Starting phenix.real_space_refine on Sun Aug 24 10:05:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmm_41394/08_2025/8tmm_41394.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmm_41394/08_2025/8tmm_41394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tmm_41394/08_2025/8tmm_41394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmm_41394/08_2025/8tmm_41394.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmm_41394/08_2025/8tmm_41394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmm_41394/08_2025/8tmm_41394.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1577 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 4 5.21 5 S 67 5.16 5 C 11579 2.51 5 N 2915 2.21 5 O 3313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17878 Number of models: 1 Model: "" Number of chains: 13 Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 794 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "A" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2804 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "B" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2925 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "C" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2805 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "D" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2925 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "E" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2925 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.68, per 1000 atoms: 0.26 Number of scatterers: 17878 At special positions: 0 Unit cell: (122.245, 133.938, 161.576, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 Mg 4 11.99 O 3313 8.00 N 2915 7.00 C 11579 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 24 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 738.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4160 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 17 sheets defined 48.1% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'G' and resid 80 through 84 removed outlier: 4.028A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.501A pdb=" N ASP F 90 " --> pdb=" O ARG F 87 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 87 through 91' Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.579A pdb=" N VAL A 50 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Proline residue: A 52 - end of helix removed outlier: 3.759A pdb=" N ASP A 55 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 80 removed outlier: 3.705A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 165 through 202 removed outlier: 3.571A pdb=" N LEU A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 238 removed outlier: 3.764A pdb=" N VAL A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 3.660A pdb=" N GLU A 230 " --> pdb=" O TRP A 226 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 247 through 283 removed outlier: 3.503A pdb=" N PHE A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 313 Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 325 through 345 removed outlier: 3.639A pdb=" N PHE A 345 " --> pdb=" O MET A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 removed outlier: 3.529A pdb=" N SER B 56 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 81 removed outlier: 3.714A pdb=" N VAL B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 165 through 202 removed outlier: 3.713A pdb=" N LEU B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 239 removed outlier: 3.519A pdb=" N VAL B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Proline residue: B 227 - end of helix removed outlier: 3.827A pdb=" N VAL B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 299 removed outlier: 3.867A pdb=" N PHE B 251 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 311 removed outlier: 3.959A pdb=" N PHE B 306 " --> pdb=" O MET B 302 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 323 removed outlier: 3.890A pdb=" N LEU B 321 " --> pdb=" O MET B 318 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TRP B 323 " --> pdb=" O GLU B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 347 removed outlier: 3.611A pdb=" N LYS B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 50 through 56 removed outlier: 3.555A pdb=" N ARG C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 56 " --> pdb=" O PRO C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 50 through 56' Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.560A pdb=" N VAL C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 92 Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.891A pdb=" N ARG C 151 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 202 removed outlier: 3.859A pdb=" N LEU C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 238 Proline residue: C 227 - end of helix removed outlier: 3.868A pdb=" N GLU C 230 " --> pdb=" O TRP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 282 removed outlier: 3.667A pdb=" N PHE C 251 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 252 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL C 278 " --> pdb=" O GLY C 274 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N TYR C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 311 removed outlier: 4.115A pdb=" N ILE C 297 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) Proline residue: C 303 - end of helix Processing helix chain 'C' and resid 318 through 323 removed outlier: 4.197A pdb=" N ARG C 322 " --> pdb=" O MET C 318 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP C 323 " --> pdb=" O PRO C 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 318 through 323' Processing helix chain 'C' and resid 325 through 345 removed outlier: 3.823A pdb=" N PHE C 345 " --> pdb=" O MET C 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 56 removed outlier: 3.897A pdb=" N ASP D 55 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER D 56 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 80 removed outlier: 3.834A pdb=" N VAL D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 160 through 164 removed outlier: 3.844A pdb=" N LYS D 164 " --> pdb=" O ILE D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 202 Processing helix chain 'D' and resid 205 through 238 removed outlier: 3.901A pdb=" N GLN D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.855A pdb=" N GLU D 230 " --> pdb=" O TRP D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 312 removed outlier: 3.624A pdb=" N LEU D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE D 300 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 325 through 349 removed outlier: 4.133A pdb=" N VAL D 329 " --> pdb=" O TRP D 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 55 removed outlier: 3.619A pdb=" N PHE E 53 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG E 54 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 80 removed outlier: 3.735A pdb=" N VAL E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 165 through 202 removed outlier: 3.656A pdb=" N LEU E 169 " --> pdb=" O ARG E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 238 removed outlier: 3.510A pdb=" N VAL E 208 " --> pdb=" O GLU E 204 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TRP E 226 " --> pdb=" O ARG E 222 " (cutoff:3.500A) Proline residue: E 227 - end of helix Processing helix chain 'E' and resid 247 through 311 removed outlier: 3.727A pdb=" N ASP E 253 " --> pdb=" O PRO E 249 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL E 254 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) Proline residue: E 303 - end of helix removed outlier: 4.070A pdb=" N TYR E 311 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 349 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'H' and resid 45 through 51 removed outlier: 6.585A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TYR H 100 " --> pdb=" O MET H 113 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N MET H 113 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR H 102 " --> pdb=" O ASN H 111 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASN H 111 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 45 through 51 removed outlier: 6.585A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 6 through 8 removed outlier: 3.624A pdb=" N THR L 75 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER L 64 " --> pdb=" O THR L 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.573A pdb=" N THR L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.693A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 5 through 8 Processing sheet with id=AA8, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.702A pdb=" N LEU G 12 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.702A pdb=" N LEU G 12 " --> pdb=" O GLU G 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.756A pdb=" N GLY F 10 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER F 33 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.756A pdb=" N GLY F 10 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N CYS F 96 " --> pdb=" O TRP F 116 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TRP F 116 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG F 98 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 39 through 44 removed outlier: 3.937A pdb=" N GLU A 121 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 98 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 40 through 44 removed outlier: 4.636A pdb=" N GLU B 121 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP B 116 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 40 through 44 removed outlier: 3.690A pdb=" N ASN C 33 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C 31 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR C 44 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE C 29 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR C 60 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N MET C 138 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE C 62 " --> pdb=" O MET C 138 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLN C 140 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C 64 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 39 through 42 removed outlier: 6.779A pdb=" N THR D 60 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N MET D 138 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE D 62 " --> pdb=" O MET D 138 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLN D 140 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE D 64 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU D 123 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR D 114 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 40 through 44 removed outlier: 4.732A pdb=" N GLU E 121 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP E 116 " --> pdb=" O GLU E 121 " (cutoff:3.500A) 1069 hydrogen bonds defined for protein. 3027 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: 3.51 Time building geometry restraints manager: 2.15 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: 5642 1.34 - 1.46: 4399 1.46 - 1.58: 8120 1.58 - 1.70: 0 1.70 - 1.82: 121 Bond restraints: 18282 Sorted by residual: bond pdb=" CG1 ILE C 192 " pdb=" CD1 ILE C 192 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.78e+00 bond pdb=" CB PHE D 306 " pdb=" CG PHE D 306 " ideal model delta sigma weight residual 1.502 1.468 0.034 2.30e-02 1.89e+03 2.22e+00 bond pdb=" CB GLN G 90 " pdb=" CG GLN G 90 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.74e+00 bond pdb=" CD GLU A 266 " pdb=" OE1 GLU A 266 " ideal model delta sigma weight residual 1.249 1.226 0.023 1.90e-02 2.77e+03 1.41e+00 bond pdb=" CG LYS D 292 " pdb=" CD LYS D 292 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.24e+00 ... (remaining 18277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 24405 2.09 - 4.18: 331 4.18 - 6.26: 44 6.26 - 8.35: 7 8.35 - 10.44: 4 Bond angle restraints: 24791 Sorted by residual: angle pdb=" C LEU B 235 " pdb=" N TYR B 236 " pdb=" CA TYR B 236 " ideal model delta sigma weight residual 122.06 114.31 7.75 1.86e+00 2.89e-01 1.74e+01 angle pdb=" CA MET C 291 " pdb=" CB MET C 291 " pdb=" CG MET C 291 " ideal model delta sigma weight residual 114.10 120.61 -6.51 2.00e+00 2.50e-01 1.06e+01 angle pdb=" C PRO E 303 " pdb=" N LEU E 304 " pdb=" CA LEU E 304 " ideal model delta sigma weight residual 122.06 116.06 6.00 1.86e+00 2.89e-01 1.04e+01 angle pdb=" CB MET D 291 " pdb=" CG MET D 291 " pdb=" SD MET D 291 " ideal model delta sigma weight residual 112.70 103.64 9.06 3.00e+00 1.11e-01 9.13e+00 angle pdb=" CA LEU E 304 " pdb=" CB LEU E 304 " pdb=" CG LEU E 304 " ideal model delta sigma weight residual 116.30 126.74 -10.44 3.50e+00 8.16e-02 8.90e+00 ... (remaining 24786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 9687 18.00 - 36.00: 1053 36.00 - 54.00: 178 54.00 - 71.99: 27 71.99 - 89.99: 19 Dihedral angle restraints: 10964 sinusoidal: 4513 harmonic: 6451 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 174.84 -81.84 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS G 24 " pdb=" SG CYS G 24 " pdb=" SG CYS G 89 " pdb=" CB CYS G 89 " ideal model delta sinusoidal sigma weight residual 93.00 155.05 -62.05 1 1.00e+01 1.00e-02 5.10e+01 dihedral pdb=" CA TRP A 323 " pdb=" C TRP A 323 " pdb=" N LYS A 324 " pdb=" CA LYS A 324 " ideal model delta harmonic sigma weight residual 180.00 155.27 24.73 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 10961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1983 0.040 - 0.080: 589 0.080 - 0.120: 204 0.120 - 0.160: 26 0.160 - 0.200: 3 Chirality restraints: 2805 Sorted by residual: chirality pdb=" CA TYR C 327 " pdb=" N TYR C 327 " pdb=" C TYR C 327 " pdb=" CB TYR C 327 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ASP C 148 " pdb=" N ASP C 148 " pdb=" C ASP C 148 " pdb=" CB ASP C 148 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CG LEU C 184 " pdb=" CB LEU C 184 " pdb=" CD1 LEU C 184 " pdb=" CD2 LEU C 184 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 2802 not shown) Planarity restraints: 3103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 350 " -0.025 2.00e-02 2.50e+03 2.78e-02 1.93e+01 pdb=" CG TRP D 350 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP D 350 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP D 350 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 350 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP D 350 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 350 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 350 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 350 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 350 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 83 " 0.065 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO C 84 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 84 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 84 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 12 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO E 13 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 13 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 13 " 0.029 5.00e-02 4.00e+02 ... (remaining 3100 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 161 2.63 - 3.20: 16423 3.20 - 3.77: 27883 3.77 - 4.33: 37495 4.33 - 4.90: 62145 Nonbonded interactions: 144107 Sorted by model distance: nonbonded pdb=" OD1 ASN D 288 " pdb=" NZ LYS D 292 " model vdw 2.065 3.120 nonbonded pdb=" O LYS E 111 " pdb=" OH TYR E 181 " model vdw 2.097 3.040 nonbonded pdb=" OG SER L 66 " pdb=" OG1 THR L 73 " model vdw 2.112 3.040 nonbonded pdb=" OG1 THR A 287 " pdb=" OD1 ASN E 288 " model vdw 2.132 3.040 nonbonded pdb=" OG SER F 55 " pdb=" O PRO B 14 " model vdw 2.176 3.040 ... (remaining 144102 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 'A' and resid 17 through 350) selection = (chain 'B' and resid 17 through 350) selection = (chain 'C' and resid 17 through 350) selection = (chain 'D' and resid 17 through 350) selection = (chain 'E' and resid 17 through 350) } ncs_group { reference = (chain 'F' and resid 1 through 122) selection = chain 'H' } ncs_group { reference = chain 'G' selection = (chain 'L' and resid 2 through 107) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.010 Find NCS groups from input model: 0.430 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 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 0.065 18286 Z= 0.148 Angle : 0.612 10.439 24799 Z= 0.324 Chirality : 0.043 0.200 2805 Planarity : 0.005 0.098 3103 Dihedral : 14.964 89.993 6792 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.18), residues: 2163 helix: 1.60 (0.17), residues: 953 sheet: 0.68 (0.25), residues: 448 loop : -1.33 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 229 TYR 0.018 0.001 TYR C 171 PHE 0.014 0.001 PHE B 315 TRP 0.072 0.002 TRP D 350 HIS 0.003 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00326 (18282) covalent geometry : angle 0.61161 (24791) SS BOND : bond 0.00192 ( 4) SS BOND : angle 1.43045 ( 8) hydrogen bonds : bond 0.12914 ( 1048) hydrogen bonds : angle 6.01205 ( 3027) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 0.712 Fit side-chains REVERT: F 13 GLN cc_start: 0.7589 (mm110) cc_final: 0.7328 (mm-40) REVERT: F 43 LYS cc_start: 0.8065 (mttm) cc_final: 0.7808 (ttmm) REVERT: F 89 GLU cc_start: 0.6568 (tm-30) cc_final: 0.5741 (tm-30) REVERT: F 100 TYR cc_start: 0.9100 (p90) cc_final: 0.8685 (p90) REVERT: F 114 ASP cc_start: 0.7534 (m-30) cc_final: 0.7118 (m-30) REVERT: A 71 ASP cc_start: 0.7785 (p0) cc_final: 0.7473 (p0) REVERT: A 111 LYS cc_start: 0.7470 (mtpt) cc_final: 0.7225 (mtmt) REVERT: A 124 SER cc_start: 0.9076 (p) cc_final: 0.8782 (p) REVERT: B 341 MET cc_start: 0.7729 (mpp) cc_final: 0.7430 (mpp) REVERT: C 115 TYR cc_start: 0.7066 (t80) cc_final: 0.6642 (t80) REVERT: C 256 ASP cc_start: 0.7232 (m-30) cc_final: 0.6661 (m-30) REVERT: C 341 MET cc_start: 0.4571 (mmt) cc_final: 0.4164 (mmt) REVERT: D 74 GLN cc_start: 0.7558 (tt0) cc_final: 0.7337 (tt0) REVERT: D 157 ASN cc_start: 0.7851 (t0) cc_final: 0.7477 (t0) REVERT: E 190 ASP cc_start: 0.7146 (m-30) cc_final: 0.6788 (m-30) REVERT: E 193 ASP cc_start: 0.6544 (m-30) cc_final: 0.6147 (m-30) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.1364 time to fit residues: 89.8161 Evaluate side-chains 389 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 GLN A 157 ASN C 140 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.200782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.158600 restraints weight = 21988.700| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.86 r_work: 0.3249 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 18286 Z= 0.202 Angle : 0.623 8.671 24799 Z= 0.332 Chirality : 0.044 0.187 2805 Planarity : 0.005 0.062 3103 Dihedral : 4.661 22.950 2417 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.30 % Allowed : 10.62 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.18), residues: 2163 helix: 1.79 (0.16), residues: 958 sheet: 0.66 (0.24), residues: 457 loop : -1.39 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 202 TYR 0.030 0.002 TYR F 103 PHE 0.023 0.002 PHE B 39 TRP 0.018 0.002 TRP C 350 HIS 0.007 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00470 (18282) covalent geometry : angle 0.62198 (24791) SS BOND : bond 0.00334 ( 4) SS BOND : angle 1.85871 ( 8) hydrogen bonds : bond 0.05786 ( 1048) hydrogen bonds : angle 4.91403 ( 3027) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 411 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: F 13 GLN cc_start: 0.8276 (mm110) cc_final: 0.8046 (mm-40) REVERT: F 43 LYS cc_start: 0.8420 (mttm) cc_final: 0.8129 (ttmm) REVERT: A 71 ASP cc_start: 0.7929 (p0) cc_final: 0.7686 (p0) REVERT: A 124 SER cc_start: 0.9259 (p) cc_final: 0.9017 (p) REVERT: C 98 LYS cc_start: 0.5745 (tmmt) cc_final: 0.5467 (tmmt) REVERT: C 139 PHE cc_start: 0.6277 (m-10) cc_final: 0.5573 (m-80) REVERT: C 198 GLU cc_start: 0.6942 (tp30) cc_final: 0.6605 (tp30) REVERT: C 244 GLU cc_start: 0.7648 (tp30) cc_final: 0.7365 (tp30) REVERT: C 256 ASP cc_start: 0.6942 (m-30) cc_final: 0.6432 (m-30) REVERT: C 334 MET cc_start: 0.5869 (ppp) cc_final: 0.3912 (mtt) REVERT: D 74 GLN cc_start: 0.7746 (tt0) cc_final: 0.7421 (tt0) REVERT: D 157 ASN cc_start: 0.7618 (t0) cc_final: 0.7083 (t0) REVERT: D 189 ASP cc_start: 0.7804 (t0) cc_final: 0.7574 (t0) REVERT: D 198 GLU cc_start: 0.6674 (tp30) cc_final: 0.6431 (tp30) REVERT: D 288 ASN cc_start: 0.8466 (t0) cc_final: 0.8178 (t0) REVERT: E 46 ASP cc_start: 0.8088 (t0) cc_final: 0.7611 (t0) REVERT: E 90 ILE cc_start: 0.7882 (mt) cc_final: 0.7646 (mt) REVERT: E 165 ARG cc_start: 0.7672 (mmp80) cc_final: 0.7203 (mtm180) REVERT: E 190 ASP cc_start: 0.7682 (m-30) cc_final: 0.7326 (m-30) REVERT: E 193 ASP cc_start: 0.6983 (m-30) cc_final: 0.6552 (m-30) REVERT: E 291 MET cc_start: 0.7410 (mmt) cc_final: 0.7001 (mmt) outliers start: 26 outliers final: 16 residues processed: 420 average time/residue: 0.1395 time to fit residues: 90.2910 Evaluate side-chains 408 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 392 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 6 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 209 optimal weight: 0.7980 chunk 160 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 187 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS C 126 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN D 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.202050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.159789 restraints weight = 22104.044| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 4.00 r_work: 0.3255 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18286 Z= 0.171 Angle : 0.582 8.126 24799 Z= 0.309 Chirality : 0.043 0.198 2805 Planarity : 0.004 0.051 3103 Dihedral : 4.606 23.256 2417 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.74 % Allowed : 13.36 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.18), residues: 2163 helix: 1.90 (0.16), residues: 959 sheet: 0.67 (0.24), residues: 462 loop : -1.37 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 229 TYR 0.024 0.001 TYR F 103 PHE 0.020 0.001 PHE B 39 TRP 0.013 0.001 TRP L 36 HIS 0.005 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00390 (18282) covalent geometry : angle 0.58086 (24791) SS BOND : bond 0.00173 ( 4) SS BOND : angle 1.74141 ( 8) hydrogen bonds : bond 0.05462 ( 1048) hydrogen bonds : angle 4.74305 ( 3027) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 401 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: H 113 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7641 (mtt) REVERT: F 43 LYS cc_start: 0.8412 (mttm) cc_final: 0.8115 (ttmm) REVERT: A 54 ARG cc_start: 0.6422 (tmm160) cc_final: 0.5889 (tmm-80) REVERT: A 71 ASP cc_start: 0.7915 (p0) cc_final: 0.7686 (p0) REVERT: A 152 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6464 (mt-10) REVERT: B 306 PHE cc_start: 0.7215 (OUTLIER) cc_final: 0.5806 (p90) REVERT: B 341 MET cc_start: 0.7650 (mpp) cc_final: 0.6965 (mpp) REVERT: C 198 GLU cc_start: 0.6925 (tp30) cc_final: 0.6565 (tp30) REVERT: C 212 HIS cc_start: 0.6969 (m90) cc_final: 0.6677 (m90) REVERT: C 244 GLU cc_start: 0.7730 (tp30) cc_final: 0.7352 (tp30) REVERT: C 256 ASP cc_start: 0.6954 (m-30) cc_final: 0.6085 (m-30) REVERT: C 313 MET cc_start: 0.3785 (ttp) cc_final: 0.2953 (ttp) REVERT: C 334 MET cc_start: 0.5840 (ppp) cc_final: 0.3836 (mtt) REVERT: D 74 GLN cc_start: 0.7729 (tt0) cc_final: 0.7481 (tt0) REVERT: D 157 ASN cc_start: 0.7668 (t0) cc_final: 0.7225 (t0) REVERT: D 198 GLU cc_start: 0.6569 (tp30) cc_final: 0.6265 (tp30) REVERT: D 288 ASN cc_start: 0.8493 (t0) cc_final: 0.8260 (t0) REVERT: E 24 ARG cc_start: 0.7945 (mtt-85) cc_final: 0.7393 (mtt180) REVERT: E 46 ASP cc_start: 0.8123 (t0) cc_final: 0.7634 (t0) REVERT: E 90 ILE cc_start: 0.7882 (mt) cc_final: 0.7646 (mt) REVERT: E 165 ARG cc_start: 0.7572 (mmp80) cc_final: 0.7021 (mtm180) REVERT: E 190 ASP cc_start: 0.7688 (m-30) cc_final: 0.7359 (m-30) REVERT: E 193 ASP cc_start: 0.6973 (m-30) cc_final: 0.6560 (m-30) outliers start: 55 outliers final: 31 residues processed: 426 average time/residue: 0.1394 time to fit residues: 91.7081 Evaluate side-chains 420 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 386 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 127 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 186 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 81 optimal weight: 0.0070 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.200706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.158827 restraints weight = 21900.034| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 4.14 r_work: 0.3237 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18286 Z= 0.172 Angle : 0.583 7.692 24799 Z= 0.309 Chirality : 0.043 0.202 2805 Planarity : 0.004 0.049 3103 Dihedral : 4.600 23.322 2417 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.89 % Allowed : 15.75 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.18), residues: 2163 helix: 1.94 (0.16), residues: 957 sheet: 0.65 (0.24), residues: 462 loop : -1.36 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 229 TYR 0.025 0.001 TYR F 103 PHE 0.020 0.001 PHE B 39 TRP 0.018 0.001 TRP L 36 HIS 0.007 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00396 (18282) covalent geometry : angle 0.58224 (24791) SS BOND : bond 0.00191 ( 4) SS BOND : angle 1.70731 ( 8) hydrogen bonds : bond 0.05345 ( 1048) hydrogen bonds : angle 4.68603 ( 3027) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 412 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.8372 (mttm) cc_final: 0.8096 (ttmm) REVERT: A 54 ARG cc_start: 0.6453 (tmm160) cc_final: 0.5922 (tmm-80) REVERT: A 87 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7969 (mm) REVERT: A 152 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6414 (mt-10) REVERT: B 306 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.5733 (p90) REVERT: B 341 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.6810 (mpp) REVERT: C 198 GLU cc_start: 0.6976 (tp30) cc_final: 0.6674 (tp30) REVERT: C 244 GLU cc_start: 0.7735 (tp30) cc_final: 0.7309 (tp30) REVERT: C 256 ASP cc_start: 0.7001 (m-30) cc_final: 0.6116 (m-30) REVERT: C 263 ASP cc_start: 0.7159 (m-30) cc_final: 0.6922 (m-30) REVERT: C 313 MET cc_start: 0.3779 (ttp) cc_final: 0.2967 (ttp) REVERT: D 74 GLN cc_start: 0.7723 (tt0) cc_final: 0.7427 (tt0) REVERT: D 157 ASN cc_start: 0.7601 (t0) cc_final: 0.7224 (t0) REVERT: D 198 GLU cc_start: 0.6562 (tp30) cc_final: 0.6250 (tp30) REVERT: D 288 ASN cc_start: 0.8492 (t0) cc_final: 0.8277 (t0) REVERT: E 24 ARG cc_start: 0.7997 (mtt-85) cc_final: 0.7462 (mtt180) REVERT: E 46 ASP cc_start: 0.8165 (t0) cc_final: 0.7701 (t0) REVERT: E 90 ILE cc_start: 0.7899 (mt) cc_final: 0.7668 (mt) REVERT: E 165 ARG cc_start: 0.7703 (mmp80) cc_final: 0.7296 (mtm180) REVERT: E 190 ASP cc_start: 0.7695 (m-30) cc_final: 0.7383 (m-30) REVERT: E 193 ASP cc_start: 0.6983 (m-30) cc_final: 0.6609 (m-30) REVERT: E 232 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8560 (mm) outliers start: 58 outliers final: 45 residues processed: 434 average time/residue: 0.1393 time to fit residues: 93.1202 Evaluate side-chains 448 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 398 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 11 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.200284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.158355 restraints weight = 21989.114| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 4.24 r_work: 0.3222 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18286 Z= 0.187 Angle : 0.591 7.361 24799 Z= 0.313 Chirality : 0.043 0.210 2805 Planarity : 0.004 0.049 3103 Dihedral : 4.635 23.599 2417 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.19 % Allowed : 17.50 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.18), residues: 2163 helix: 1.90 (0.16), residues: 958 sheet: 0.62 (0.24), residues: 462 loop : -1.39 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 229 TYR 0.026 0.001 TYR F 103 PHE 0.019 0.001 PHE B 39 TRP 0.027 0.001 TRP L 36 HIS 0.005 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00433 (18282) covalent geometry : angle 0.59005 (24791) SS BOND : bond 0.00111 ( 4) SS BOND : angle 1.88957 ( 8) hydrogen bonds : bond 0.05357 ( 1048) hydrogen bonds : angle 4.68974 ( 3027) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 410 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 67 ARG cc_start: 0.7683 (tmm-80) cc_final: 0.7435 (tmm-80) REVERT: F 43 LYS cc_start: 0.8365 (mttm) cc_final: 0.8093 (ttmm) REVERT: A 54 ARG cc_start: 0.6443 (tmm160) cc_final: 0.5929 (tmm-80) REVERT: A 87 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8040 (mm) REVERT: A 152 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6474 (mt-10) REVERT: B 260 GLN cc_start: 0.8357 (mt0) cc_final: 0.8087 (mt0) REVERT: B 306 PHE cc_start: 0.7069 (OUTLIER) cc_final: 0.5578 (p90) REVERT: B 341 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.6745 (mpp) REVERT: C 198 GLU cc_start: 0.6989 (tp30) cc_final: 0.6673 (tp30) REVERT: C 244 GLU cc_start: 0.7753 (tp30) cc_final: 0.7290 (tp30) REVERT: C 313 MET cc_start: 0.3904 (ttp) cc_final: 0.3130 (ttp) REVERT: D 74 GLN cc_start: 0.7716 (tt0) cc_final: 0.7403 (tt0) REVERT: D 157 ASN cc_start: 0.7716 (t0) cc_final: 0.7402 (t0) REVERT: D 198 GLU cc_start: 0.6586 (tp30) cc_final: 0.6270 (tp30) REVERT: D 288 ASN cc_start: 0.8512 (t0) cc_final: 0.8206 (t0) REVERT: D 341 MET cc_start: 0.5394 (mmt) cc_final: 0.4967 (mmp) REVERT: E 24 ARG cc_start: 0.7979 (mtt-85) cc_final: 0.7431 (mtt180) REVERT: E 46 ASP cc_start: 0.8170 (t0) cc_final: 0.7743 (t0) REVERT: E 90 ILE cc_start: 0.7947 (mt) cc_final: 0.7715 (mt) REVERT: E 165 ARG cc_start: 0.7715 (mmp80) cc_final: 0.7242 (mtm180) REVERT: E 190 ASP cc_start: 0.7774 (m-30) cc_final: 0.7494 (m-30) REVERT: E 193 ASP cc_start: 0.6955 (m-30) cc_final: 0.6503 (m-30) REVERT: E 232 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8556 (mm) outliers start: 64 outliers final: 48 residues processed: 442 average time/residue: 0.1359 time to fit residues: 93.7931 Evaluate side-chains 460 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 407 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 125 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 204 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN B 288 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.199817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.157856 restraints weight = 21804.768| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 4.03 r_work: 0.3232 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18286 Z= 0.189 Angle : 0.595 7.428 24799 Z= 0.315 Chirality : 0.043 0.214 2805 Planarity : 0.004 0.047 3103 Dihedral : 4.663 23.673 2417 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.64 % Allowed : 18.49 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.18), residues: 2163 helix: 1.89 (0.16), residues: 958 sheet: 0.57 (0.24), residues: 465 loop : -1.40 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 229 TYR 0.025 0.002 TYR F 103 PHE 0.019 0.002 PHE B 39 TRP 0.028 0.001 TRP L 36 HIS 0.007 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00438 (18282) covalent geometry : angle 0.59393 (24791) SS BOND : bond 0.00103 ( 4) SS BOND : angle 1.88082 ( 8) hydrogen bonds : bond 0.05340 ( 1048) hydrogen bonds : angle 4.69539 ( 3027) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 411 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.8366 (mttm) cc_final: 0.8097 (ttmm) REVERT: A 54 ARG cc_start: 0.6446 (tmm160) cc_final: 0.5934 (tmm-80) REVERT: A 71 ASP cc_start: 0.8121 (p0) cc_final: 0.7750 (p0) REVERT: A 87 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8011 (mm) REVERT: A 152 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6428 (mt-10) REVERT: B 202 ARG cc_start: 0.6969 (mtm-85) cc_final: 0.6712 (mtm-85) REVERT: B 260 GLN cc_start: 0.8363 (mt0) cc_final: 0.8089 (mt0) REVERT: B 306 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.5424 (p90) REVERT: B 341 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.6814 (mpp) REVERT: C 139 PHE cc_start: 0.6085 (m-10) cc_final: 0.5353 (m-80) REVERT: C 198 GLU cc_start: 0.7015 (tp30) cc_final: 0.6687 (tp30) REVERT: C 244 GLU cc_start: 0.7829 (tp30) cc_final: 0.7355 (tp30) REVERT: C 313 MET cc_start: 0.3942 (ttp) cc_final: 0.3188 (ttp) REVERT: D 74 GLN cc_start: 0.7730 (tt0) cc_final: 0.7382 (tt0) REVERT: D 157 ASN cc_start: 0.7710 (t0) cc_final: 0.7409 (t0) REVERT: D 198 GLU cc_start: 0.6564 (tp30) cc_final: 0.6258 (tp30) REVERT: D 288 ASN cc_start: 0.8533 (t0) cc_final: 0.8235 (t0) REVERT: D 291 MET cc_start: 0.8233 (ttm) cc_final: 0.7849 (mtp) REVERT: D 331 LEU cc_start: 0.5468 (OUTLIER) cc_final: 0.5163 (tt) REVERT: D 341 MET cc_start: 0.5447 (mmt) cc_final: 0.4999 (mmp) REVERT: E 24 ARG cc_start: 0.7971 (mtt-85) cc_final: 0.7416 (mtt180) REVERT: E 29 ILE cc_start: 0.7790 (mt) cc_final: 0.7466 (mt) REVERT: E 46 ASP cc_start: 0.8209 (t0) cc_final: 0.7698 (t0) REVERT: E 90 ILE cc_start: 0.7953 (mt) cc_final: 0.7700 (mt) REVERT: E 132 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8448 (t) REVERT: E 165 ARG cc_start: 0.7738 (mmp80) cc_final: 0.7289 (mtm180) REVERT: E 190 ASP cc_start: 0.7741 (m-30) cc_final: 0.7496 (m-30) REVERT: E 193 ASP cc_start: 0.6871 (m-30) cc_final: 0.6471 (m-30) REVERT: E 232 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8557 (mm) REVERT: E 291 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7195 (mmt) outliers start: 73 outliers final: 52 residues processed: 445 average time/residue: 0.1359 time to fit residues: 94.0298 Evaluate side-chains 466 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 406 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 291 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 210 optimal weight: 0.7980 chunk 181 optimal weight: 0.0030 chunk 126 optimal weight: 0.2980 chunk 123 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 66 optimal weight: 0.0060 chunk 9 optimal weight: 1.9990 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS A 140 GLN B 288 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.203292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.161641 restraints weight = 21979.162| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 4.14 r_work: 0.3261 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18286 Z= 0.136 Angle : 0.568 7.243 24799 Z= 0.299 Chirality : 0.043 0.212 2805 Planarity : 0.004 0.046 3103 Dihedral : 4.533 23.622 2417 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.94 % Allowed : 20.09 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.19), residues: 2163 helix: 2.04 (0.16), residues: 957 sheet: 0.65 (0.24), residues: 469 loop : -1.32 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 222 TYR 0.045 0.001 TYR D 19 PHE 0.020 0.001 PHE B 39 TRP 0.020 0.001 TRP L 36 HIS 0.004 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00297 (18282) covalent geometry : angle 0.56748 (24791) SS BOND : bond 0.00144 ( 4) SS BOND : angle 1.55820 ( 8) hydrogen bonds : bond 0.04954 ( 1048) hydrogen bonds : angle 4.55836 ( 3027) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 421 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.6676 (tt0) cc_final: 0.6386 (tt0) REVERT: F 43 LYS cc_start: 0.8248 (mttm) cc_final: 0.7985 (ttmm) REVERT: A 54 ARG cc_start: 0.6626 (tmm160) cc_final: 0.6070 (tmm-80) REVERT: A 71 ASP cc_start: 0.8089 (p0) cc_final: 0.7684 (p0) REVERT: A 87 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8046 (mm) REVERT: A 152 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6395 (mt-10) REVERT: B 186 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7755 (tp30) REVERT: B 260 GLN cc_start: 0.8294 (mt0) cc_final: 0.8018 (mt0) REVERT: B 306 PHE cc_start: 0.6900 (OUTLIER) cc_final: 0.5423 (p90) REVERT: B 341 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.6719 (mpp) REVERT: C 139 PHE cc_start: 0.6070 (m-10) cc_final: 0.5332 (m-80) REVERT: C 198 GLU cc_start: 0.6968 (tp30) cc_final: 0.6664 (tp30) REVERT: C 244 GLU cc_start: 0.7845 (tp30) cc_final: 0.7351 (tp30) REVERT: C 263 ASP cc_start: 0.7039 (m-30) cc_final: 0.6801 (m-30) REVERT: C 313 MET cc_start: 0.3850 (ttp) cc_final: 0.3094 (ttp) REVERT: D 74 GLN cc_start: 0.7716 (tt0) cc_final: 0.7369 (tt0) REVERT: D 157 ASN cc_start: 0.7676 (t0) cc_final: 0.7358 (t0) REVERT: D 198 GLU cc_start: 0.6558 (tp30) cc_final: 0.6297 (tp30) REVERT: D 288 ASN cc_start: 0.8534 (t0) cc_final: 0.8254 (t0) REVERT: D 291 MET cc_start: 0.8173 (ttm) cc_final: 0.7881 (mtp) REVERT: D 331 LEU cc_start: 0.5443 (OUTLIER) cc_final: 0.5138 (tt) REVERT: D 341 MET cc_start: 0.5469 (mmt) cc_final: 0.5025 (mmp) REVERT: E 24 ARG cc_start: 0.7968 (mtt-85) cc_final: 0.7406 (mtt180) REVERT: E 29 ILE cc_start: 0.7750 (mt) cc_final: 0.7434 (mt) REVERT: E 46 ASP cc_start: 0.8109 (t0) cc_final: 0.7584 (t0) REVERT: E 90 ILE cc_start: 0.7871 (mt) cc_final: 0.7629 (mt) REVERT: E 132 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8324 (t) REVERT: E 165 ARG cc_start: 0.7629 (mmp80) cc_final: 0.7227 (mtm180) REVERT: E 181 TYR cc_start: 0.8481 (m-80) cc_final: 0.8044 (m-80) REVERT: E 190 ASP cc_start: 0.7742 (m-30) cc_final: 0.7495 (m-30) REVERT: E 193 ASP cc_start: 0.6806 (m-30) cc_final: 0.6449 (m-30) REVERT: E 291 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7202 (mmt) outliers start: 59 outliers final: 40 residues processed: 448 average time/residue: 0.1331 time to fit residues: 92.5023 Evaluate side-chains 447 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 400 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 291 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 141 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 146 optimal weight: 0.0170 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 36 optimal weight: 0.0670 chunk 81 optimal weight: 0.9980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN C 217 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.203188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.161235 restraints weight = 21801.571| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.93 r_work: 0.3263 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18286 Z= 0.135 Angle : 0.568 8.254 24799 Z= 0.298 Chirality : 0.043 0.221 2805 Planarity : 0.004 0.045 3103 Dihedral : 4.439 23.547 2417 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.94 % Allowed : 20.34 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.19), residues: 2163 helix: 2.09 (0.16), residues: 957 sheet: 0.68 (0.24), residues: 464 loop : -1.30 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 210 TYR 0.031 0.001 TYR D 19 PHE 0.018 0.001 PHE B 39 TRP 0.035 0.001 TRP L 36 HIS 0.005 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00298 (18282) covalent geometry : angle 0.56738 (24791) SS BOND : bond 0.00141 ( 4) SS BOND : angle 1.61115 ( 8) hydrogen bonds : bond 0.04797 ( 1048) hydrogen bonds : angle 4.45375 ( 3027) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 414 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.8348 (mttm) cc_final: 0.8088 (ttmm) REVERT: A 54 ARG cc_start: 0.6639 (tmm160) cc_final: 0.6079 (tmm-80) REVERT: A 71 ASP cc_start: 0.8115 (p0) cc_final: 0.7702 (p0) REVERT: A 87 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8049 (mm) REVERT: A 152 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6434 (mt-10) REVERT: B 186 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7688 (tp30) REVERT: B 197 GLU cc_start: 0.7622 (tp30) cc_final: 0.7337 (tp30) REVERT: B 260 GLN cc_start: 0.8238 (mt0) cc_final: 0.7951 (mt0) REVERT: B 292 LYS cc_start: 0.7875 (mtmt) cc_final: 0.7622 (mttt) REVERT: B 306 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.5428 (p90) REVERT: B 341 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.6238 (mpp) REVERT: C 139 PHE cc_start: 0.6033 (m-10) cc_final: 0.5250 (m-80) REVERT: C 198 GLU cc_start: 0.6989 (tp30) cc_final: 0.6685 (tp30) REVERT: C 244 GLU cc_start: 0.7894 (tp30) cc_final: 0.7391 (tp30) REVERT: C 263 ASP cc_start: 0.6997 (m-30) cc_final: 0.6782 (m-30) REVERT: C 313 MET cc_start: 0.3912 (ttp) cc_final: 0.3153 (ttp) REVERT: D 28 GLU cc_start: 0.7545 (mm-30) cc_final: 0.5894 (mt-10) REVERT: D 74 GLN cc_start: 0.7701 (tt0) cc_final: 0.7356 (tt0) REVERT: D 75 ARG cc_start: 0.8000 (ttt180) cc_final: 0.7727 (ttt180) REVERT: D 157 ASN cc_start: 0.7686 (t0) cc_final: 0.7366 (t0) REVERT: D 198 GLU cc_start: 0.6522 (tp30) cc_final: 0.6257 (tp30) REVERT: D 210 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.7605 (mtp85) REVERT: D 288 ASN cc_start: 0.8520 (t0) cc_final: 0.8249 (t0) REVERT: D 331 LEU cc_start: 0.5318 (OUTLIER) cc_final: 0.5032 (tt) REVERT: D 341 MET cc_start: 0.5552 (mmt) cc_final: 0.5106 (mmp) REVERT: E 24 ARG cc_start: 0.7939 (mtt-85) cc_final: 0.7353 (mtt180) REVERT: E 46 ASP cc_start: 0.8075 (t0) cc_final: 0.7636 (t0) REVERT: E 90 ILE cc_start: 0.7846 (mt) cc_final: 0.7617 (mt) REVERT: E 132 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8260 (t) REVERT: E 165 ARG cc_start: 0.7603 (mmp80) cc_final: 0.7031 (mtm180) REVERT: E 190 ASP cc_start: 0.7728 (m-30) cc_final: 0.7488 (m-30) REVERT: E 193 ASP cc_start: 0.6757 (m-30) cc_final: 0.6409 (m-30) REVERT: E 204 GLU cc_start: 0.7870 (mp0) cc_final: 0.7631 (mp0) REVERT: E 232 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8429 (mm) REVERT: E 291 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7125 (mmt) REVERT: E 334 MET cc_start: 0.4696 (mmt) cc_final: 0.4416 (mmt) outliers start: 59 outliers final: 44 residues processed: 442 average time/residue: 0.1325 time to fit residues: 90.4371 Evaluate side-chains 464 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 412 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 291 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 188 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 137 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 184 optimal weight: 0.0970 chunk 79 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN B 288 ASN C 260 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.202190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.159997 restraints weight = 21960.916| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 4.05 r_work: 0.3264 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18286 Z= 0.159 Angle : 0.584 8.166 24799 Z= 0.307 Chirality : 0.043 0.224 2805 Planarity : 0.004 0.046 3103 Dihedral : 4.473 23.618 2417 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.04 % Allowed : 20.54 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.19), residues: 2163 helix: 2.05 (0.16), residues: 957 sheet: 0.68 (0.25), residues: 460 loop : -1.33 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 210 TYR 0.026 0.001 TYR D 19 PHE 0.029 0.001 PHE D 251 TRP 0.034 0.001 TRP H 47 HIS 0.004 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00365 (18282) covalent geometry : angle 0.58340 (24791) SS BOND : bond 0.00073 ( 4) SS BOND : angle 1.75215 ( 8) hydrogen bonds : bond 0.04914 ( 1048) hydrogen bonds : angle 4.50921 ( 3027) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 420 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.6548 (tt0) cc_final: 0.6258 (tt0) REVERT: F 13 GLN cc_start: 0.8307 (mm110) cc_final: 0.8035 (mm-40) REVERT: F 43 LYS cc_start: 0.8325 (mttm) cc_final: 0.8071 (ttmm) REVERT: A 54 ARG cc_start: 0.6646 (tmm160) cc_final: 0.6084 (tmm-80) REVERT: A 71 ASP cc_start: 0.8109 (p0) cc_final: 0.7696 (p0) REVERT: A 87 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8009 (mm) REVERT: A 152 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6426 (mt-10) REVERT: B 197 GLU cc_start: 0.7516 (tp30) cc_final: 0.7221 (tp30) REVERT: B 306 PHE cc_start: 0.6930 (OUTLIER) cc_final: 0.5395 (p90) REVERT: B 341 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.6383 (mpp) REVERT: C 139 PHE cc_start: 0.5666 (m-10) cc_final: 0.4883 (m-80) REVERT: C 198 GLU cc_start: 0.6988 (tp30) cc_final: 0.6681 (tp30) REVERT: C 244 GLU cc_start: 0.7820 (tp30) cc_final: 0.7299 (tp30) REVERT: C 263 ASP cc_start: 0.6963 (m-30) cc_final: 0.6742 (m-30) REVERT: C 313 MET cc_start: 0.3971 (ttp) cc_final: 0.3258 (ttp) REVERT: C 318 MET cc_start: 0.4317 (tpt) cc_final: 0.3842 (tpt) REVERT: D 28 GLU cc_start: 0.7564 (mm-30) cc_final: 0.5974 (mt-10) REVERT: D 74 GLN cc_start: 0.7724 (tt0) cc_final: 0.7367 (tt0) REVERT: D 75 ARG cc_start: 0.8042 (ttt180) cc_final: 0.7796 (ttt180) REVERT: D 157 ASN cc_start: 0.7679 (t0) cc_final: 0.7376 (t0) REVERT: D 198 GLU cc_start: 0.6492 (tp30) cc_final: 0.6211 (tp30) REVERT: D 210 ARG cc_start: 0.8286 (mmm-85) cc_final: 0.7654 (mtp85) REVERT: D 288 ASN cc_start: 0.8530 (t0) cc_final: 0.8255 (t0) REVERT: D 331 LEU cc_start: 0.5318 (OUTLIER) cc_final: 0.5040 (tt) REVERT: D 341 MET cc_start: 0.5646 (mmt) cc_final: 0.5198 (mmp) REVERT: E 24 ARG cc_start: 0.7964 (mtt-85) cc_final: 0.7375 (mtt180) REVERT: E 29 ILE cc_start: 0.7793 (mt) cc_final: 0.7499 (mt) REVERT: E 46 ASP cc_start: 0.8101 (t0) cc_final: 0.7579 (t0) REVERT: E 132 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8354 (t) REVERT: E 165 ARG cc_start: 0.7605 (mmp80) cc_final: 0.7166 (mtm180) REVERT: E 190 ASP cc_start: 0.7726 (m-30) cc_final: 0.7498 (m-30) REVERT: E 193 ASP cc_start: 0.6769 (m-30) cc_final: 0.6421 (m-30) REVERT: E 232 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8482 (mm) outliers start: 61 outliers final: 47 residues processed: 448 average time/residue: 0.1354 time to fit residues: 93.8146 Evaluate side-chains 465 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 411 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 110 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 197 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 0.0040 chunk 106 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 189 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.205147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.161356 restraints weight = 21770.512| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.95 r_work: 0.3277 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18286 Z= 0.152 Angle : 0.596 11.592 24799 Z= 0.311 Chirality : 0.043 0.225 2805 Planarity : 0.004 0.046 3103 Dihedral : 4.472 23.659 2417 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.79 % Allowed : 21.14 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.18), residues: 2163 helix: 2.05 (0.16), residues: 954 sheet: 0.71 (0.25), residues: 461 loop : -1.36 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 210 TYR 0.024 0.001 TYR D 19 PHE 0.020 0.001 PHE D 251 TRP 0.031 0.001 TRP H 47 HIS 0.004 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00346 (18282) covalent geometry : angle 0.59517 (24791) SS BOND : bond 0.00079 ( 4) SS BOND : angle 1.71875 ( 8) hydrogen bonds : bond 0.04884 ( 1048) hydrogen bonds : angle 4.51973 ( 3027) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 422 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.6518 (tt0) cc_final: 0.6231 (tt0) REVERT: F 13 GLN cc_start: 0.8271 (mm110) cc_final: 0.7994 (mm-40) REVERT: F 43 LYS cc_start: 0.8306 (mttm) cc_final: 0.8059 (ttmm) REVERT: A 54 ARG cc_start: 0.6617 (tmm160) cc_final: 0.6056 (tmm-80) REVERT: A 71 ASP cc_start: 0.8081 (p0) cc_final: 0.7657 (p0) REVERT: A 87 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7993 (mm) REVERT: A 152 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6420 (mt-10) REVERT: B 186 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7682 (tp30) REVERT: B 288 ASN cc_start: 0.6955 (m110) cc_final: 0.6664 (m-40) REVERT: B 306 PHE cc_start: 0.6920 (OUTLIER) cc_final: 0.5331 (p90) REVERT: B 341 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.6402 (mpp) REVERT: C 139 PHE cc_start: 0.5640 (m-10) cc_final: 0.4820 (m-80) REVERT: C 198 GLU cc_start: 0.7005 (tp30) cc_final: 0.6699 (tp30) REVERT: C 244 GLU cc_start: 0.7827 (tp30) cc_final: 0.7315 (tp30) REVERT: C 263 ASP cc_start: 0.6924 (m-30) cc_final: 0.6710 (m-30) REVERT: C 313 MET cc_start: 0.3946 (ttp) cc_final: 0.3244 (ttp) REVERT: C 318 MET cc_start: 0.4245 (tpt) cc_final: 0.3775 (tpt) REVERT: D 28 GLU cc_start: 0.7543 (mm-30) cc_final: 0.5895 (mt-10) REVERT: D 74 GLN cc_start: 0.7719 (tt0) cc_final: 0.7356 (tt0) REVERT: D 75 ARG cc_start: 0.7943 (ttt180) cc_final: 0.7726 (ttt180) REVERT: D 157 ASN cc_start: 0.7671 (t0) cc_final: 0.7351 (t0) REVERT: D 198 GLU cc_start: 0.6504 (tp30) cc_final: 0.6227 (tp30) REVERT: D 210 ARG cc_start: 0.8268 (mmm-85) cc_final: 0.7643 (mtp85) REVERT: D 288 ASN cc_start: 0.8480 (t0) cc_final: 0.8203 (t0) REVERT: D 331 LEU cc_start: 0.5258 (OUTLIER) cc_final: 0.4983 (tt) REVERT: D 341 MET cc_start: 0.5691 (mmt) cc_final: 0.5232 (mmp) REVERT: E 24 ARG cc_start: 0.7907 (mtt-85) cc_final: 0.7306 (mtt180) REVERT: E 29 ILE cc_start: 0.7773 (mt) cc_final: 0.7488 (mt) REVERT: E 46 ASP cc_start: 0.8076 (t0) cc_final: 0.7552 (t0) REVERT: E 132 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8343 (t) REVERT: E 165 ARG cc_start: 0.7632 (mmp80) cc_final: 0.7203 (mtm180) REVERT: E 181 TYR cc_start: 0.8449 (m-80) cc_final: 0.8011 (m-80) REVERT: E 190 ASP cc_start: 0.7684 (m-30) cc_final: 0.7459 (m-30) REVERT: E 193 ASP cc_start: 0.6711 (m-30) cc_final: 0.6336 (m-30) REVERT: E 204 GLU cc_start: 0.7836 (mp0) cc_final: 0.7595 (mp0) REVERT: E 232 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8464 (mm) outliers start: 56 outliers final: 46 residues processed: 447 average time/residue: 0.1377 time to fit residues: 95.3874 Evaluate side-chains 468 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 415 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 1 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 125 optimal weight: 3.9990 chunk 161 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 69 optimal weight: 0.0970 chunk 200 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.203523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.162094 restraints weight = 21903.489| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 4.23 r_work: 0.3263 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18286 Z= 0.147 Angle : 0.589 11.512 24799 Z= 0.308 Chirality : 0.043 0.230 2805 Planarity : 0.004 0.046 3103 Dihedral : 4.451 23.715 2417 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.84 % Allowed : 21.29 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.18), residues: 2163 helix: 2.08 (0.16), residues: 954 sheet: 0.74 (0.25), residues: 456 loop : -1.39 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 210 TYR 0.023 0.001 TYR D 19 PHE 0.030 0.001 PHE D 251 TRP 0.028 0.001 TRP H 47 HIS 0.005 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00333 (18282) covalent geometry : angle 0.58800 (24791) SS BOND : bond 0.00112 ( 4) SS BOND : angle 1.68656 ( 8) hydrogen bonds : bond 0.04821 ( 1048) hydrogen bonds : angle 4.49224 ( 3027) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5260.26 seconds wall clock time: 90 minutes 58.04 seconds (5458.04 seconds total)