Starting phenix.real_space_refine on Mon May 12 17:22:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwv_38743/05_2025/8xwv_38743.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwv_38743/05_2025/8xwv_38743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xwv_38743/05_2025/8xwv_38743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwv_38743/05_2025/8xwv_38743.map" model { file = "/net/cci-nas-00/data/ceres_data/8xwv_38743/05_2025/8xwv_38743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwv_38743/05_2025/8xwv_38743.cif" } resolution = 3.07 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5868 2.51 5 N 1594 2.21 5 O 1691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9211 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 465 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 62} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 387 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 55} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "R" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2354 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 286} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1542 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 4, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2416 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 389 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1658 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Time building chain proxies: 5.17, per 1000 atoms: 0.56 Number of scatterers: 9211 At special positions: 0 Unit cell: (87.15, 122.425, 151.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1691 8.00 N 1594 7.00 C 5868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 35 " distance=2.03 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 35 " distance=2.03 Simple disulfide: pdb=" SG CYS E 11 " - pdb=" SG CYS E 51 " distance=2.03 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.1 seconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 14 sheets defined 37.2% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'D' and resid 19 through 21 No H-bonds generated for 'chain 'D' and resid 19 through 21' Processing helix chain 'D' and resid 56 through 67 removed outlier: 3.529A pdb=" N LYS D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 21 No H-bonds generated for 'chain 'E' and resid 19 through 21' Processing helix chain 'E' and resid 56 through 68 Processing helix chain 'R' and resid 44 through 76 removed outlier: 4.369A pdb=" N LYS R 48 " --> pdb=" O LEU R 44 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR R 49 " --> pdb=" O GLU R 45 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE R 50 " --> pdb=" O ILE R 46 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N SER R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 99 Processing helix chain 'R' and resid 100 through 111 Processing helix chain 'R' and resid 115 through 150 removed outlier: 4.078A pdb=" N SER R 123 " --> pdb=" O CYS R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 160 removed outlier: 3.707A pdb=" N THR R 156 " --> pdb=" O ARG R 153 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR R 160 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 177 Processing helix chain 'R' and resid 177 through 183 removed outlier: 3.617A pdb=" N LEU R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 212 removed outlier: 3.684A pdb=" N MET R 209 " --> pdb=" O ALA R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 218 removed outlier: 3.691A pdb=" N GLN R 216 " --> pdb=" O ARG R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 241 removed outlier: 3.785A pdb=" N LYS R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA R 241 " --> pdb=" O THR R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 279 Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 285 through 304 Processing helix chain 'R' and resid 305 through 315 Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 318 through 330 removed outlier: 3.735A pdb=" N ALA R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.566A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.975A pdb=" N ILE A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.587A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.527A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.778A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.901A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.595A pdb=" N ASP H 223 " --> pdb=" O GLU H 220 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 220 through 224' Processing sheet with id=AA1, first strand: chain 'D' and resid 49 through 52 removed outlier: 4.189A pdb=" N VAL D 40 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.957A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N HIS A 322 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A 267 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.606A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.689A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.129A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.130A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.501A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.597A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.428A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.973A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.446A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.593A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 149 removed outlier: 3.598A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 479 hydrogen bonds defined for protein. 1359 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: 2.49 Time building geometry restraints manager: 2.49 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: 2943 1.34 - 1.46: 1525 1.46 - 1.58: 4852 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 9396 Sorted by residual: bond pdb=" N TYR H 235 " pdb=" CA TYR H 235 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.53e-02 4.27e+03 3.99e+00 bond pdb=" N LEU R 325 " pdb=" CA LEU R 325 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.23e-02 6.61e+03 3.80e+00 bond pdb=" CA SER A 6 " pdb=" CB SER A 6 " ideal model delta sigma weight residual 1.530 1.491 0.039 2.00e-02 2.50e+03 3.76e+00 bond pdb=" CA ALA A 41 " pdb=" CB ALA A 41 " ideal model delta sigma weight residual 1.527 1.501 0.026 1.49e-02 4.50e+03 3.13e+00 bond pdb=" N LEU R 68 " pdb=" CA LEU R 68 " ideal model delta sigma weight residual 1.459 1.479 -0.020 1.19e-02 7.06e+03 2.72e+00 ... (remaining 9391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 12627 1.87 - 3.73: 152 3.73 - 5.60: 16 5.60 - 7.46: 4 7.46 - 9.33: 3 Bond angle restraints: 12802 Sorted by residual: angle pdb=" C GLY A 40 " pdb=" N ALA A 41 " pdb=" CA ALA A 41 " ideal model delta sigma weight residual 122.12 115.87 6.25 1.76e+00 3.23e-01 1.26e+01 angle pdb=" CA TYR H 235 " pdb=" C TYR H 235 " pdb=" O TYR H 235 " ideal model delta sigma weight residual 120.23 116.61 3.62 1.02e+00 9.61e-01 1.26e+01 angle pdb=" N LEU R 325 " pdb=" CA LEU R 325 " pdb=" C LEU R 325 " ideal model delta sigma weight residual 111.36 107.94 3.42 1.09e+00 8.42e-01 9.84e+00 angle pdb=" CA TYR H 235 " pdb=" C TYR H 235 " pdb=" N PRO H 236 " ideal model delta sigma weight residual 118.03 121.73 -3.70 1.19e+00 7.06e-01 9.69e+00 angle pdb=" CA GLN B 13 " pdb=" CB GLN B 13 " pdb=" CG GLN B 13 " ideal model delta sigma weight residual 114.10 119.48 -5.38 2.00e+00 2.50e-01 7.25e+00 ... (remaining 12797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4903 17.56 - 35.11: 500 35.11 - 52.67: 119 52.67 - 70.22: 22 70.22 - 87.78: 6 Dihedral angle restraints: 5550 sinusoidal: 1912 harmonic: 3638 Sorted by residual: dihedral pdb=" CB CYS D 11 " pdb=" SG CYS D 11 " pdb=" SG CYS D 51 " pdb=" CB CYS D 51 " ideal model delta sinusoidal sigma weight residual 93.00 171.62 -78.62 1 1.00e+01 1.00e-02 7.71e+01 dihedral pdb=" CB CYS R 119 " pdb=" SG CYS R 119 " pdb=" SG CYS R 196 " pdb=" CB CYS R 196 " ideal model delta sinusoidal sigma weight residual 93.00 143.19 -50.19 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" SG CYS R 119 " pdb=" CB CYS R 196 " pdb=" SG CYS R 196 " pdb=" CA CYS R 196 " ideal model delta sinusoidal sigma weight residual -73.00 -10.41 -62.59 1 2.00e+01 2.50e-03 1.30e+01 ... (remaining 5547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1092 0.041 - 0.081: 296 0.081 - 0.122: 119 0.122 - 0.162: 6 0.162 - 0.203: 2 Chirality restraints: 1515 Sorted by residual: chirality pdb=" CA LEU R 68 " pdb=" N LEU R 68 " pdb=" C LEU R 68 " pdb=" CB LEU R 68 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CG LEU R 88 " pdb=" CB LEU R 88 " pdb=" CD1 LEU R 88 " pdb=" CD2 LEU R 88 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.36e-01 chirality pdb=" CA ILE H 189 " pdb=" N ILE H 189 " pdb=" C ILE H 189 " pdb=" CB ILE H 189 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 1512 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 30 " 0.035 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO E 31 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO E 31 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 31 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO B 194 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 193 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO R 194 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO R 194 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 194 " 0.022 5.00e-02 4.00e+02 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2216 2.79 - 3.32: 8271 3.32 - 3.85: 14763 3.85 - 4.37: 16682 4.37 - 4.90: 30633 Nonbonded interactions: 72565 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.265 3.040 nonbonded pdb=" OG SER H 161 " pdb=" O LYS H 163 " model vdw 2.292 3.040 nonbonded pdb=" O LEU R 64 " pdb=" OG SER R 67 " model vdw 2.293 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.314 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.320 3.040 ... (remaining 72560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 9 or (resid 10 and (name N or name CA or name C or name O \ or name CB )) or resid 11 or (resid 12 through 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 or (resid 15 through 16 and (name N or na \ me CA or name C or name O or name CB )) or resid 17 through 28 or (resid 29 and \ (name N or name CA or name C or name O or name CB )) or resid 30 through 33 or ( \ resid 34 and (name N or name CA or name C or name O or name CB )) or resid 35 th \ rough 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) o \ r resid 38 or (resid 39 and (name N or name CA or name C or name O or name CB )) \ or resid 40 through 51 or (resid 52 and (name N or name CA or name C or name O \ or name CB )) or resid 53 through 59 or (resid 60 through 61 and (name N or name \ CA or name C or name O or name CB )) or resid 62 through 66 or (resid 67 and (n \ ame N or name CA or name C or name O or name CB )) or resid 68)) selection = (chain 'E' and (resid 9 through 21 or (resid 22 and (name N or name CA or name C \ or name O or name CB )) or resid 23 through 44 or (resid 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 through 64 or (resid 65 and (n \ ame N or name CA or name C or name O or name CB )) or resid 66 through 68)) } 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: 0.920 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.830 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9404 Z= 0.134 Angle : 0.524 9.326 12818 Z= 0.286 Chirality : 0.042 0.203 1515 Planarity : 0.003 0.054 1630 Dihedral : 15.238 87.780 3174 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.11 % Allowed : 21.87 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1235 helix: 2.06 (0.26), residues: 405 sheet: 0.50 (0.29), residues: 331 loop : -0.31 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 211 HIS 0.002 0.001 HIS R 242 PHE 0.010 0.001 PHE B 151 TYR 0.016 0.001 TYR A 354 ARG 0.001 0.000 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.17793 ( 474) hydrogen bonds : angle 6.70063 ( 1359) SS BOND : bond 0.00187 ( 8) SS BOND : angle 0.73911 ( 16) covalent geometry : bond 0.00285 ( 9396) covalent geometry : angle 0.52373 (12802) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.947 Fit side-chains REVERT: H 83 MET cc_start: 0.8881 (mtp) cc_final: 0.8680 (mtp) outliers start: 1 outliers final: 0 residues processed: 127 average time/residue: 0.2002 time to fit residues: 36.2206 Evaluate side-chains 124 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN ** R 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 295 ASN G 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.187219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.128971 restraints weight = 11069.406| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.81 r_work: 0.3299 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9404 Z= 0.152 Angle : 0.550 12.395 12818 Z= 0.287 Chirality : 0.043 0.148 1515 Planarity : 0.004 0.054 1630 Dihedral : 3.876 16.704 1336 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.19 % Allowed : 19.89 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.24), residues: 1235 helix: 2.27 (0.26), residues: 405 sheet: 0.42 (0.29), residues: 334 loop : -0.26 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 211 HIS 0.004 0.001 HIS B 91 PHE 0.011 0.001 PHE H 29 TYR 0.021 0.002 TYR A 354 ARG 0.002 0.000 ARG H 72 Details of bonding type rmsd hydrogen bonds : bond 0.04624 ( 474) hydrogen bonds : angle 4.74751 ( 1359) SS BOND : bond 0.00304 ( 8) SS BOND : angle 0.92055 ( 16) covalent geometry : bond 0.00346 ( 9396) covalent geometry : angle 0.54947 (12802) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.955 Fit side-chains REVERT: D 10 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7456 (tt0) outliers start: 29 outliers final: 15 residues processed: 154 average time/residue: 0.1896 time to fit residues: 41.7270 Evaluate side-chains 142 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 GLN Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 63 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 86 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 119 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 6 optimal weight: 20.0000 chunk 76 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.187819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.129621 restraints weight = 11297.556| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.87 r_work: 0.3301 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9404 Z= 0.123 Angle : 0.508 13.544 12818 Z= 0.266 Chirality : 0.042 0.141 1515 Planarity : 0.003 0.055 1630 Dihedral : 3.792 16.962 1336 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.64 % Allowed : 21.43 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.18 (0.24), residues: 1235 helix: 2.31 (0.26), residues: 405 sheet: 0.55 (0.29), residues: 328 loop : -0.29 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE H 29 TYR 0.018 0.001 TYR H 190 ARG 0.002 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.04033 ( 474) hydrogen bonds : angle 4.45136 ( 1359) SS BOND : bond 0.00221 ( 8) SS BOND : angle 0.84966 ( 16) covalent geometry : bond 0.00279 ( 9396) covalent geometry : angle 0.50773 (12802) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.013 Fit side-chains REVERT: D 10 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: B 32 GLN cc_start: 0.8353 (mt0) cc_final: 0.8098 (mt0) outliers start: 24 outliers final: 13 residues processed: 149 average time/residue: 0.1850 time to fit residues: 39.7639 Evaluate side-chains 149 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 GLN Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 74 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 90 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 295 ASN B 259 GLN H 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.185315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.127848 restraints weight = 11154.833| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.93 r_work: 0.3248 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9404 Z= 0.197 Angle : 0.574 14.738 12818 Z= 0.300 Chirality : 0.044 0.149 1515 Planarity : 0.004 0.055 1630 Dihedral : 4.033 17.359 1336 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.29 % Allowed : 20.22 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.24), residues: 1235 helix: 2.28 (0.25), residues: 404 sheet: 0.33 (0.28), residues: 336 loop : -0.28 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 211 HIS 0.004 0.001 HIS B 91 PHE 0.012 0.002 PHE B 151 TYR 0.025 0.002 TYR A 354 ARG 0.002 0.000 ARG R 278 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 474) hydrogen bonds : angle 4.45495 ( 1359) SS BOND : bond 0.00325 ( 8) SS BOND : angle 0.97615 ( 16) covalent geometry : bond 0.00463 ( 9396) covalent geometry : angle 0.57285 (12802) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 128 time to evaluate : 0.960 Fit side-chains REVERT: D 10 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7387 (tt0) outliers start: 39 outliers final: 24 residues processed: 154 average time/residue: 0.1841 time to fit residues: 41.0823 Evaluate side-chains 152 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 GLN Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 263 CYS Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 7 optimal weight: 30.0000 chunk 87 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 49 optimal weight: 0.0270 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.182227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 119)---------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125439 restraints weight = 11216.292| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.83 r_work: 0.3224 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 9404 Z= 0.273 Angle : 0.641 15.810 12818 Z= 0.335 Chirality : 0.047 0.187 1515 Planarity : 0.004 0.054 1630 Dihedral : 4.357 17.979 1336 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.84 % Allowed : 20.66 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.82 (0.24), residues: 1235 helix: 2.11 (0.26), residues: 404 sheet: 0.10 (0.28), residues: 337 loop : -0.38 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 211 HIS 0.006 0.001 HIS B 91 PHE 0.015 0.002 PHE B 151 TYR 0.029 0.002 TYR A 354 ARG 0.007 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 474) hydrogen bonds : angle 4.56130 ( 1359) SS BOND : bond 0.00379 ( 8) SS BOND : angle 1.31550 ( 16) covalent geometry : bond 0.00650 ( 9396) covalent geometry : angle 0.63973 (12802) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 0.949 Fit side-chains outliers start: 44 outliers final: 29 residues processed: 157 average time/residue: 0.1885 time to fit residues: 42.5439 Evaluate side-chains 153 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 263 CYS Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 115 optimal weight: 0.0970 chunk 91 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.186427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.129218 restraints weight = 11151.814| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.81 r_work: 0.3292 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9404 Z= 0.110 Angle : 0.514 15.633 12818 Z= 0.269 Chirality : 0.042 0.162 1515 Planarity : 0.003 0.052 1630 Dihedral : 3.901 17.888 1336 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.19 % Allowed : 22.42 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.00 (0.24), residues: 1235 helix: 2.25 (0.26), residues: 404 sheet: 0.30 (0.28), residues: 335 loop : -0.35 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 211 HIS 0.002 0.001 HIS H 35 PHE 0.014 0.001 PHE R 59 TYR 0.019 0.001 TYR H 190 ARG 0.005 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 474) hydrogen bonds : angle 4.28435 ( 1359) SS BOND : bond 0.00219 ( 8) SS BOND : angle 1.02784 ( 16) covalent geometry : bond 0.00243 ( 9396) covalent geometry : angle 0.51290 (12802) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8579 (m-80) cc_final: 0.8131 (m-80) outliers start: 29 outliers final: 18 residues processed: 156 average time/residue: 0.1764 time to fit residues: 39.8531 Evaluate side-chains 152 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 0.0670 chunk 3 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.183729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.125941 restraints weight = 11211.859| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.86 r_work: 0.3245 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9404 Z= 0.196 Angle : 0.591 17.643 12818 Z= 0.304 Chirality : 0.044 0.166 1515 Planarity : 0.004 0.051 1630 Dihedral : 4.089 17.494 1336 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.85 % Allowed : 21.87 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.95 (0.24), residues: 1235 helix: 2.23 (0.26), residues: 404 sheet: 0.24 (0.28), residues: 338 loop : -0.40 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 211 HIS 0.005 0.001 HIS B 91 PHE 0.014 0.002 PHE R 59 TYR 0.023 0.002 TYR A 354 ARG 0.005 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 474) hydrogen bonds : angle 4.37381 ( 1359) SS BOND : bond 0.00339 ( 8) SS BOND : angle 1.03507 ( 16) covalent geometry : bond 0.00464 ( 9396) covalent geometry : angle 0.59025 (12802) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.952 Fit side-chains REVERT: B 32 GLN cc_start: 0.8334 (mt0) cc_final: 0.8080 (mt0) REVERT: B 59 TYR cc_start: 0.8681 (m-80) cc_final: 0.8311 (m-80) outliers start: 35 outliers final: 30 residues processed: 150 average time/residue: 0.1722 time to fit residues: 38.0465 Evaluate side-chains 154 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 263 CYS Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 48 optimal weight: 0.0670 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 94 optimal weight: 0.4980 chunk 45 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 191 ASN ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.195583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.130180 restraints weight = 11104.691| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.33 r_work: 0.3481 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9404 Z= 0.119 Angle : 0.535 16.713 12818 Z= 0.275 Chirality : 0.042 0.189 1515 Planarity : 0.003 0.051 1630 Dihedral : 3.876 17.698 1336 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.19 % Allowed : 22.86 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.03 (0.24), residues: 1235 helix: 2.28 (0.26), residues: 404 sheet: 0.33 (0.28), residues: 341 loop : -0.37 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 211 HIS 0.002 0.001 HIS H 35 PHE 0.017 0.001 PHE R 59 TYR 0.018 0.001 TYR H 190 ARG 0.004 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 474) hydrogen bonds : angle 4.25752 ( 1359) SS BOND : bond 0.00248 ( 8) SS BOND : angle 0.95095 ( 16) covalent geometry : bond 0.00271 ( 9396) covalent geometry : angle 0.53388 (12802) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: B 32 GLN cc_start: 0.8324 (mt0) cc_final: 0.8107 (mt0) REVERT: B 59 TYR cc_start: 0.8665 (m-80) cc_final: 0.8317 (m-80) outliers start: 29 outliers final: 25 residues processed: 148 average time/residue: 0.1725 time to fit residues: 37.8559 Evaluate side-chains 152 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 45 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 33 optimal weight: 0.0770 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 150 HIS ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.192764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.127016 restraints weight = 10886.036| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.30 r_work: 0.3451 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9404 Z= 0.205 Angle : 0.594 18.994 12818 Z= 0.307 Chirality : 0.045 0.163 1515 Planarity : 0.004 0.051 1630 Dihedral : 4.095 17.339 1336 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.74 % Allowed : 22.20 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.95 (0.24), residues: 1235 helix: 2.27 (0.25), residues: 404 sheet: 0.22 (0.28), residues: 332 loop : -0.40 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 211 HIS 0.005 0.001 HIS B 91 PHE 0.017 0.002 PHE R 59 TYR 0.023 0.002 TYR A 354 ARG 0.004 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 474) hydrogen bonds : angle 4.38039 ( 1359) SS BOND : bond 0.00358 ( 8) SS BOND : angle 1.01993 ( 16) covalent geometry : bond 0.00488 ( 9396) covalent geometry : angle 0.59319 (12802) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 1.051 Fit side-chains REVERT: B 32 GLN cc_start: 0.8318 (mt0) cc_final: 0.8013 (mt0) REVERT: B 59 TYR cc_start: 0.8728 (m-80) cc_final: 0.8460 (m-80) outliers start: 34 outliers final: 30 residues processed: 147 average time/residue: 0.1763 time to fit residues: 38.4167 Evaluate side-chains 156 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 263 CYS Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.193028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.130622 restraints weight = 11066.860| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.75 r_work: 0.3419 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9404 Z= 0.197 Angle : 0.595 18.925 12818 Z= 0.306 Chirality : 0.045 0.157 1515 Planarity : 0.004 0.051 1630 Dihedral : 4.117 18.342 1336 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.96 % Allowed : 22.20 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.92 (0.24), residues: 1235 helix: 2.28 (0.25), residues: 404 sheet: 0.15 (0.28), residues: 341 loop : -0.41 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.018 0.002 PHE R 59 TYR 0.020 0.002 TYR A 354 ARG 0.004 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 474) hydrogen bonds : angle 4.40198 ( 1359) SS BOND : bond 0.00349 ( 8) SS BOND : angle 1.04328 ( 16) covalent geometry : bond 0.00468 ( 9396) covalent geometry : angle 0.59373 (12802) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: R 82 VAL cc_start: 0.6989 (m) cc_final: 0.6662 (t) REVERT: B 32 GLN cc_start: 0.8319 (mt0) cc_final: 0.8043 (mt0) REVERT: B 59 TYR cc_start: 0.8723 (m-80) cc_final: 0.8443 (m-80) outliers start: 36 outliers final: 31 residues processed: 154 average time/residue: 0.1762 time to fit residues: 40.2329 Evaluate side-chains 160 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 263 CYS Chi-restraints excluded: chain R residue 276 LEU Chi-restraints excluded: chain R residue 285 THR Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 158 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 99 optimal weight: 0.0570 chunk 8 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.192457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.126814 restraints weight = 10996.963| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.28 r_work: 0.3446 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9404 Z= 0.204 Angle : 0.612 18.607 12818 Z= 0.313 Chirality : 0.045 0.147 1515 Planarity : 0.004 0.051 1630 Dihedral : 4.153 17.796 1336 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.96 % Allowed : 22.31 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.93 (0.24), residues: 1235 helix: 2.29 (0.25), residues: 403 sheet: 0.18 (0.28), residues: 337 loop : -0.42 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 211 HIS 0.005 0.001 HIS B 91 PHE 0.014 0.002 PHE R 183 TYR 0.023 0.002 TYR A 354 ARG 0.004 0.000 ARG A 209 Details of bonding type rmsd hydrogen bonds : bond 0.04240 ( 474) hydrogen bonds : angle 4.42393 ( 1359) SS BOND : bond 0.00362 ( 8) SS BOND : angle 1.04282 ( 16) covalent geometry : bond 0.00485 ( 9396) covalent geometry : angle 0.61123 (12802) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6427.34 seconds wall clock time: 111 minutes 15.45 seconds (6675.45 seconds total)