Starting phenix.real_space_refine on Mon May 19 19:02:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tml_41393/05_2025/8tml_41393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tml_41393/05_2025/8tml_41393.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/8tml_41393/05_2025/8tml_41393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tml_41393/05_2025/8tml_41393.map" model { file = "/net/cci-nas-00/data/ceres_data/8tml_41393/05_2025/8tml_41393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tml_41393/05_2025/8tml_41393.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 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 65 5.16 5 C 11503 2.51 5 N 2895 2.21 5 O 3292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17759 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" 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: "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: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2805 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2909 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 15, 'TRANS': 333} Chain: "C" 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: "D" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2935 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "E" 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: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.33, per 1000 atoms: 0.64 Number of scatterers: 17759 At special positions: 0 Unit cell: (122.245, 142.442, 140.316, 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 65 16.00 Mg 4 11.99 O 3292 8.00 N 2895 7.00 C 11503 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=2.04 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: 4.60 Conformation dependent library (CDL) restraints added in 2.4 seconds 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4132 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 17 sheets defined 49.1% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.697A pdb=" N TYR F 31 " --> pdb=" O ASN F 28 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR F 32 " --> pdb=" O VAL F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.798A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.667A pdb=" N VAL A 50 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 69 through 81 removed outlier: 3.794A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 removed outlier: 3.683A pdb=" N LEU A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 165 through 202 removed outlier: 4.097A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 239 Proline residue: A 227 - end of helix removed outlier: 3.504A pdb=" N VAL A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 276 removed outlier: 4.251A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 285 through 312 removed outlier: 3.521A pdb=" N GLU A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 325 through 345 removed outlier: 3.564A pdb=" N VAL A 329 " --> pdb=" O TRP A 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 removed outlier: 3.825A pdb=" N ASP B 55 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 56 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 80 removed outlier: 3.504A 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 156 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 165 through 202 removed outlier: 3.506A pdb=" N LEU B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 238 removed outlier: 3.594A pdb=" N VAL B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Proline residue: B 227 - end of helix removed outlier: 4.297A pdb=" N ASP B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 300 removed outlier: 3.547A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASP B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 311 removed outlier: 3.563A pdb=" N THR B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE B 306 " --> pdb=" O MET B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 348 Processing helix chain 'C' and resid 51 through 56 removed outlier: 3.605A pdb=" N ARG C 54 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP C 55 " --> pdb=" O PRO C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.591A pdb=" N VAL C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 92 removed outlier: 3.785A pdb=" N ASP C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 165 through 202 removed outlier: 3.540A pdb=" N LEU C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 237 Proline residue: C 227 - end of helix removed outlier: 3.734A 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: 3.904A pdb=" N PHE C 251 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 252 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL C 278 " --> pdb=" O GLY C 274 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 312 removed outlier: 3.748A pdb=" N ILE C 300 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Proline residue: C 303 - end of helix Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.916A pdb=" N ARG C 322 " --> pdb=" O MET C 318 " (cutoff:3.500A) removed outlier: 4.003A 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 348 removed outlier: 3.832A pdb=" N LYS C 348 " --> pdb=" O TYR C 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 Proline residue: D 52 - end of helix removed outlier: 3.937A pdb=" N ASP D 55 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 81 removed outlier: 3.546A 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 165 through 202 Processing helix chain 'D' and resid 205 through 238 removed outlier: 4.027A pdb=" N GLN D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Proline residue: D 227 - end of helix Processing helix chain 'D' and resid 240 through 244 removed outlier: 3.754A pdb=" N GLU D 244 " --> pdb=" O PRO D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 311 removed outlier: 3.563A pdb=" N PHE D 251 " --> pdb=" O THR D 247 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG D 252 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP D 253 " --> pdb=" O PRO D 249 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL D 254 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL D 290 " --> pdb=" O LYS D 286 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE D 300 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Proline residue: D 303 - end of helix removed outlier: 3.804A pdb=" N TYR D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 349 Processing helix chain 'E' and resid 46 through 51 removed outlier: 4.345A pdb=" N VAL E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU E 51 " --> pdb=" O VAL E 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 46 through 51' Processing helix chain 'E' and resid 52 through 56 removed outlier: 4.447A pdb=" N ASP E 55 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER E 56 " --> pdb=" O PHE E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 56' Processing helix chain 'E' and resid 69 through 80 removed outlier: 3.696A 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 157 Processing helix chain 'E' and resid 165 through 202 removed outlier: 3.906A pdb=" N TYR E 181 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE E 182 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL E 183 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 239 Proline residue: E 227 - end of helix removed outlier: 3.661A pdb=" N ASP E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 311 Proline residue: E 303 - end of helix removed outlier: 3.559A pdb=" N TYR E 311 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 349 removed outlier: 4.113A pdb=" N PHE E 345 " --> pdb=" O MET E 341 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS E 347 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS E 348 " --> pdb=" O TYR E 344 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 60 removed outlier: 6.637A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR H 100 " --> pdb=" O MET H 113 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N MET H 113 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TYR H 102 " --> pdb=" O ASN H 111 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN H 111 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 57 through 60 removed outlier: 6.637A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER H 33 " --> pdb=" O SER H 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.663A pdb=" N TYR L 87 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.529A 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 14 removed outlier: 3.663A pdb=" N TYR L 87 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 3.587A 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: 6.437A pdb=" N LEU G 12 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N TYR G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.407A 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: 6.437A pdb=" N LEU G 12 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR G 98 " --> pdb=" O GLN G 91 " (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 58 through 60 removed outlier: 6.573A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER F 33 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY F 110 " --> pdb=" O TYR F 102 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 58 through 60 removed outlier: 6.573A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER F 33 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 40 through 43 removed outlier: 3.527A pdb=" N VAL A 109 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 98 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 41 through 44 removed outlier: 4.427A pdb=" N GLU B 121 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP B 116 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 39 through 41 removed outlier: 4.899A pdb=" N GLU C 121 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP C 116 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 127 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 106 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 39 through 44 removed outlier: 6.562A pdb=" N THR D 60 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N MET D 138 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE D 62 " --> pdb=" O MET D 138 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N GLN D 140 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE D 64 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU D 121 " --> pdb=" O ASP D 116 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP D 116 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS D 98 " --> pdb=" O VAL D 109 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 39 through 41 removed outlier: 3.798A pdb=" N PHE E 139 " --> pdb=" O SER E 128 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER E 128 " --> pdb=" O PHE E 139 " (cutoff:3.500A) 1080 hydrogen bonds defined for protein. 3072 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: 5.88 Time building geometry restraints manager: 5.32 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: 5593 1.34 - 1.46: 4189 1.46 - 1.58: 8263 1.58 - 1.70: 0 1.70 - 1.82: 117 Bond restraints: 18162 Sorted by residual: bond pdb=" CD LYS C 292 " pdb=" CE LYS C 292 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 3.98e+00 bond pdb=" CB PRO A 59 " pdb=" CG PRO A 59 " ideal model delta sigma weight residual 1.492 1.565 -0.073 5.00e-02 4.00e+02 2.16e+00 bond pdb=" CG LEU D 184 " pdb=" CD1 LEU D 184 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 1.99e+00 bond pdb=" N LYS C 349 " pdb=" CA LYS C 349 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.53e+00 bond pdb=" CB VAL A 290 " pdb=" CG2 VAL A 290 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.43e+00 ... (remaining 18157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 24301 2.40 - 4.79: 287 4.79 - 7.19: 42 7.19 - 9.58: 2 9.58 - 11.98: 1 Bond angle restraints: 24633 Sorted by residual: angle pdb=" CA PRO A 59 " pdb=" N PRO A 59 " pdb=" CD PRO A 59 " ideal model delta sigma weight residual 112.00 105.65 6.35 1.40e+00 5.10e-01 2.06e+01 angle pdb=" CB MET A 291 " pdb=" CG MET A 291 " pdb=" SD MET A 291 " ideal model delta sigma weight residual 112.70 100.72 11.98 3.00e+00 1.11e-01 1.59e+01 angle pdb=" C LYS D 117 " pdb=" N ASN D 118 " pdb=" CA ASN D 118 " ideal model delta sigma weight residual 121.54 128.51 -6.97 1.91e+00 2.74e-01 1.33e+01 angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 128.12 -6.58 1.91e+00 2.74e-01 1.19e+01 angle pdb=" C THR E 211 " pdb=" N HIS E 212 " pdb=" CA HIS E 212 " ideal model delta sigma weight residual 121.14 115.13 6.01 1.75e+00 3.27e-01 1.18e+01 ... (remaining 24628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9736 17.97 - 35.94: 956 35.94 - 53.91: 145 53.91 - 71.88: 30 71.88 - 89.85: 13 Dihedral angle restraints: 10880 sinusoidal: 4473 harmonic: 6407 Sorted by residual: 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 93.00 169.68 -76.68 1 1.00e+01 1.00e-02 7.39e+01 dihedral pdb=" CA CYS G 89 " pdb=" C CYS G 89 " pdb=" N GLN G 90 " pdb=" CA GLN G 90 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA PRO B 240 " pdb=" C PRO B 240 " pdb=" N PRO B 241 " pdb=" CA PRO B 241 " ideal model delta harmonic sigma weight residual -180.00 -158.54 -21.46 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 10877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2034 0.046 - 0.092: 602 0.092 - 0.138: 135 0.138 - 0.183: 16 0.183 - 0.229: 1 Chirality restraints: 2788 Sorted by residual: chirality pdb=" CB VAL B 265 " pdb=" CA VAL B 265 " pdb=" CG1 VAL B 265 " pdb=" CG2 VAL B 265 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB ILE E 64 " pdb=" CA ILE E 64 " pdb=" CG1 ILE E 64 " pdb=" CG2 ILE E 64 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CA GLU B 266 " pdb=" N GLU B 266 " pdb=" C GLU B 266 " pdb=" CB GLU B 266 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.84e-01 ... (remaining 2785 not shown) Planarity restraints: 3083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 58 " -0.053 5.00e-02 4.00e+02 7.73e-02 9.55e+00 pdb=" N PRO A 59 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 59 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 59 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 292 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C LYS B 292 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS B 292 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL B 293 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 263 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C ASP B 263 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP B 263 " 0.013 2.00e-02 2.50e+03 pdb=" N THR B 264 " 0.012 2.00e-02 2.50e+03 ... (remaining 3080 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 844 2.72 - 3.27: 18587 3.27 - 3.81: 29798 3.81 - 4.36: 35213 4.36 - 4.90: 60966 Nonbonded interactions: 145408 Sorted by model distance: nonbonded pdb=" OD1 ASN B 288 " pdb=" OG1 THR C 287 " model vdw 2.178 3.040 nonbonded pdb=" O GLU A 204 " pdb=" OG1 THR A 207 " model vdw 2.195 3.040 nonbonded pdb=" OE1 GLN D 260 " pdb=" NH2 ARG E 96 " model vdw 2.216 3.120 nonbonded pdb=" NE2 GLN A 140 " pdb=" OD2 ASP A 145 " model vdw 2.226 3.120 nonbonded pdb=" NH1 ARG A 216 " pdb=" OD1 ASP E 193 " model vdw 2.237 3.120 ... (remaining 145403 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' 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 41.520 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 18166 Z= 0.182 Angle : 0.668 11.976 24641 Z= 0.360 Chirality : 0.045 0.229 2788 Planarity : 0.005 0.077 3083 Dihedral : 14.467 89.853 6736 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.05 % Allowed : 0.30 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.18), residues: 2147 helix: 1.60 (0.16), residues: 940 sheet: 0.32 (0.24), residues: 471 loop : -1.70 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 61 HIS 0.009 0.001 HIS E 212 PHE 0.019 0.002 PHE G 99 TYR 0.015 0.001 TYR D 236 ARG 0.008 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.13084 ( 1048) hydrogen bonds : angle 6.23281 ( 3072) SS BOND : bond 0.00501 ( 4) SS BOND : angle 1.34861 ( 8) covalent geometry : bond 0.00416 (18162) covalent geometry : angle 0.66736 (24633) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 413 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 92 SER cc_start: 0.8702 (p) cc_final: 0.8427 (p) REVERT: A 121 GLU cc_start: 0.6012 (pm20) cc_final: 0.5743 (pm20) REVERT: A 129 LEU cc_start: 0.7915 (mm) cc_final: 0.7653 (mt) REVERT: A 151 ARG cc_start: 0.6300 (ttm170) cc_final: 0.5857 (ttp-170) REVERT: A 155 ARG cc_start: 0.6072 (ttm110) cc_final: 0.5680 (ttm110) REVERT: A 181 TYR cc_start: 0.6794 (m-80) cc_final: 0.6464 (m-80) REVERT: A 193 ASP cc_start: 0.6921 (t0) cc_final: 0.6589 (t0) REVERT: A 214 LEU cc_start: 0.8256 (tp) cc_final: 0.7973 (tp) REVERT: A 291 MET cc_start: 0.7610 (mmm) cc_final: 0.7132 (mmt) REVERT: B 121 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6570 (mt-10) REVERT: B 198 GLU cc_start: 0.6851 (tp30) cc_final: 0.6604 (tp30) REVERT: C 112 MET cc_start: 0.8150 (mtp) cc_final: 0.7822 (mtp) REVERT: C 186 GLU cc_start: 0.7087 (tt0) cc_final: 0.6587 (tt0) REVERT: C 263 ASP cc_start: 0.7555 (m-30) cc_final: 0.7341 (m-30) REVERT: C 313 MET cc_start: 0.4985 (tpp) cc_final: 0.4605 (tpp) REVERT: C 341 MET cc_start: 0.4917 (mmt) cc_final: 0.4572 (mmp) REVERT: D 220 GLU cc_start: 0.7243 (tt0) cc_final: 0.7027 (mt-10) REVERT: D 259 ILE cc_start: 0.8462 (mm) cc_final: 0.7879 (mm) REVERT: E 164 LYS cc_start: 0.7465 (mttt) cc_final: 0.7098 (mtpt) outliers start: 1 outliers final: 0 residues processed: 413 average time/residue: 0.2944 time to fit residues: 183.1954 Evaluate side-chains 365 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 4.9990 chunk 160 optimal weight: 0.1980 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 192 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN F 39 GLN ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 HIS B 157 ASN ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN E 212 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.193723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.151151 restraints weight = 20718.864| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.64 r_work: 0.3187 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18166 Z= 0.173 Angle : 0.618 9.335 24641 Z= 0.325 Chirality : 0.044 0.221 2788 Planarity : 0.005 0.053 3083 Dihedral : 4.706 21.568 2400 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.30 % Allowed : 8.93 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 2147 helix: 2.02 (0.16), residues: 949 sheet: 0.43 (0.24), residues: 446 loop : -1.58 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 61 HIS 0.015 0.001 HIS E 212 PHE 0.023 0.002 PHE B 306 TYR 0.021 0.001 TYR E 344 ARG 0.006 0.001 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.05751 ( 1048) hydrogen bonds : angle 4.97916 ( 3072) SS BOND : bond 0.00407 ( 4) SS BOND : angle 1.12711 ( 8) covalent geometry : bond 0.00393 (18162) covalent geometry : angle 0.61765 (24633) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 372 time to evaluate : 1.877 Fit side-chains revert: symmetry clash REVERT: H 21 SER cc_start: 0.8993 (t) cc_final: 0.8743 (m) REVERT: L 25 ARG cc_start: 0.8100 (mtp-110) cc_final: 0.7691 (mtp-110) REVERT: L 90 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: A 111 LYS cc_start: 0.7325 (mtpp) cc_final: 0.7099 (mtpp) REVERT: A 121 GLU cc_start: 0.6221 (pm20) cc_final: 0.5850 (pm20) REVERT: A 151 ARG cc_start: 0.6645 (ttm170) cc_final: 0.6414 (ttp-170) REVERT: A 202 ARG cc_start: 0.6078 (mtm180) cc_final: 0.5822 (ptt180) REVERT: A 214 LEU cc_start: 0.8338 (tp) cc_final: 0.7955 (tp) REVERT: A 296 ILE cc_start: 0.7764 (pt) cc_final: 0.7472 (pt) REVERT: B 157 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8089 (t0) REVERT: B 198 GLU cc_start: 0.7127 (tp30) cc_final: 0.6828 (tp30) REVERT: B 291 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.7001 (mtp) REVERT: B 318 MET cc_start: 0.3521 (tmm) cc_final: 0.1775 (mmm) REVERT: C 112 MET cc_start: 0.8510 (mtp) cc_final: 0.8143 (mtp) REVERT: C 186 GLU cc_start: 0.7481 (tt0) cc_final: 0.7030 (tt0) REVERT: C 292 LYS cc_start: 0.7554 (mmtp) cc_final: 0.7141 (mmtp) REVERT: C 313 MET cc_start: 0.4811 (tpp) cc_final: 0.4585 (tpp) REVERT: C 341 MET cc_start: 0.4829 (mmt) cc_final: 0.4483 (mmp) REVERT: D 190 ASP cc_start: 0.7430 (m-30) cc_final: 0.6957 (m-30) REVERT: D 193 ASP cc_start: 0.6254 (t0) cc_final: 0.6024 (t0) REVERT: D 196 GLU cc_start: 0.7750 (tt0) cc_final: 0.7474 (tt0) REVERT: D 220 GLU cc_start: 0.8013 (tt0) cc_final: 0.7689 (mt-10) REVERT: E 40 ARG cc_start: 0.4890 (tpt90) cc_final: 0.4562 (tpt90) REVERT: E 134 ASN cc_start: 0.6878 (p0) cc_final: 0.6526 (p0) REVERT: E 164 LYS cc_start: 0.7178 (mttt) cc_final: 0.6627 (mtpt) outliers start: 26 outliers final: 19 residues processed: 378 average time/residue: 0.2820 time to fit residues: 161.2787 Evaluate side-chains 382 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 360 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 219 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 157 optimal weight: 0.2980 chunk 94 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 chunk 149 optimal weight: 0.0770 chunk 10 optimal weight: 0.9990 chunk 88 optimal weight: 0.0050 chunk 121 optimal weight: 0.1980 overall best weight: 0.2752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN G 39 GLN F 39 GLN A 63 ASN B 260 GLN ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.195328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.152245 restraints weight = 20752.457| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.57 r_work: 0.3230 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18166 Z= 0.133 Angle : 0.569 9.492 24641 Z= 0.298 Chirality : 0.043 0.311 2788 Planarity : 0.004 0.049 3083 Dihedral : 4.484 21.421 2400 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.81 % Allowed : 11.39 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.18), residues: 2147 helix: 2.26 (0.16), residues: 954 sheet: 0.49 (0.24), residues: 449 loop : -1.58 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 61 HIS 0.005 0.001 HIS D 257 PHE 0.021 0.001 PHE B 306 TYR 0.025 0.001 TYR C 19 ARG 0.007 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.05163 ( 1048) hydrogen bonds : angle 4.65826 ( 3072) SS BOND : bond 0.00559 ( 4) SS BOND : angle 0.70536 ( 8) covalent geometry : bond 0.00281 (18162) covalent geometry : angle 0.56883 (24633) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 362 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 37 VAL cc_start: 0.8760 (p) cc_final: 0.8413 (t) REVERT: H 83 MET cc_start: 0.8153 (mtm) cc_final: 0.7799 (mtt) REVERT: A 151 ARG cc_start: 0.6511 (ttm170) cc_final: 0.6246 (ttp-170) REVERT: A 202 ARG cc_start: 0.6176 (mtm180) cc_final: 0.5943 (ptt180) REVERT: A 222 ARG cc_start: 0.6957 (ttm-80) cc_final: 0.6181 (tpp80) REVERT: B 121 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7211 (pt0) REVERT: B 156 TYR cc_start: 0.7308 (m-80) cc_final: 0.6635 (m-80) REVERT: B 157 ASN cc_start: 0.8320 (t0) cc_final: 0.7907 (t0) REVERT: B 163 LYS cc_start: 0.7819 (mmmt) cc_final: 0.7375 (mmtp) REVERT: B 198 GLU cc_start: 0.7096 (tp30) cc_final: 0.6800 (tp30) REVERT: B 247 THR cc_start: 0.7832 (OUTLIER) cc_final: 0.7627 (p) REVERT: B 252 ARG cc_start: 0.7473 (tpt-90) cc_final: 0.6553 (mmm160) REVERT: B 266 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: B 318 MET cc_start: 0.3314 (tmm) cc_final: 0.1618 (mmm) REVERT: C 112 MET cc_start: 0.8518 (mtp) cc_final: 0.8116 (mtp) REVERT: C 191 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7331 (mm-30) REVERT: C 292 LYS cc_start: 0.7434 (mmtp) cc_final: 0.7005 (mmtp) REVERT: C 313 MET cc_start: 0.4438 (tpp) cc_final: 0.4153 (tpp) REVERT: C 341 MET cc_start: 0.4891 (mmt) cc_final: 0.4578 (mmp) REVERT: D 190 ASP cc_start: 0.7295 (m-30) cc_final: 0.6847 (m-30) REVERT: D 193 ASP cc_start: 0.6255 (t0) cc_final: 0.6016 (t0) REVERT: D 220 GLU cc_start: 0.7998 (tt0) cc_final: 0.7682 (mt-10) REVERT: D 289 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7661 (tp30) REVERT: E 134 ASN cc_start: 0.6827 (p0) cc_final: 0.6463 (p0) REVERT: E 164 LYS cc_start: 0.7112 (mttt) cc_final: 0.6548 (mtpt) outliers start: 36 outliers final: 21 residues processed: 376 average time/residue: 0.2892 time to fit residues: 164.9680 Evaluate side-chains 372 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 347 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 266 GLU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain E residue 219 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 91 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 27 optimal weight: 0.0770 chunk 110 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 78 optimal weight: 0.0050 chunk 150 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.8156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN G 90 GLN ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 GLN B 94 HIS ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.192750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.149414 restraints weight = 20754.243| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.62 r_work: 0.3165 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18166 Z= 0.193 Angle : 0.596 10.377 24641 Z= 0.312 Chirality : 0.044 0.248 2788 Planarity : 0.005 0.047 3083 Dihedral : 4.564 21.788 2400 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.31 % Allowed : 13.85 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2147 helix: 2.15 (0.16), residues: 955 sheet: 0.40 (0.24), residues: 456 loop : -1.65 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 350 HIS 0.007 0.001 HIS D 257 PHE 0.020 0.002 PHE B 306 TYR 0.017 0.002 TYR H 103 ARG 0.007 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.05441 ( 1048) hydrogen bonds : angle 4.68699 ( 3072) SS BOND : bond 0.00390 ( 4) SS BOND : angle 1.09008 ( 8) covalent geometry : bond 0.00454 (18162) covalent geometry : angle 0.59540 (24633) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 371 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 37 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8518 (t) REVERT: H 83 MET cc_start: 0.8253 (mtm) cc_final: 0.7906 (mtt) REVERT: F 39 GLN cc_start: 0.6237 (tt0) cc_final: 0.5606 (tt0) REVERT: A 87 LEU cc_start: 0.7838 (tp) cc_final: 0.7607 (tp) REVERT: A 129 LEU cc_start: 0.7227 (mt) cc_final: 0.6768 (mm) REVERT: A 151 ARG cc_start: 0.6550 (ttm170) cc_final: 0.6322 (ttp-170) REVERT: A 202 ARG cc_start: 0.6117 (mtm180) cc_final: 0.5894 (ptt180) REVERT: A 300 ILE cc_start: 0.7962 (mt) cc_final: 0.7761 (mt) REVERT: B 157 ASN cc_start: 0.8471 (t0) cc_final: 0.7942 (t0) REVERT: B 163 LYS cc_start: 0.7913 (mmmt) cc_final: 0.7527 (mmtp) REVERT: B 202 ARG cc_start: 0.6678 (mmm-85) cc_final: 0.6469 (mtm110) REVERT: B 247 THR cc_start: 0.7925 (OUTLIER) cc_final: 0.7687 (p) REVERT: B 252 ARG cc_start: 0.7495 (tpt-90) cc_final: 0.6577 (mmm160) REVERT: B 318 MET cc_start: 0.3346 (tmm) cc_final: 0.1630 (mmm) REVERT: C 112 MET cc_start: 0.8547 (mtp) cc_final: 0.8198 (mtp) REVERT: C 292 LYS cc_start: 0.7492 (mmtp) cc_final: 0.7090 (mmtp) REVERT: C 341 MET cc_start: 0.5099 (mmt) cc_final: 0.4786 (mmp) REVERT: D 190 ASP cc_start: 0.7454 (m-30) cc_final: 0.6972 (m-30) REVERT: D 220 GLU cc_start: 0.7974 (tt0) cc_final: 0.7637 (mt-10) REVERT: D 289 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7675 (tp30) REVERT: E 134 ASN cc_start: 0.6805 (p0) cc_final: 0.6438 (p0) REVERT: E 164 LYS cc_start: 0.7168 (mttt) cc_final: 0.6529 (mtpt) outliers start: 46 outliers final: 31 residues processed: 391 average time/residue: 0.2877 time to fit residues: 170.7492 Evaluate side-chains 392 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 358 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 219 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 79 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 205 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 135 optimal weight: 0.4980 chunk 13 optimal weight: 0.0980 chunk 127 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** C 140 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 = 0.4001 r_free = 0.4001 target = 0.194299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.151458 restraints weight = 21022.089| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.80 r_work: 0.3189 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18166 Z= 0.140 Angle : 0.561 9.449 24641 Z= 0.295 Chirality : 0.043 0.156 2788 Planarity : 0.004 0.046 3083 Dihedral : 4.449 21.555 2400 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.41 % Allowed : 15.10 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.18), residues: 2147 helix: 2.28 (0.16), residues: 957 sheet: 0.43 (0.24), residues: 447 loop : -1.56 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 350 HIS 0.006 0.001 HIS D 257 PHE 0.022 0.001 PHE E 53 TYR 0.031 0.001 TYR C 19 ARG 0.008 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.05024 ( 1048) hydrogen bonds : angle 4.54320 ( 3072) SS BOND : bond 0.00557 ( 4) SS BOND : angle 0.92562 ( 8) covalent geometry : bond 0.00310 (18162) covalent geometry : angle 0.56072 (24633) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 353 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 37 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8533 (t) REVERT: H 76 LYS cc_start: 0.7790 (ptmm) cc_final: 0.7509 (ptpt) REVERT: L 90 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: F 39 GLN cc_start: 0.6181 (tt0) cc_final: 0.5577 (tt0) REVERT: A 38 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: A 87 LEU cc_start: 0.7694 (tp) cc_final: 0.7428 (tp) REVERT: A 151 ARG cc_start: 0.6558 (ttm170) cc_final: 0.6301 (ttp-170) REVERT: A 222 ARG cc_start: 0.7034 (ttm-80) cc_final: 0.5818 (ttm-80) REVERT: B 157 ASN cc_start: 0.8487 (t0) cc_final: 0.7913 (t0) REVERT: B 163 LYS cc_start: 0.7802 (mmmt) cc_final: 0.7518 (mmtm) REVERT: B 318 MET cc_start: 0.3271 (tmm) cc_final: 0.1606 (mmm) REVERT: C 112 MET cc_start: 0.8549 (mtp) cc_final: 0.8259 (mtp) REVERT: C 191 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7312 (mm-30) REVERT: C 292 LYS cc_start: 0.7497 (mmtp) cc_final: 0.7089 (mmtp) REVERT: C 341 MET cc_start: 0.5102 (mmt) cc_final: 0.4793 (mmp) REVERT: D 10 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7841 (tttp) REVERT: D 190 ASP cc_start: 0.7401 (m-30) cc_final: 0.6891 (m-30) REVERT: D 220 GLU cc_start: 0.8051 (tt0) cc_final: 0.7712 (mt-10) REVERT: D 289 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7700 (tp30) REVERT: E 53 PHE cc_start: 0.5934 (t80) cc_final: 0.5722 (t80) REVERT: E 74 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.6806 (tp-100) REVERT: E 134 ASN cc_start: 0.6844 (p0) cc_final: 0.6491 (p0) REVERT: E 164 LYS cc_start: 0.7156 (mttt) cc_final: 0.6516 (mtpt) outliers start: 48 outliers final: 31 residues processed: 375 average time/residue: 0.2791 time to fit residues: 158.5618 Evaluate side-chains 381 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 343 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 219 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 93 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN B 63 ASN B 157 ASN ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.189604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.146033 restraints weight = 20752.013| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.69 r_work: 0.3125 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 18166 Z= 0.241 Angle : 0.638 11.098 24641 Z= 0.333 Chirality : 0.045 0.283 2788 Planarity : 0.005 0.055 3083 Dihedral : 4.683 22.765 2400 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.11 % Allowed : 15.81 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 2147 helix: 1.95 (0.16), residues: 957 sheet: 0.27 (0.24), residues: 456 loop : -1.72 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 226 HIS 0.005 0.001 HIS C 257 PHE 0.017 0.002 PHE C 27 TYR 0.018 0.002 TYR H 103 ARG 0.007 0.001 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.05682 ( 1048) hydrogen bonds : angle 4.76026 ( 3072) SS BOND : bond 0.00600 ( 4) SS BOND : angle 1.35729 ( 8) covalent geometry : bond 0.00575 (18162) covalent geometry : angle 0.63715 (24633) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 374 time to evaluate : 2.101 Fit side-chains REVERT: H 37 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8509 (t) REVERT: F 39 GLN cc_start: 0.6233 (tt0) cc_final: 0.5658 (tt0) REVERT: A 38 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6659 (mm-30) REVERT: A 87 LEU cc_start: 0.7818 (tp) cc_final: 0.7557 (tp) REVERT: A 151 ARG cc_start: 0.6349 (ttm170) cc_final: 0.6148 (ttp-170) REVERT: A 202 ARG cc_start: 0.6080 (mtm180) cc_final: 0.5755 (ptp-170) REVERT: B 157 ASN cc_start: 0.8521 (t0) cc_final: 0.8148 (t0) REVERT: B 163 LYS cc_start: 0.7900 (mmmt) cc_final: 0.7619 (mmtm) REVERT: B 252 ARG cc_start: 0.7444 (tpt-90) cc_final: 0.6534 (mmm160) REVERT: B 318 MET cc_start: 0.3263 (tmm) cc_final: 0.1565 (mmm) REVERT: C 112 MET cc_start: 0.8634 (mtp) cc_final: 0.8323 (mtp) REVERT: C 313 MET cc_start: 0.4449 (tpp) cc_final: 0.4194 (tpp) REVERT: C 341 MET cc_start: 0.5240 (mmt) cc_final: 0.4910 (mmp) REVERT: D 10 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8250 (tttp) REVERT: D 38 GLU cc_start: 0.7765 (pp20) cc_final: 0.7492 (pp20) REVERT: D 190 ASP cc_start: 0.7560 (m-30) cc_final: 0.7103 (m-30) REVERT: D 220 GLU cc_start: 0.8023 (tt0) cc_final: 0.7680 (mt-10) REVERT: D 289 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7690 (tp30) REVERT: E 53 PHE cc_start: 0.5975 (t80) cc_final: 0.5600 (t80) REVERT: E 74 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.6816 (tp-100) REVERT: E 138 MET cc_start: 0.5354 (pmm) cc_final: 0.4597 (pmm) REVERT: E 164 LYS cc_start: 0.7127 (mttt) cc_final: 0.6484 (mtpt) outliers start: 62 outliers final: 41 residues processed: 404 average time/residue: 0.2864 time to fit residues: 175.9062 Evaluate side-chains 408 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 362 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 166 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 125 optimal weight: 0.0970 chunk 27 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 157 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.192767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.149855 restraints weight = 20606.752| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.71 r_work: 0.3163 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 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 = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18166 Z= 0.153 Angle : 0.581 11.404 24641 Z= 0.304 Chirality : 0.043 0.308 2788 Planarity : 0.004 0.046 3083 Dihedral : 4.491 22.487 2400 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.66 % Allowed : 17.36 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2147 helix: 2.15 (0.16), residues: 958 sheet: 0.28 (0.25), residues: 431 loop : -1.63 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 226 HIS 0.006 0.001 HIS D 257 PHE 0.017 0.001 PHE C 27 TYR 0.039 0.001 TYR C 19 ARG 0.007 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.05136 ( 1048) hydrogen bonds : angle 4.57979 ( 3072) SS BOND : bond 0.00361 ( 4) SS BOND : angle 0.93415 ( 8) covalent geometry : bond 0.00349 (18162) covalent geometry : angle 0.58102 (24633) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 369 time to evaluate : 1.909 Fit side-chains revert: symmetry clash REVERT: H 37 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8530 (t) REVERT: H 76 LYS cc_start: 0.7932 (ptmm) cc_final: 0.7611 (ptpt) REVERT: L 28 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8089 (mm-40) REVERT: F 113 MET cc_start: 0.8685 (mtt) cc_final: 0.8119 (mtt) REVERT: A 38 GLU cc_start: 0.7086 (tp30) cc_final: 0.6783 (mm-30) REVERT: A 87 LEU cc_start: 0.7708 (tp) cc_final: 0.7479 (tp) REVERT: A 191 GLU cc_start: 0.8016 (tt0) cc_final: 0.7765 (tt0) REVERT: A 301 PHE cc_start: 0.7262 (m-80) cc_final: 0.6963 (m-80) REVERT: B 157 ASN cc_start: 0.8417 (t0) cc_final: 0.8111 (t0) REVERT: B 266 GLU cc_start: 0.7928 (tt0) cc_final: 0.7593 (tt0) REVERT: B 313 MET cc_start: 0.5721 (OUTLIER) cc_final: 0.5511 (mmm) REVERT: B 318 MET cc_start: 0.3250 (tmm) cc_final: 0.1730 (mmm) REVERT: C 112 MET cc_start: 0.8575 (mtp) cc_final: 0.8289 (mtp) REVERT: C 191 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7351 (mm-30) REVERT: C 292 LYS cc_start: 0.7327 (mmtp) cc_final: 0.6948 (mmtp) REVERT: C 313 MET cc_start: 0.4421 (tpp) cc_final: 0.4198 (tpp) REVERT: C 341 MET cc_start: 0.5195 (mmt) cc_final: 0.4887 (mmp) REVERT: D 10 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8099 (tttp) REVERT: D 190 ASP cc_start: 0.7566 (m-30) cc_final: 0.7050 (m-30) REVERT: D 220 GLU cc_start: 0.8097 (tt0) cc_final: 0.7750 (mt-10) REVERT: E 53 PHE cc_start: 0.5999 (t80) cc_final: 0.5508 (t80) REVERT: E 74 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6818 (tp-100) REVERT: E 164 LYS cc_start: 0.7169 (mttt) cc_final: 0.6508 (mtpt) outliers start: 53 outliers final: 39 residues processed: 397 average time/residue: 0.2791 time to fit residues: 167.9870 Evaluate side-chains 400 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 355 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 122 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 121 optimal weight: 0.4980 chunk 104 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN A 217 ASN ** C 140 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 = 0.3956 r_free = 0.3956 target = 0.190088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.146845 restraints weight = 20691.302| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.79 r_work: 0.3137 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18166 Z= 0.204 Angle : 0.616 10.898 24641 Z= 0.321 Chirality : 0.045 0.331 2788 Planarity : 0.005 0.048 3083 Dihedral : 4.596 22.341 2400 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.16 % Allowed : 17.56 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 2147 helix: 2.01 (0.16), residues: 957 sheet: 0.24 (0.25), residues: 438 loop : -1.74 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 226 HIS 0.005 0.001 HIS D 257 PHE 0.016 0.002 PHE C 27 TYR 0.028 0.002 TYR C 19 ARG 0.008 0.001 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.05434 ( 1048) hydrogen bonds : angle 4.66744 ( 3072) SS BOND : bond 0.00436 ( 4) SS BOND : angle 1.06333 ( 8) covalent geometry : bond 0.00483 (18162) covalent geometry : angle 0.61584 (24633) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 362 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 37 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8520 (t) REVERT: H 76 LYS cc_start: 0.7970 (ptmm) cc_final: 0.7644 (ptpt) REVERT: L 28 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8148 (mm-40) REVERT: G 90 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: F 113 MET cc_start: 0.8669 (mtt) cc_final: 0.8158 (mtt) REVERT: A 38 GLU cc_start: 0.7095 (tp30) cc_final: 0.6772 (mm-30) REVERT: A 87 LEU cc_start: 0.7781 (tp) cc_final: 0.7556 (tp) REVERT: A 191 GLU cc_start: 0.8110 (tt0) cc_final: 0.7895 (tt0) REVERT: A 301 PHE cc_start: 0.7274 (m-80) cc_final: 0.6959 (m-80) REVERT: B 157 ASN cc_start: 0.8501 (t0) cc_final: 0.8207 (t0) REVERT: B 266 GLU cc_start: 0.7925 (tt0) cc_final: 0.7678 (tt0) REVERT: B 313 MET cc_start: 0.5882 (OUTLIER) cc_final: 0.5487 (mmm) REVERT: B 318 MET cc_start: 0.3342 (tmm) cc_final: 0.1754 (mmm) REVERT: C 112 MET cc_start: 0.8595 (mtp) cc_final: 0.8291 (mtp) REVERT: C 313 MET cc_start: 0.4511 (tpp) cc_final: 0.4231 (tpp) REVERT: C 341 MET cc_start: 0.5194 (mmt) cc_final: 0.4917 (mmp) REVERT: D 10 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8261 (tttp) REVERT: D 190 ASP cc_start: 0.7561 (m-30) cc_final: 0.7055 (m-30) REVERT: D 220 GLU cc_start: 0.8062 (tt0) cc_final: 0.7717 (mt-10) REVERT: D 226 TRP cc_start: 0.9129 (m-10) cc_final: 0.8838 (m-10) REVERT: D 236 TYR cc_start: 0.8149 (t80) cc_final: 0.7588 (t80) REVERT: E 40 ARG cc_start: 0.3978 (tpt90) cc_final: 0.3775 (tpt90) REVERT: E 53 PHE cc_start: 0.6098 (t80) cc_final: 0.5531 (t80) REVERT: E 74 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.6831 (tp-100) REVERT: E 164 LYS cc_start: 0.7153 (mttt) cc_final: 0.6495 (mtpt) REVERT: E 278 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8294 (p) outliers start: 63 outliers final: 49 residues processed: 397 average time/residue: 0.2761 time to fit residues: 168.3095 Evaluate side-chains 412 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 356 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 173 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 chunk 4 optimal weight: 0.0270 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 197 optimal weight: 0.6980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 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 = 0.3973 r_free = 0.3973 target = 0.191778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.148171 restraints weight = 20759.160| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.79 r_work: 0.3176 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 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 = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18166 Z= 0.153 Angle : 0.587 11.490 24641 Z= 0.307 Chirality : 0.043 0.338 2788 Planarity : 0.004 0.045 3083 Dihedral : 4.499 22.430 2400 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.91 % Allowed : 17.76 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.18), residues: 2147 helix: 2.14 (0.16), residues: 958 sheet: 0.27 (0.25), residues: 435 loop : -1.71 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 226 HIS 0.006 0.001 HIS D 257 PHE 0.016 0.001 PHE C 27 TYR 0.019 0.001 TYR B 311 ARG 0.009 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.05108 ( 1048) hydrogen bonds : angle 4.56719 ( 3072) SS BOND : bond 0.00463 ( 4) SS BOND : angle 0.96931 ( 8) covalent geometry : bond 0.00350 (18162) covalent geometry : angle 0.58694 (24633) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 358 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8518 (t) REVERT: H 76 LYS cc_start: 0.7924 (ptmm) cc_final: 0.7612 (ptpt) REVERT: L 28 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8150 (mm-40) REVERT: G 90 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: F 39 GLN cc_start: 0.6136 (tt0) cc_final: 0.5744 (tt0) REVERT: F 82 GLN cc_start: 0.6400 (tm-30) cc_final: 0.6107 (tm-30) REVERT: F 113 MET cc_start: 0.8667 (mtt) cc_final: 0.8126 (mtt) REVERT: A 38 GLU cc_start: 0.7073 (tp30) cc_final: 0.6754 (mm-30) REVERT: A 87 LEU cc_start: 0.7691 (tp) cc_final: 0.7451 (tp) REVERT: A 109 VAL cc_start: 0.7765 (OUTLIER) cc_final: 0.7565 (m) REVERT: A 318 MET cc_start: 0.6243 (tmm) cc_final: 0.5101 (mmm) REVERT: B 157 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8095 (t0) REVERT: B 266 GLU cc_start: 0.7832 (tt0) cc_final: 0.7329 (tt0) REVERT: B 313 MET cc_start: 0.5748 (OUTLIER) cc_final: 0.5363 (mmm) REVERT: B 318 MET cc_start: 0.2781 (tmm) cc_final: 0.1418 (mmm) REVERT: C 112 MET cc_start: 0.8556 (mtp) cc_final: 0.8264 (mtp) REVERT: C 313 MET cc_start: 0.4475 (tpp) cc_final: 0.4212 (tpp) REVERT: C 341 MET cc_start: 0.5164 (mmt) cc_final: 0.4898 (mmp) REVERT: D 10 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8126 (tttp) REVERT: D 190 ASP cc_start: 0.7537 (m-30) cc_final: 0.7023 (m-30) REVERT: D 220 GLU cc_start: 0.8034 (tt0) cc_final: 0.7687 (mt-10) REVERT: D 226 TRP cc_start: 0.9075 (m-10) cc_final: 0.8668 (m-10) REVERT: D 236 TYR cc_start: 0.8123 (t80) cc_final: 0.7599 (t80) REVERT: E 40 ARG cc_start: 0.3983 (tpt90) cc_final: 0.3773 (tpt90) REVERT: E 74 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.6828 (tp-100) REVERT: E 164 LYS cc_start: 0.7164 (mttt) cc_final: 0.6522 (mtpt) outliers start: 58 outliers final: 44 residues processed: 391 average time/residue: 0.2786 time to fit residues: 167.3378 Evaluate side-chains 402 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 350 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 5 optimal weight: 0.3980 chunk 119 optimal weight: 0.0980 chunk 88 optimal weight: 0.3980 chunk 184 optimal weight: 0.3980 chunk 205 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 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 = 0.3983 r_free = 0.3983 target = 0.192817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.149522 restraints weight = 20695.577| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.82 r_work: 0.3179 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 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 = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18166 Z= 0.147 Angle : 0.589 11.532 24641 Z= 0.306 Chirality : 0.043 0.345 2788 Planarity : 0.004 0.049 3083 Dihedral : 4.502 23.640 2400 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.91 % Allowed : 18.06 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2147 helix: 2.19 (0.16), residues: 958 sheet: 0.30 (0.25), residues: 433 loop : -1.66 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 226 HIS 0.005 0.001 HIS D 257 PHE 0.020 0.001 PHE E 301 TYR 0.019 0.001 TYR B 311 ARG 0.010 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.04997 ( 1048) hydrogen bonds : angle 4.52653 ( 3072) SS BOND : bond 0.00328 ( 4) SS BOND : angle 1.90154 ( 8) covalent geometry : bond 0.00334 (18162) covalent geometry : angle 0.58771 (24633) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 354 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 37 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8525 (t) REVERT: H 76 LYS cc_start: 0.7910 (ptmm) cc_final: 0.7594 (ptpt) REVERT: L 28 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8148 (mm-40) REVERT: G 90 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7187 (tt0) REVERT: F 39 GLN cc_start: 0.6123 (tt0) cc_final: 0.5737 (tt0) REVERT: F 82 GLN cc_start: 0.6378 (tm-30) cc_final: 0.6081 (tm-30) REVERT: F 113 MET cc_start: 0.8698 (mtt) cc_final: 0.8126 (mtt) REVERT: A 38 GLU cc_start: 0.7087 (tp30) cc_final: 0.6776 (mm-30) REVERT: A 87 LEU cc_start: 0.7577 (tp) cc_final: 0.7348 (tp) REVERT: A 155 ARG cc_start: 0.5741 (ttm110) cc_final: 0.5311 (ttm110) REVERT: A 222 ARG cc_start: 0.7028 (ttm-80) cc_final: 0.6275 (tpp80) REVERT: A 318 MET cc_start: 0.5877 (tmm) cc_final: 0.4956 (mmm) REVERT: B 54 ARG cc_start: 0.7214 (ttm170) cc_final: 0.6822 (ttm170) REVERT: B 157 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8149 (t0) REVERT: B 201 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6590 (pp20) REVERT: B 266 GLU cc_start: 0.7873 (tt0) cc_final: 0.7319 (tt0) REVERT: B 313 MET cc_start: 0.5713 (OUTLIER) cc_final: 0.5438 (mmm) REVERT: B 318 MET cc_start: 0.2763 (tmm) cc_final: 0.1417 (mmm) REVERT: C 112 MET cc_start: 0.8543 (mtp) cc_final: 0.8256 (mtp) REVERT: C 140 GLN cc_start: 0.8329 (mp10) cc_final: 0.8126 (mp10) REVERT: C 191 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7335 (mm-30) REVERT: C 313 MET cc_start: 0.4472 (tpp) cc_final: 0.4206 (tpp) REVERT: C 341 MET cc_start: 0.5197 (mmt) cc_final: 0.4906 (mmp) REVERT: D 10 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8077 (tttp) REVERT: D 50 VAL cc_start: 0.9230 (OUTLIER) cc_final: 0.9020 (m) REVERT: D 190 ASP cc_start: 0.7511 (m-30) cc_final: 0.6984 (m-30) REVERT: D 220 GLU cc_start: 0.8091 (tt0) cc_final: 0.7741 (mt-10) REVERT: D 226 TRP cc_start: 0.9066 (m-10) cc_final: 0.8634 (m-10) REVERT: D 236 TYR cc_start: 0.8149 (t80) cc_final: 0.7631 (t80) REVERT: E 40 ARG cc_start: 0.3983 (tpt90) cc_final: 0.3767 (tpt90) REVERT: E 53 PHE cc_start: 0.5948 (t80) cc_final: 0.5317 (t80) REVERT: E 74 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.6826 (tp-100) REVERT: E 125 GLU cc_start: 0.7839 (tp30) cc_final: 0.7029 (tm-30) REVERT: E 164 LYS cc_start: 0.7161 (mttt) cc_final: 0.6301 (mtpt) outliers start: 58 outliers final: 46 residues processed: 388 average time/residue: 0.2918 time to fit residues: 173.4673 Evaluate side-chains 405 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 349 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 59 SER Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 135 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 189 optimal weight: 6.9990 chunk 27 optimal weight: 0.0980 chunk 44 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 174 optimal weight: 0.3980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 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 = 0.3980 r_free = 0.3980 target = 0.192519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.149458 restraints weight = 20677.808| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.79 r_work: 0.3174 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 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 = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18166 Z= 0.157 Angle : 0.594 13.782 24641 Z= 0.308 Chirality : 0.044 0.380 2788 Planarity : 0.004 0.047 3083 Dihedral : 4.490 22.120 2400 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.06 % Allowed : 18.21 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2147 helix: 2.17 (0.16), residues: 958 sheet: 0.29 (0.25), residues: 435 loop : -1.68 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 226 HIS 0.004 0.001 HIS D 257 PHE 0.018 0.001 PHE E 301 TYR 0.019 0.001 TYR C 19 ARG 0.009 0.000 ARG B 216 Details of bonding type rmsd hydrogen bonds : bond 0.05022 ( 1048) hydrogen bonds : angle 4.51644 ( 3072) SS BOND : bond 0.00299 ( 4) SS BOND : angle 1.68836 ( 8) covalent geometry : bond 0.00363 (18162) covalent geometry : angle 0.59335 (24633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9247.59 seconds wall clock time: 161 minutes 17.17 seconds (9677.17 seconds total)