=" N LYS A 16 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 284 " 0.085 2.00e-02 2.50e+03 5.15e-02 5.30e+01 pdb=" CG TYR A 284 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR A 284 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR A 284 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 284 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 284 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR A 284 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 284 " 0.088 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 60 2.43 - 3.05: 5806 3.05 - 3.66: 14076 3.66 - 4.28: 20177 4.28 - 4.90: 33368 Nonbonded interactions: 73487 Sorted by model distance: nonbonded pdb=" O ILE A 182 " pdb=" CG1 ILE A 182 " model vdw 1.812 3.440 nonbonded pdb=" O ILE A 182 " pdb=" CD1 ILE A 182 " model vdw 1.865 3.460 nonbonded pdb=" OG SER A 298 " pdb=" O GLY C 352 " model vdw 1.963 2.440 nonbonded pdb=" O ARG S 67 " pdb=" OG1 THR S 84 " model vdw 2.106 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.125 2.440 ... (remaining 73482 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: 1.200 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: 3.950 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.380 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.008 0.188 8911 Z= 0.505 Angle : 1.204 23.902 12096 Z= 0.725 Chirality : 0.066 0.823 1374 Planarity : 0.008 0.122 1540 Dihedral : 16.918 89.280 3132 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.30 % Allowed : 30.85 % Favored : 66.85 % Cbeta Deviations : 0.94 % Peptide Plane: Cis-proline : 3.23 % 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: -0.43 (0.26), residues: 1120 helix: 0.46 (0.27), residues: 368 sheet: 0.03 (0.32), residues: 273 loop : -0.99 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP A 91 HIS 0.006 0.001 HIS A 259 PHE 0.050 0.002 PHE A 277 TYR 0.088 0.003 TYR A 284 ARG 0.008 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.8382 (tmm) cc_final: 0.7819 (tmm) REVERT: A 137 ASN cc_start: 0.8762 (m-40) cc_final: 0.8550 (m110) REVERT: A 217 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8847 (tm-30) REVERT: C 294 ASN cc_start: 0.8170 (m-40) cc_final: 0.7963 (t0) REVERT: C 350 ASP cc_start: 0.8947 (t0) cc_final: 0.8741 (m-30) REVERT: G 27 ARG cc_start: 0.8342 (tpp80) cc_final: 0.7778 (tpp80) REVERT: S 190 ARG cc_start: 0.7867 (mtp180) cc_final: 0.7517 (mtp180) outliers start: 21 outliers final: 9 residues processed: 194 average time/residue: 0.2325 time to fit residues: 60.1983 Evaluate side-chains 174 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 165 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 177 CYS Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 180 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 28 optimal weight: 0.0870 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 91 HIS B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8911 Z= 0.185 Angle : 0.645 9.622 12096 Z= 0.330 Chirality : 0.044 0.162 1374 Planarity : 0.004 0.056 1540 Dihedral : 7.939 71.477 1266 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.60 % Allowed : 26.15 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.07 (0.26), residues: 1120 helix: 1.10 (0.28), residues: 369 sheet: 0.02 (0.32), residues: 275 loop : -0.95 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP S 164 HIS 0.014 0.001 HIS A 189 PHE 0.022 0.001 PHE A 180 TYR 0.014 0.001 TYR S 223 ARG 0.005 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 189 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.8881 (tmm) cc_final: 0.8593 (tmm) REVERT: A 112 GLN cc_start: 0.8003 (tp40) cc_final: 0.7677 (tp40) REVERT: A 137 ASN cc_start: 0.8763 (m-40) cc_final: 0.8559 (m110) REVERT: B 289 TYR cc_start: 0.8829 (m-80) cc_final: 0.8581 (m-80) REVERT: C 308 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.8737 (mt-10) REVERT: G 27 ARG cc_start: 0.8331 (tpp80) cc_final: 0.7925 (tpp80) REVERT: S 82 GLN cc_start: 0.8635 (mm110) cc_final: 0.8369 (mm110) REVERT: S 87 ARG cc_start: 0.7944 (mpp80) cc_final: 0.7735 (mpp80) REVERT: S 190 ARG cc_start: 0.7866 (mtp180) cc_final: 0.7468 (mtp180) REVERT: S 206 ARG cc_start: 0.8724 (tpp80) cc_final: 0.7975 (tpp80) REVERT: S 208 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8256 (pm20) outliers start: 42 outliers final: 15 residues processed: 223 average time/residue: 0.2233 time to fit residues: 66.5852 Evaluate side-chains 191 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 174 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 0.1980 chunk 109 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8911 Z= 0.359 Angle : 0.678 8.129 12096 Z= 0.350 Chirality : 0.045 0.151 1374 Planarity : 0.004 0.051 1540 Dihedral : 7.266 72.822 1253 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 5.69 % Allowed : 27.24 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.05 (0.26), residues: 1120 helix: 1.23 (0.28), residues: 368 sheet: -0.11 (0.32), residues: 273 loop : -0.95 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP S 164 HIS 0.011 0.001 HIS A 189 PHE 0.015 0.002 PHE A 197 TYR 0.018 0.002 TYR S 178 ARG 0.006 0.001 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 176 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8589 (m) cc_final: 0.8082 (m) REVERT: A 109 MET cc_start: 0.8855 (tmm) cc_final: 0.8585 (tmm) REVERT: A 112 GLN cc_start: 0.8224 (tp40) cc_final: 0.7959 (tp40) REVERT: A 137 ASN cc_start: 0.8680 (m-40) cc_final: 0.8449 (m110) REVERT: A 238 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8923 (tp) REVERT: B 220 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8632 (mp10) REVERT: B 289 TYR cc_start: 0.8906 (m-80) cc_final: 0.8601 (m-80) REVERT: C 294 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.8095 (t0) REVERT: C 308 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.8759 (mt-10) REVERT: G 27 ARG cc_start: 0.8457 (tpp80) cc_final: 0.7948 (tpp80) REVERT: S 190 ARG cc_start: 0.7903 (mtp180) cc_final: 0.7687 (mtp180) REVERT: S 206 ARG cc_start: 0.8832 (tpp80) cc_final: 0.8176 (tpp80) REVERT: S 208 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8295 (pm20) outliers start: 52 outliers final: 31 residues processed: 212 average time/residue: 0.2416 time to fit residues: 69.3013 Evaluate side-chains 200 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 164 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 28 optimal weight: 0.0770 chunk 89 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8911 Z= 0.277 Angle : 0.638 8.365 12096 Z= 0.329 Chirality : 0.044 0.146 1374 Planarity : 0.004 0.050 1540 Dihedral : 7.204 71.572 1253 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 6.46 % Allowed : 27.35 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.05 (0.26), residues: 1120 helix: 1.31 (0.28), residues: 369 sheet: -0.08 (0.32), residues: 274 loop : -0.86 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP S 164 HIS 0.009 0.001 HIS A 189 PHE 0.011 0.001 PHE A 193 TYR 0.017 0.001 TYR S 178 ARG 0.005 0.000 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 178 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8667 (m) cc_final: 0.8202 (m) REVERT: A 109 MET cc_start: 0.8771 (tmm) cc_final: 0.8537 (tmm) REVERT: A 112 GLN cc_start: 0.8152 (tp40) cc_final: 0.7874 (tp40) REVERT: A 137 ASN cc_start: 0.8673 (m-40) cc_final: 0.8434 (m110) REVERT: B 37 ILE cc_start: 0.8833 (mt) cc_final: 0.8585 (mp) REVERT: B 262 MET cc_start: 0.7793 (mmm) cc_final: 0.7222 (mmm) REVERT: B 289 TYR cc_start: 0.8913 (m-80) cc_final: 0.8680 (m-80) REVERT: C 274 PHE cc_start: 0.9479 (t80) cc_final: 0.9267 (t80) REVERT: C 294 ASN cc_start: 0.8351 (t0) cc_final: 0.8075 (t0) REVERT: C 308 GLU cc_start: 0.9274 (OUTLIER) cc_final: 0.8746 (mt-10) REVERT: G 27 ARG cc_start: 0.8446 (tpp80) cc_final: 0.7915 (tpp80) REVERT: S 82 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8626 (mm-40) REVERT: S 171 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7825 (pm20) REVERT: S 190 ARG cc_start: 0.7905 (mtp180) cc_final: 0.7283 (mtp180) REVERT: S 206 ARG cc_start: 0.8908 (tpp80) cc_final: 0.8347 (tpp80) REVERT: S 208 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8335 (pm20) REVERT: S 232 LYS cc_start: 0.8919 (tppt) cc_final: 0.8679 (tppt) outliers start: 59 outliers final: 32 residues processed: 220 average time/residue: 0.2267 time to fit residues: 66.6843 Evaluate side-chains 203 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 171 GLN Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8911 Z= 0.279 Angle : 0.644 8.434 12096 Z= 0.328 Chirality : 0.044 0.168 1374 Planarity : 0.004 0.052 1540 Dihedral : 7.062 71.305 1253 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 6.89 % Allowed : 27.79 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.04 (0.26), residues: 1120 helix: 1.37 (0.28), residues: 368 sheet: -0.09 (0.32), residues: 270 loop : -0.92 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP S 164 HIS 0.009 0.001 HIS A 189 PHE 0.019 0.001 PHE A 186 TYR 0.016 0.001 TYR S 223 ARG 0.006 0.000 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 179 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8721 (m) cc_final: 0.8341 (m) REVERT: A 109 MET cc_start: 0.8741 (tmm) cc_final: 0.8281 (tmm) REVERT: A 112 GLN cc_start: 0.8121 (tp40) cc_final: 0.7823 (tp40) REVERT: A 238 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8941 (tp) REVERT: B 37 ILE cc_start: 0.8776 (mt) cc_final: 0.8494 (mp) REVERT: B 97 SER cc_start: 0.9064 (OUTLIER) cc_final: 0.8762 (p) REVERT: B 289 TYR cc_start: 0.8873 (m-80) cc_final: 0.8589 (m-80) REVERT: C 274 PHE cc_start: 0.9525 (t80) cc_final: 0.9324 (t80) REVERT: C 294 ASN cc_start: 0.8369 (t0) cc_final: 0.8119 (t0) REVERT: C 308 GLU cc_start: 0.9279 (OUTLIER) cc_final: 0.8770 (mt-10) REVERT: G 27 ARG cc_start: 0.8437 (tpp80) cc_final: 0.7710 (tpp80) REVERT: S 82 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8600 (mm-40) REVERT: S 171 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7843 (pm20) REVERT: S 190 ARG cc_start: 0.7917 (mtp180) cc_final: 0.7284 (mtp180) REVERT: S 206 ARG cc_start: 0.8938 (tpp80) cc_final: 0.8383 (tpp80) REVERT: S 208 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8353 (pm20) outliers start: 63 outliers final: 43 residues processed: 225 average time/residue: 0.2126 time to fit residues: 65.0287 Evaluate side-chains 216 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 168 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 171 GLN Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 107 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8911 Z= 0.217 Angle : 0.644 8.588 12096 Z= 0.326 Chirality : 0.044 0.142 1374 Planarity : 0.004 0.050 1540 Dihedral : 6.915 71.157 1253 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.36 % Allowed : 29.54 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.08 (0.26), residues: 1120 helix: 1.37 (0.28), residues: 368 sheet: -0.01 (0.32), residues: 266 loop : -0.89 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP S 164 HIS 0.007 0.001 HIS A 189 PHE 0.012 0.001 PHE A 186 TYR 0.016 0.001 TYR S 223 ARG 0.007 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 182 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8845 (m) cc_final: 0.8375 (m) REVERT: A 109 MET cc_start: 0.8693 (tmm) cc_final: 0.8311 (tmm) REVERT: A 137 ASN cc_start: 0.8619 (m110) cc_final: 0.8204 (m110) REVERT: A 238 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8963 (tp) REVERT: B 37 ILE cc_start: 0.8784 (mt) cc_final: 0.8404 (mp) REVERT: B 97 SER cc_start: 0.9042 (OUTLIER) cc_final: 0.8721 (p) REVERT: B 289 TYR cc_start: 0.8871 (m-80) cc_final: 0.8555 (m-80) REVERT: C 294 ASN cc_start: 0.8371 (t0) cc_final: 0.8128 (t0) REVERT: C 308 GLU cc_start: 0.9278 (OUTLIER) cc_final: 0.8729 (mt-10) REVERT: C 313 ARG cc_start: 0.8901 (mpp80) cc_final: 0.8430 (mtm-85) REVERT: G 27 ARG cc_start: 0.8444 (tpp80) cc_final: 0.7659 (tpp80) REVERT: S 43 LYS cc_start: 0.9377 (mmmm) cc_final: 0.9001 (mmtm) REVERT: S 171 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7873 (pm20) REVERT: S 190 ARG cc_start: 0.7914 (mtp180) cc_final: 0.7449 (mtp180) REVERT: S 206 ARG cc_start: 0.8959 (tpp80) cc_final: 0.8297 (tpp80) REVERT: S 208 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8312 (pm20) outliers start: 49 outliers final: 33 residues processed: 219 average time/residue: 0.2330 time to fit residues: 69.0978 Evaluate side-chains 213 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 175 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 171 GLN Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 90 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8911 Z= 0.286 Angle : 0.671 8.969 12096 Z= 0.338 Chirality : 0.044 0.144 1374 Planarity : 0.004 0.050 1540 Dihedral : 7.150 71.415 1253 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.09 % Favored : 94.82 % Rotamer: Outliers : 6.24 % Allowed : 28.77 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.07 (0.26), residues: 1120 helix: 1.48 (0.28), residues: 366 sheet: -0.09 (0.32), residues: 270 loop : -0.95 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP S 164 HIS 0.007 0.001 HIS A 189 PHE 0.014 0.001 PHE A 197 TYR 0.017 0.001 TYR S 223 ARG 0.006 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 175 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8818 (m) cc_final: 0.8360 (m) REVERT: A 85 ASP cc_start: 0.9301 (t0) cc_final: 0.9031 (t0) REVERT: A 109 MET cc_start: 0.8705 (tmm) cc_final: 0.8321 (tmm) REVERT: A 238 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8986 (tp) REVERT: B 97 SER cc_start: 0.9059 (OUTLIER) cc_final: 0.8750 (p) REVERT: B 220 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8638 (mp10) REVERT: B 289 TYR cc_start: 0.8896 (m-80) cc_final: 0.8627 (m-80) REVERT: C 294 ASN cc_start: 0.8381 (t0) cc_final: 0.8137 (t0) REVERT: C 308 GLU cc_start: 0.9281 (OUTLIER) cc_final: 0.8741 (mt-10) REVERT: G 27 ARG cc_start: 0.8423 (tpp80) cc_final: 0.7607 (tpp80) REVERT: S 82 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8411 (mm-40) REVERT: S 171 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: S 190 ARG cc_start: 0.7951 (mtp180) cc_final: 0.7290 (mtp180) REVERT: S 206 ARG cc_start: 0.8979 (tpp80) cc_final: 0.8442 (tpp80) REVERT: S 208 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8363 (pm20) outliers start: 57 outliers final: 44 residues processed: 218 average time/residue: 0.2370 time to fit residues: 70.0894 Evaluate side-chains 221 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 171 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 22 ASN Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 171 GLN Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.0370 chunk 84 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8911 Z= 0.301 Angle : 0.684 8.574 12096 Z= 0.346 Chirality : 0.045 0.155 1374 Planarity : 0.004 0.048 1540 Dihedral : 7.192 71.495 1253 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.91 % Favored : 95.00 % Rotamer: Outliers : 6.24 % Allowed : 29.10 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.08 (0.26), residues: 1120 helix: 1.45 (0.27), residues: 368 sheet: -0.17 (0.32), residues: 278 loop : -0.88 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP S 164 HIS 0.007 0.001 HIS A 189 PHE 0.020 0.001 PHE A 95 TYR 0.018 0.002 TYR S 223 ARG 0.007 0.000 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 173 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8836 (m) cc_final: 0.8392 (m) REVERT: A 109 MET cc_start: 0.8704 (tmm) cc_final: 0.8344 (tmm) REVERT: A 238 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8995 (tp) REVERT: B 97 SER cc_start: 0.9071 (OUTLIER) cc_final: 0.8768 (p) REVERT: B 220 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8635 (mp10) REVERT: B 289 TYR cc_start: 0.8905 (m-80) cc_final: 0.8668 (m-80) REVERT: C 294 ASN cc_start: 0.8328 (t0) cc_final: 0.8090 (t0) REVERT: C 308 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.8754 (mt-10) REVERT: C 313 ARG cc_start: 0.8943 (mpp80) cc_final: 0.8496 (mtm-85) REVERT: G 27 ARG cc_start: 0.8436 (tpp80) cc_final: 0.7569 (tpp80) REVERT: S 43 LYS cc_start: 0.9456 (mmmm) cc_final: 0.9082 (mmtm) REVERT: S 82 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8557 (mm-40) REVERT: S 171 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7877 (pm20) REVERT: S 190 ARG cc_start: 0.7959 (mtp180) cc_final: 0.7323 (mtp180) REVERT: S 206 ARG cc_start: 0.9000 (tpp80) cc_final: 0.8430 (tpp80) REVERT: S 208 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8323 (pm20) outliers start: 57 outliers final: 45 residues processed: 214 average time/residue: 0.2206 time to fit residues: 63.6786 Evaluate side-chains 220 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 169 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 171 GLN Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8911 Z= 0.283 Angle : 0.695 9.150 12096 Z= 0.350 Chirality : 0.045 0.185 1374 Planarity : 0.004 0.048 1540 Dihedral : 7.205 71.567 1253 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 5.91 % Allowed : 29.32 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.10 (0.26), residues: 1120 helix: 1.48 (0.27), residues: 368 sheet: -0.11 (0.32), residues: 276 loop : -0.91 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP S 164 HIS 0.007 0.001 HIS A 161 PHE 0.021 0.001 PHE A 95 TYR 0.023 0.002 TYR C 302 ARG 0.007 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 172 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8828 (m) cc_final: 0.8375 (m) REVERT: A 238 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8992 (tp) REVERT: B 97 SER cc_start: 0.9065 (OUTLIER) cc_final: 0.8758 (p) REVERT: B 220 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8660 (mp10) REVERT: B 289 TYR cc_start: 0.8899 (m-80) cc_final: 0.8671 (m-80) REVERT: C 294 ASN cc_start: 0.8354 (t0) cc_final: 0.8113 (t0) REVERT: C 308 GLU cc_start: 0.9288 (OUTLIER) cc_final: 0.8729 (mt-10) REVERT: C 313 ARG cc_start: 0.8953 (mpp80) cc_final: 0.8502 (mtm-85) REVERT: G 27 ARG cc_start: 0.8435 (tpp80) cc_final: 0.7560 (tpp80) REVERT: G 38 MET cc_start: 0.8843 (ppp) cc_final: 0.8538 (ppp) REVERT: S 43 LYS cc_start: 0.9462 (mmmm) cc_final: 0.9116 (mmtm) REVERT: S 82 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8571 (mm-40) REVERT: S 171 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7892 (pm20) REVERT: S 190 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7359 (mtp180) outliers start: 54 outliers final: 46 residues processed: 210 average time/residue: 0.2265 time to fit residues: 64.1399 Evaluate side-chains 220 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 169 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 171 GLN Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 9 optimal weight: 0.0030 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8911 Z= 0.214 Angle : 0.681 8.937 12096 Z= 0.343 Chirality : 0.044 0.162 1374 Planarity : 0.004 0.047 1540 Dihedral : 7.119 71.377 1253 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 4.70 % Allowed : 30.53 % Favored : 64.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.12 (0.26), residues: 1120 helix: 1.45 (0.27), residues: 370 sheet: 0.09 (0.33), residues: 266 loop : -0.98 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP S 164 HIS 0.006 0.001 HIS A 259 PHE 0.020 0.001 PHE A 95 TYR 0.019 0.001 TYR C 302 ARG 0.008 0.000 ARG S 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 181 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.8850 (m) cc_final: 0.8394 (m) REVERT: A 238 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8926 (tp) REVERT: B 97 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8715 (p) REVERT: B 220 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8678 (mp10) REVERT: B 262 MET cc_start: 0.7850 (mmm) cc_final: 0.7260 (mmm) REVERT: B 289 TYR cc_start: 0.8887 (m-80) cc_final: 0.8641 (m-80) REVERT: C 294 ASN cc_start: 0.8340 (t0) cc_final: 0.8068 (t0) REVERT: C 308 GLU cc_start: 0.9285 (OUTLIER) cc_final: 0.8701 (mt-10) REVERT: C 313 ARG cc_start: 0.8953 (mpp80) cc_final: 0.8498 (mtm-85) REVERT: G 27 ARG cc_start: 0.8403 (tpp80) cc_final: 0.7524 (tpp80) REVERT: G 38 MET cc_start: 0.8754 (ppp) cc_final: 0.8483 (ppp) REVERT: S 43 LYS cc_start: 0.9507 (mmmm) cc_final: 0.9205 (mmtm) REVERT: S 82 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8600 (mm-40) REVERT: S 171 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7948 (pm20) REVERT: S 190 ARG cc_start: 0.7985 (mtp180) cc_final: 0.7605 (mtp180) REVERT: S 232 LYS cc_start: 0.8932 (tppp) cc_final: 0.8568 (tptp) outliers start: 43 outliers final: 37 residues processed: 211 average time/residue: 0.2312 time to fit residues: 65.9018 Evaluate side-chains 214 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 172 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 157 ASN Chi-restraints excluded: chain S residue 171 GLN Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.0980 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 90 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 0.0980 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.102534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.072796 restraints weight = 20259.255| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 3.96 r_work: 0.2886 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8911 Z= 0.182 Angle : 0.704 10.195 12096 Z= 0.352 Chirality : 0.045 0.173 1374 Planarity : 0.004 0.046 1540 Dihedral : 7.119 70.548 1253 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.00 % Favored : 94.91 % Rotamer: Outliers : 3.72 % Allowed : 31.95 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.14 (0.26), residues: 1120 helix: 1.43 (0.27), residues: 370 sheet: 0.13 (0.34), residues: 267 loop : -0.95 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP S 164 HIS 0.015 0.001 HIS A 9 PHE 0.020 0.001 PHE A 95 TYR 0.019 0.002 TYR C 302 ARG 0.008 0.001 ARG S 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2394.88 seconds wall clock time: 44 minutes 6.94 seconds (2646.94 seconds total)