Starting phenix.real_space_refine on Sat Apr 6 22:50:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jil_36317/04_2024/8jil_36317_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jil_36317/04_2024/8jil_36317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jil_36317/04_2024/8jil_36317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jil_36317/04_2024/8jil_36317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jil_36317/04_2024/8jil_36317_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jil_36317/04_2024/8jil_36317_neut_updated.pdb" } resolution = 3.5 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= 0.011 sd= 0.078 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 69 5.16 5 C 5765 2.51 5 N 1535 2.21 5 O 1659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S ARG 218": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ARG 270": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9028 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 1796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1796 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2364 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 9, 'TRANS': 278} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'CLR': 1, 'NIO': 1} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Time building chain proxies: 4.90, per 1000 atoms: 0.54 Number of scatterers: 9028 At special positions: 0 Unit cell: (109.48, 135.24, 104.88, 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 69 16.00 O 1659 8.00 N 1535 7.00 C 5765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.05 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.04 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " 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: 3.16 Conformation dependent library (CDL) restraints added in 1.8 seconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 14 sheets defined 30.2% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.614A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'C' and resid 7 through 22 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'D' and resid 12 through 28 removed outlier: 3.845A pdb=" N GLU D 28 " --> pdb=" O ARG D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 52 Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 257 through 259 No H-bonds generated for 'chain 'D' and resid 257 through 259' Processing helix chain 'D' and resid 271 through 280 removed outlier: 3.945A pdb=" N GLU D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 310 removed outlier: 4.113A pdb=" N LEU D 310 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 350 removed outlier: 3.506A pdb=" N VAL D 342 " --> pdb=" O ALA D 338 " (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 'A' and resid 26 through 54 Proline residue: A 31 - end of helix removed outlier: 4.211A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 78 removed outlier: 3.676A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASN A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 88 Processing helix chain 'A' and resid 98 through 113 removed outlier: 4.251A pdb=" N PHE A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 107 " --> pdb=" O MET A 103 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 121 through 129 removed outlier: 4.231A pdb=" N TYR A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 145 through 158 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 188 through 214 removed outlier: 4.236A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 4.390A pdb=" N PHE A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 260 Proline residue: A 246 - end of helix removed outlier: 3.528A pdb=" N ARG A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 272 through 282 removed outlier: 4.570A pdb=" N SER A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 291 through 294 No H-bonds generated for 'chain 'A' and resid 291 through 294' Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.860A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.857A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.685A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.507A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.746A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 294 through 298 Processing sheet with id= G, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.883A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 319 through 323 removed outlier: 6.505A pdb=" N ILE D 264 " --> pdb=" O TYR D 320 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N HIS D 322 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU D 266 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA D 220 " --> pdb=" O LYS D 35 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE D 189 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.676A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 146 through 148 removed outlier: 7.155A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'S' and resid 226 through 231 removed outlier: 6.218A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 11 through 13 341 hydrogen bonds defined for protein. 972 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: 2.78 Time building geometry restraints manager: 3.50 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: 2903 1.34 - 1.47: 2302 1.47 - 1.60: 3920 1.60 - 1.72: 0 1.72 - 1.85: 100 Bond restraints: 9225 Sorted by residual: bond pdb=" CA SER A 179 " pdb=" CB SER A 179 " ideal model delta sigma weight residual 1.537 1.480 0.057 1.38e-02 5.25e+03 1.70e+01 bond pdb=" N CYS A 183 " pdb=" CA CYS A 183 " ideal model delta sigma weight residual 1.453 1.496 -0.043 1.39e-02 5.18e+03 9.61e+00 bond pdb=" N PHE A 186 " pdb=" CA PHE A 186 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.22e-02 6.72e+03 9.25e+00 bond pdb=" N ILE A 77 " pdb=" CA ILE A 77 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.18e-02 7.18e+03 7.87e+00 bond pdb=" N SER A 179 " pdb=" CA SER A 179 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.31e-02 5.83e+03 7.82e+00 ... (remaining 9220 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.42: 126 105.42 - 112.62: 4777 112.62 - 119.83: 3112 119.83 - 127.04: 4361 127.04 - 134.24: 109 Bond angle restraints: 12485 Sorted by residual: angle pdb=" CB MET S 230 " pdb=" CG MET S 230 " pdb=" SD MET S 230 " ideal model delta sigma weight residual 112.70 126.87 -14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" N SER A 178 " pdb=" CA SER A 178 " pdb=" C SER A 178 " ideal model delta sigma weight residual 108.96 114.78 -5.82 1.49e+00 4.50e-01 1.53e+01 angle pdb=" N SER A 179 " pdb=" CA SER A 179 " pdb=" C SER A 179 " ideal model delta sigma weight residual 114.31 109.31 5.00 1.29e+00 6.01e-01 1.50e+01 angle pdb=" CA MET C 21 " pdb=" CB MET C 21 " pdb=" CG MET C 21 " ideal model delta sigma weight residual 114.10 121.68 -7.58 2.00e+00 2.50e-01 1.44e+01 angle pdb=" C CYS A 183 " pdb=" CA CYS A 183 " pdb=" CB CYS A 183 " ideal model delta sigma weight residual 112.43 105.21 7.22 1.91e+00 2.74e-01 1.43e+01 ... (remaining 12480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 4887 16.33 - 32.67: 506 32.67 - 49.00: 100 49.00 - 65.34: 10 65.34 - 81.67: 8 Dihedral angle restraints: 5511 sinusoidal: 2208 harmonic: 3303 Sorted by residual: dihedral pdb=" CA PHE S 239 " pdb=" C PHE S 239 " pdb=" N GLY S 240 " pdb=" CA GLY S 240 " ideal model delta harmonic sigma weight residual 180.00 154.39 25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA ASP A 14 " pdb=" C ASP A 14 " pdb=" N LYS A 15 " pdb=" CA LYS A 15 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLU D 8 " pdb=" C GLU D 8 " pdb=" N ASP D 9 " pdb=" CA ASP D 9 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 5508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 837 0.037 - 0.075: 371 0.075 - 0.112: 146 0.112 - 0.150: 39 0.150 - 0.187: 10 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA VAL S 37 " pdb=" N VAL S 37 " pdb=" C VAL S 37 " pdb=" CB VAL S 37 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.76e-01 chirality pdb=" CA LEU A 76 " pdb=" N LEU A 76 " pdb=" C LEU A 76 " pdb=" CB LEU A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.08e-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 2.68 -0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 1400 not shown) Planarity restraints: 1574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 182 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C ILE A 182 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE A 182 " -0.019 2.00e-02 2.50e+03 pdb=" N CYS A 183 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " -0.045 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO C 49 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.038 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO S 75 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.033 5.00e-02 4.00e+02 ... (remaining 1571 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1064 2.75 - 3.29: 8602 3.29 - 3.82: 14246 3.82 - 4.36: 17138 4.36 - 4.90: 30059 Nonbonded interactions: 71109 Sorted by model distance: nonbonded pdb=" O ALA C 56 " pdb=" NH1 ARG C 62 " model vdw 2.209 2.520 nonbonded pdb=" NH1 ARG B 49 " pdb=" O PHE C 61 " model vdw 2.216 2.520 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.241 2.440 nonbonded pdb=" NH2 ARG B 22 " pdb=" O THR B 221 " model vdw 2.254 2.520 nonbonded pdb=" OG SER S 30 " pdb=" OD1 ASP S 74 " model vdw 2.279 2.440 ... (remaining 71104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.010 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 26.790 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 9225 Z= 0.363 Angle : 0.876 14.172 12485 Z= 0.502 Chirality : 0.050 0.187 1403 Planarity : 0.005 0.069 1574 Dihedral : 13.683 81.670 3365 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.10 % Allowed : 0.41 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.81 (0.24), residues: 1127 helix: -0.21 (0.29), residues: 325 sheet: -0.34 (0.30), residues: 273 loop : -2.35 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 169 HIS 0.010 0.002 HIS A 189 PHE 0.023 0.002 PHE A 105 TYR 0.022 0.002 TYR S 50 ARG 0.005 0.001 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.946 Fit side-chains REVERT: A 167 MET cc_start: 0.5256 (tpt) cc_final: 0.5011 (tpp) REVERT: A 217 GLN cc_start: 0.7802 (pp30) cc_final: 0.7594 (pp30) outliers start: 1 outliers final: 1 residues processed: 116 average time/residue: 0.2794 time to fit residues: 42.5362 Evaluate side-chains 98 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 45 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS C 18 GLN A 184 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9225 Z= 0.203 Angle : 0.642 10.795 12485 Z= 0.326 Chirality : 0.044 0.145 1403 Planarity : 0.004 0.055 1574 Dihedral : 5.974 51.363 1300 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.81 % Allowed : 7.43 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.37 (0.24), residues: 1127 helix: 0.40 (0.29), residues: 330 sheet: -0.19 (0.30), residues: 279 loop : -2.25 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 169 HIS 0.008 0.001 HIS A 184 PHE 0.018 0.002 PHE A 67 TYR 0.013 0.002 TYR B 105 ARG 0.003 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 167 MET cc_start: 0.5027 (tpt) cc_final: 0.4780 (tpp) outliers start: 8 outliers final: 4 residues processed: 113 average time/residue: 0.2635 time to fit residues: 40.0638 Evaluate side-chains 102 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain A residue 130 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN D 188 HIS S 167 HIS A 45 ASN A 184 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9225 Z= 0.215 Angle : 0.616 9.148 12485 Z= 0.314 Chirality : 0.044 0.192 1403 Planarity : 0.004 0.051 1574 Dihedral : 5.788 50.831 1300 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.63 % Allowed : 10.48 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.22 (0.24), residues: 1127 helix: 0.66 (0.30), residues: 331 sheet: -0.30 (0.30), residues: 275 loop : -2.12 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 169 HIS 0.007 0.001 HIS A 133 PHE 0.017 0.002 PHE A 105 TYR 0.015 0.001 TYR B 105 ARG 0.005 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 MET cc_start: 0.7353 (ppp) cc_final: 0.7030 (ppp) REVERT: B 172 GLU cc_start: 0.7023 (pm20) cc_final: 0.6739 (pm20) REVERT: D 227 LEU cc_start: 0.5396 (OUTLIER) cc_final: 0.5030 (pp) REVERT: D 276 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6663 (mp0) outliers start: 16 outliers final: 6 residues processed: 119 average time/residue: 0.2471 time to fit residues: 39.7749 Evaluate side-chains 106 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 242 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 0.3980 chunk 53 optimal weight: 0.6980 chunk 96 optimal weight: 0.0670 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9225 Z= 0.173 Angle : 0.569 10.199 12485 Z= 0.289 Chirality : 0.042 0.200 1403 Planarity : 0.004 0.049 1574 Dihedral : 5.512 47.542 1300 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.03 % Allowed : 11.09 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.98 (0.25), residues: 1127 helix: 0.86 (0.30), residues: 336 sheet: -0.11 (0.30), residues: 274 loop : -2.04 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.006 0.001 HIS A 133 PHE 0.013 0.001 PHE S 203 TYR 0.010 0.001 TYR S 95 ARG 0.005 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: B 155 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7216 (t0) REVERT: B 172 GLU cc_start: 0.7067 (pm20) cc_final: 0.6676 (pm20) REVERT: D 227 LEU cc_start: 0.5344 (OUTLIER) cc_final: 0.4964 (pp) REVERT: D 276 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: A 103 MET cc_start: 0.6231 (ttt) cc_final: 0.5835 (ttt) outliers start: 20 outliers final: 9 residues processed: 117 average time/residue: 0.2408 time to fit residues: 38.6318 Evaluate side-chains 108 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.082 9225 Z= 0.657 Angle : 0.891 14.409 12485 Z= 0.452 Chirality : 0.056 0.246 1403 Planarity : 0.006 0.069 1574 Dihedral : 6.734 62.659 1300 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.21 % Favored : 93.70 % Rotamer: Outliers : 2.44 % Allowed : 13.43 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.68 (0.24), residues: 1127 helix: -0.02 (0.28), residues: 340 sheet: -0.37 (0.30), residues: 277 loop : -2.35 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 169 HIS 0.018 0.002 HIS A 189 PHE 0.026 0.004 PHE A 105 TYR 0.036 0.004 TYR S 50 ARG 0.006 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: D 227 LEU cc_start: 0.5299 (OUTLIER) cc_final: 0.4860 (pp) REVERT: D 276 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6414 (mp0) outliers start: 24 outliers final: 13 residues processed: 123 average time/residue: 0.2469 time to fit residues: 41.9256 Evaluate side-chains 115 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 188 HIS ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9225 Z= 0.213 Angle : 0.616 10.567 12485 Z= 0.315 Chirality : 0.044 0.176 1403 Planarity : 0.004 0.055 1574 Dihedral : 5.887 53.840 1300 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.03 % Allowed : 14.85 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.23 (0.24), residues: 1127 helix: 0.62 (0.30), residues: 332 sheet: -0.28 (0.30), residues: 276 loop : -2.12 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.010 0.001 HIS A 133 PHE 0.015 0.002 PHE A 105 TYR 0.027 0.002 TYR S 95 ARG 0.005 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 227 LEU cc_start: 0.5241 (OUTLIER) cc_final: 0.4826 (pp) REVERT: D 276 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6551 (mp0) REVERT: A 103 MET cc_start: 0.6049 (ttt) cc_final: 0.5771 (ttt) outliers start: 20 outliers final: 11 residues processed: 122 average time/residue: 0.2358 time to fit residues: 38.9986 Evaluate side-chains 119 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 242 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9225 Z= 0.191 Angle : 0.581 10.177 12485 Z= 0.298 Chirality : 0.043 0.156 1403 Planarity : 0.004 0.051 1574 Dihedral : 5.603 41.664 1300 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.03 % Allowed : 15.67 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.24), residues: 1127 helix: 0.80 (0.30), residues: 337 sheet: -0.13 (0.30), residues: 275 loop : -2.05 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.009 0.001 HIS A 133 PHE 0.016 0.001 PHE A 105 TYR 0.011 0.001 TYR B 105 ARG 0.006 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: D 227 LEU cc_start: 0.5009 (OUTLIER) cc_final: 0.4663 (pp) REVERT: D 272 ASP cc_start: 0.4923 (m-30) cc_final: 0.4475 (p0) REVERT: D 276 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: S 6 GLU cc_start: 0.6308 (pt0) cc_final: 0.6022 (pt0) outliers start: 20 outliers final: 12 residues processed: 122 average time/residue: 0.2409 time to fit residues: 39.9637 Evaluate side-chains 121 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 10 optimal weight: 0.0270 chunk 84 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9225 Z= 0.183 Angle : 0.570 9.926 12485 Z= 0.292 Chirality : 0.043 0.151 1403 Planarity : 0.004 0.050 1574 Dihedral : 5.460 39.972 1300 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.83 % Allowed : 15.87 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.92 (0.25), residues: 1127 helix: 0.89 (0.30), residues: 337 sheet: -0.06 (0.30), residues: 274 loop : -1.99 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.008 0.001 HIS A 133 PHE 0.015 0.001 PHE A 105 TYR 0.024 0.001 TYR S 95 ARG 0.002 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 227 LEU cc_start: 0.5094 (OUTLIER) cc_final: 0.4741 (pp) REVERT: A 40 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.6578 (m-10) outliers start: 18 outliers final: 14 residues processed: 119 average time/residue: 0.2379 time to fit residues: 38.2668 Evaluate side-chains 119 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 95 TYR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 290 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.0980 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9225 Z= 0.167 Angle : 0.562 10.085 12485 Z= 0.287 Chirality : 0.042 0.139 1403 Planarity : 0.004 0.049 1574 Dihedral : 5.332 38.099 1300 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.83 % Allowed : 15.87 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.81 (0.25), residues: 1127 helix: 0.99 (0.30), residues: 337 sheet: 0.01 (0.30), residues: 274 loop : -1.94 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.009 0.001 HIS A 184 PHE 0.014 0.001 PHE A 105 TYR 0.015 0.001 TYR S 95 ARG 0.004 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 227 LEU cc_start: 0.5119 (OUTLIER) cc_final: 0.4799 (pp) REVERT: S 96 CYS cc_start: 0.7041 (p) cc_final: 0.6778 (p) REVERT: A 40 PHE cc_start: 0.6840 (OUTLIER) cc_final: 0.6579 (m-10) outliers start: 18 outliers final: 13 residues processed: 119 average time/residue: 0.2433 time to fit residues: 39.5614 Evaluate side-chains 118 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 235 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 0.0070 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9225 Z= 0.176 Angle : 0.568 10.460 12485 Z= 0.290 Chirality : 0.043 0.148 1403 Planarity : 0.004 0.049 1574 Dihedral : 5.295 37.794 1300 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.73 % Allowed : 16.28 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.75 (0.25), residues: 1127 helix: 1.03 (0.30), residues: 337 sheet: 0.11 (0.30), residues: 269 loop : -1.92 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.015 0.002 HIS A 184 PHE 0.015 0.001 PHE A 105 TYR 0.028 0.001 TYR S 95 ARG 0.009 0.000 ARG A 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: B 332 TRP cc_start: 0.8266 (m-10) cc_final: 0.8053 (m-10) REVERT: D 227 LEU cc_start: 0.5171 (OUTLIER) cc_final: 0.4876 (pp) REVERT: S 96 CYS cc_start: 0.6873 (p) cc_final: 0.6635 (p) REVERT: A 40 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.6521 (m-10) REVERT: A 221 ASP cc_start: 0.6853 (p0) cc_final: 0.6636 (p0) outliers start: 17 outliers final: 14 residues processed: 114 average time/residue: 0.2438 time to fit residues: 38.0293 Evaluate side-chains 117 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 95 TYR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 235 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.146505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.127204 restraints weight = 15338.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.126795 restraints weight = 21477.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.127233 restraints weight = 19804.460| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9225 Z= 0.194 Angle : 0.578 10.188 12485 Z= 0.296 Chirality : 0.043 0.154 1403 Planarity : 0.004 0.049 1574 Dihedral : 5.333 37.654 1300 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.93 % Allowed : 16.07 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.74 (0.25), residues: 1127 helix: 1.02 (0.30), residues: 337 sheet: 0.16 (0.30), residues: 274 loop : -1.94 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.021 0.002 HIS A 184 PHE 0.015 0.001 PHE A 105 TYR 0.029 0.001 TYR S 95 ARG 0.008 0.000 ARG A 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1863.98 seconds wall clock time: 35 minutes 6.37 seconds (2106.37 seconds total)