Starting phenix.real_space_refine on Sat Oct 11 23:27:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tml_41393/10_2025/8tml_41393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tml_41393/10_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_41393/10_2025/8tml_41393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tml_41393/10_2025/8tml_41393.map" model { file = "/net/cci-nas-00/data/ceres_data/8tml_41393/10_2025/8tml_41393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tml_41393/10_2025/8tml_41393.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 4.33, per 1000 atoms: 0.24 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: 1.80 Conformation dependent library (CDL) restraints added in 754.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.80 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: 3.27 Time building geometry restraints manager: 2.39 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: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.680 Find NCS groups from input model: 0.390 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.780 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (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 ARG 0.008 0.000 ARG A 155 TYR 0.015 0.001 TYR D 236 PHE 0.019 0.002 PHE G 99 TRP 0.030 0.001 TRP A 61 HIS 0.009 0.001 HIS E 212 Details of bonding type rmsd covalent geometry : bond 0.00416 (18162) covalent geometry : angle 0.66736 (24633) SS BOND : bond 0.00501 ( 4) SS BOND : angle 1.34861 ( 8) hydrogen bonds : bond 0.13084 ( 1048) hydrogen bonds : angle 6.23281 ( 3072) *********************** 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 : 0.605 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: 0.1360 time to fit residues: 85.2394 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 : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 120 HIS B 63 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.192331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.149255 restraints weight = 20792.733| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.65 r_work: 0.3170 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18166 Z= 0.196 Angle : 0.632 8.829 24641 Z= 0.333 Chirality : 0.045 0.230 2788 Planarity : 0.005 0.051 3083 Dihedral : 4.761 21.932 2400 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.46 % Allowed : 9.13 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.18), residues: 2147 helix: 1.97 (0.16), residues: 949 sheet: 0.36 (0.24), residues: 447 loop : -1.60 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 216 TYR 0.021 0.002 TYR E 344 PHE 0.023 0.002 PHE B 306 TRP 0.028 0.001 TRP A 61 HIS 0.016 0.001 HIS E 212 Details of bonding type rmsd covalent geometry : bond 0.00453 (18162) covalent geometry : angle 0.63173 (24633) SS BOND : bond 0.01699 ( 4) SS BOND : angle 1.10119 ( 8) hydrogen bonds : bond 0.05826 ( 1048) hydrogen bonds : angle 4.99223 ( 3072) *********************** 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 402 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 373 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: H 21 SER cc_start: 0.9036 (t) cc_final: 0.8803 (m) REVERT: L 90 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: A 111 LYS cc_start: 0.7335 (mtpp) cc_final: 0.7086 (mtpp) REVERT: A 151 ARG cc_start: 0.6632 (ttm170) cc_final: 0.6388 (ttp-170) REVERT: A 202 ARG cc_start: 0.6026 (mtm180) cc_final: 0.5774 (ptt180) REVERT: A 214 LEU cc_start: 0.8351 (tp) cc_final: 0.7987 (tp) REVERT: A 296 ILE cc_start: 0.7792 (pt) cc_final: 0.7499 (pt) REVERT: B 157 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.8071 (t0) REVERT: B 198 GLU cc_start: 0.7164 (tp30) cc_final: 0.6857 (tp30) REVERT: B 291 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7168 (mtp) REVERT: C 19 TYR cc_start: 0.7787 (t80) cc_final: 0.7460 (t80) REVERT: C 112 MET cc_start: 0.8557 (mtp) cc_final: 0.8154 (mtp) REVERT: C 292 LYS cc_start: 0.7576 (mmtp) cc_final: 0.7145 (mmtp) REVERT: C 313 MET cc_start: 0.4875 (tpp) cc_final: 0.4621 (tpp) REVERT: C 341 MET cc_start: 0.4860 (mmt) cc_final: 0.4512 (mmp) REVERT: D 193 ASP cc_start: 0.6292 (t0) cc_final: 0.6063 (t0) REVERT: D 196 GLU cc_start: 0.7844 (tt0) cc_final: 0.7565 (tt0) REVERT: D 220 GLU cc_start: 0.8001 (tt0) cc_final: 0.7700 (mt-10) REVERT: E 40 ARG cc_start: 0.4894 (tpt90) cc_final: 0.4666 (tpt90) REVERT: E 53 PHE cc_start: 0.5860 (t80) cc_final: 0.5517 (t80) REVERT: E 134 ASN cc_start: 0.6884 (p0) cc_final: 0.6542 (p0) REVERT: E 164 LYS cc_start: 0.7197 (mttt) cc_final: 0.6641 (mtpt) outliers start: 29 outliers final: 21 residues processed: 380 average time/residue: 0.1307 time to fit residues: 75.8548 Evaluate side-chains 382 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 358 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 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 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 157 ASN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 20 THR 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 72 optimal weight: 0.4980 chunk 195 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 chunk 126 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 155 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** G 39 GLN F 39 GLN A 63 ASN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 GLN ** 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 = 0.192806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.149369 restraints weight = 20939.667| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.54 r_work: 0.3203 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18166 Z= 0.167 Angle : 0.592 10.005 24641 Z= 0.310 Chirality : 0.044 0.324 2788 Planarity : 0.005 0.045 3083 Dihedral : 4.620 21.845 2400 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.86 % Allowed : 12.49 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.18), residues: 2147 helix: 2.09 (0.16), residues: 952 sheet: 0.38 (0.24), residues: 449 loop : -1.64 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 216 TYR 0.017 0.001 TYR C 279 PHE 0.021 0.001 PHE B 306 TRP 0.017 0.001 TRP A 61 HIS 0.006 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00384 (18162) covalent geometry : angle 0.59227 (24633) SS BOND : bond 0.00344 ( 4) SS BOND : angle 0.94380 ( 8) hydrogen bonds : bond 0.05513 ( 1048) hydrogen bonds : angle 4.77028 ( 3072) *********************** 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 414 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 377 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: H 21 SER cc_start: 0.8969 (t) cc_final: 0.8758 (m) REVERT: H 83 MET cc_start: 0.8226 (mtm) cc_final: 0.7884 (mtt) REVERT: G 90 GLN cc_start: 0.6701 (mt0) cc_final: 0.6455 (mt0) REVERT: A 87 LEU cc_start: 0.7697 (tp) cc_final: 0.7485 (tp) REVERT: A 121 GLU cc_start: 0.6244 (pm20) cc_final: 0.5864 (pm20) REVERT: A 129 LEU cc_start: 0.7197 (mt) cc_final: 0.6802 (mm) REVERT: A 151 ARG cc_start: 0.6471 (ttm170) cc_final: 0.6215 (ttp-170) REVERT: A 202 ARG cc_start: 0.6181 (mtm180) cc_final: 0.5956 (ptt180) REVERT: B 121 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7274 (pt0) REVERT: B 156 TYR cc_start: 0.7368 (m-80) cc_final: 0.6687 (m-80) REVERT: B 157 ASN cc_start: 0.8414 (t0) cc_final: 0.8001 (t0) REVERT: B 163 LYS cc_start: 0.7847 (mmmt) cc_final: 0.7384 (mmtp) REVERT: B 198 GLU cc_start: 0.7146 (tp30) cc_final: 0.6909 (tp30) REVERT: B 202 ARG cc_start: 0.6678 (mmm-85) cc_final: 0.6347 (mmm-85) REVERT: B 252 ARG cc_start: 0.7371 (tpt-90) cc_final: 0.6491 (mmm160) REVERT: B 266 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7540 (tt0) REVERT: B 318 MET cc_start: 0.3366 (tmm) cc_final: 0.1577 (mmm) REVERT: C 19 TYR cc_start: 0.7839 (t80) cc_final: 0.7455 (t80) REVERT: C 112 MET cc_start: 0.8526 (mtp) cc_final: 0.8128 (mtp) REVERT: C 291 MET cc_start: 0.8483 (mmm) cc_final: 0.8250 (tpt) REVERT: C 292 LYS cc_start: 0.7450 (mmtp) cc_final: 0.7004 (mmtp) REVERT: C 313 MET cc_start: 0.4604 (tpp) cc_final: 0.4321 (tpp) REVERT: C 341 MET cc_start: 0.5009 (mmt) cc_final: 0.4697 (mmp) REVERT: D 190 ASP cc_start: 0.7397 (m-30) cc_final: 0.6911 (m-30) REVERT: D 220 GLU cc_start: 0.7917 (tt0) cc_final: 0.7572 (mt-10) REVERT: D 289 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7611 (tp30) REVERT: E 53 PHE cc_start: 0.5894 (t80) cc_final: 0.5430 (t80) REVERT: E 134 ASN cc_start: 0.6800 (p0) cc_final: 0.6423 (p0) REVERT: E 164 LYS cc_start: 0.7154 (mttt) cc_final: 0.6554 (mtpt) REVERT: E 195 LEU cc_start: 0.7136 (mt) cc_final: 0.6904 (mt) outliers start: 37 outliers final: 25 residues processed: 389 average time/residue: 0.1316 time to fit residues: 77.7549 Evaluate side-chains 386 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 359 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 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 A residue 318 MET Chi-restraints excluded: chain B residue 135 CYS 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 236 TYR Chi-restraints excluded: chain D residue 20 THR 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 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 22 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 170 optimal weight: 0.5980 chunk 164 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 209 GLN ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.190966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.147867 restraints weight = 20958.095| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.64 r_work: 0.3148 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18166 Z= 0.199 Angle : 0.608 9.466 24641 Z= 0.318 Chirality : 0.044 0.228 2788 Planarity : 0.005 0.047 3083 Dihedral : 4.655 23.006 2400 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.61 % Allowed : 14.35 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.18), residues: 2147 helix: 2.03 (0.16), residues: 957 sheet: 0.30 (0.24), residues: 451 loop : -1.66 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 155 TYR 0.017 0.002 TYR H 103 PHE 0.021 0.002 PHE B 306 TRP 0.016 0.001 TRP C 350 HIS 0.007 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00469 (18162) covalent geometry : angle 0.60721 (24633) SS BOND : bond 0.00538 ( 4) SS BOND : angle 1.24346 ( 8) hydrogen bonds : bond 0.05586 ( 1048) hydrogen bonds : angle 4.76738 ( 3072) *********************** 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 431 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 379 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 21 SER cc_start: 0.9021 (t) cc_final: 0.8788 (m) REVERT: H 37 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8505 (t) REVERT: H 83 MET cc_start: 0.8387 (mtm) cc_final: 0.8015 (mtt) REVERT: F 39 GLN cc_start: 0.6285 (tt0) cc_final: 0.5669 (tt0) REVERT: A 87 LEU cc_start: 0.7816 (tp) cc_final: 0.7530 (tp) REVERT: A 151 ARG cc_start: 0.6619 (ttm170) cc_final: 0.6374 (ttp-170) REVERT: A 202 ARG cc_start: 0.6246 (mtm180) cc_final: 0.5984 (ptt180) REVERT: A 300 ILE cc_start: 0.8083 (mt) cc_final: 0.7852 (mt) REVERT: B 157 ASN cc_start: 0.8541 (t0) cc_final: 0.7975 (t0) REVERT: B 163 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7554 (mmtp) REVERT: B 318 MET cc_start: 0.3335 (tmm) cc_final: 0.1612 (mmm) REVERT: C 19 TYR cc_start: 0.7905 (t80) cc_final: 0.7371 (t80) REVERT: C 112 MET cc_start: 0.8584 (mtp) cc_final: 0.8259 (mtp) REVERT: C 191 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7430 (mm-30) REVERT: C 341 MET cc_start: 0.5172 (mmt) cc_final: 0.4830 (mmp) REVERT: D 10 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8033 (tttp) REVERT: D 190 ASP cc_start: 0.7498 (m-30) cc_final: 0.6989 (m-30) REVERT: D 220 GLU cc_start: 0.8008 (tt0) cc_final: 0.7666 (mt-10) REVERT: D 289 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7728 (tp30) REVERT: E 40 ARG cc_start: 0.4704 (tpt90) cc_final: 0.4422 (tpt90) REVERT: E 134 ASN cc_start: 0.6853 (p0) cc_final: 0.6497 (p0) REVERT: E 164 LYS cc_start: 0.7162 (mttt) cc_final: 0.6545 (mtpt) outliers start: 52 outliers final: 36 residues processed: 403 average time/residue: 0.1383 time to fit residues: 84.1185 Evaluate side-chains 407 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 367 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 69 THR 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 50 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 195 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 296 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 160 ILE 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 20 THR 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 74 GLN Chi-restraints excluded: chain E residue 109 VAL 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 186 optimal weight: 8.9990 chunk 206 optimal weight: 0.9990 chunk 190 optimal weight: 0.6980 chunk 201 optimal weight: 0.9980 chunk 99 optimal weight: 0.0980 chunk 55 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** 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 = 0.3967 r_free = 0.3967 target = 0.191199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.147626 restraints weight = 20605.921| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.59 r_work: 0.3163 rms_B_bonded: 3.53 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: 0.7585 moved from start: 0.1468 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= 0.168 Angle : 0.587 10.052 24641 Z= 0.308 Chirality : 0.044 0.347 2788 Planarity : 0.004 0.048 3083 Dihedral : 4.573 22.279 2400 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.91 % Allowed : 15.70 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.18), residues: 2147 helix: 2.09 (0.16), residues: 958 sheet: 0.30 (0.24), residues: 454 loop : -1.68 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 216 TYR 0.016 0.001 TYR B 311 PHE 0.018 0.001 PHE C 27 TRP 0.017 0.001 TRP C 350 HIS 0.006 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00390 (18162) covalent geometry : angle 0.58732 (24633) SS BOND : bond 0.00722 ( 4) SS BOND : angle 0.93885 ( 8) hydrogen bonds : bond 0.05340 ( 1048) hydrogen bonds : angle 4.67779 ( 3072) *********************** 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 422 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 364 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 21 SER cc_start: 0.9025 (t) cc_final: 0.8816 (m) REVERT: H 37 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8509 (t) REVERT: H 83 MET cc_start: 0.8304 (mtm) cc_final: 0.7945 (mtt) REVERT: L 28 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8074 (mm-40) REVERT: F 39 GLN cc_start: 0.6201 (tt0) cc_final: 0.5602 (tt0) REVERT: A 38 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6689 (mm-30) REVERT: A 87 LEU cc_start: 0.7713 (tp) cc_final: 0.7472 (tp) REVERT: A 151 ARG cc_start: 0.6365 (ttm170) cc_final: 0.6135 (ttp-170) REVERT: A 217 ASN cc_start: 0.8741 (m-40) cc_final: 0.8445 (m110) REVERT: B 157 ASN cc_start: 0.8525 (t0) cc_final: 0.7966 (t0) REVERT: B 163 LYS cc_start: 0.7872 (mmmt) cc_final: 0.7541 (mmtp) REVERT: B 318 MET cc_start: 0.3308 (tmm) cc_final: 0.1600 (mmm) REVERT: C 112 MET cc_start: 0.8559 (mtp) cc_final: 0.8244 (mtp) REVERT: C 132 THR cc_start: 0.8345 (p) cc_final: 0.8139 (p) REVERT: C 191 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7316 (mm-30) REVERT: C 291 MET cc_start: 0.8486 (mmm) cc_final: 0.8222 (tpp) REVERT: C 313 MET cc_start: 0.4288 (tpp) cc_final: 0.4058 (tpp) REVERT: C 341 MET cc_start: 0.5135 (mmt) cc_final: 0.4838 (mmp) REVERT: D 10 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8041 (tttp) REVERT: D 190 ASP cc_start: 0.7524 (m-30) cc_final: 0.7055 (m-30) REVERT: D 220 GLU cc_start: 0.8024 (tt0) cc_final: 0.7668 (mt-10) REVERT: E 134 ASN cc_start: 0.6849 (p0) cc_final: 0.6491 (p0) REVERT: E 164 LYS cc_start: 0.7135 (mttt) cc_final: 0.6505 (mtpt) outliers start: 58 outliers final: 43 residues processed: 393 average time/residue: 0.1335 time to fit residues: 80.3786 Evaluate side-chains 400 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 352 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 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 195 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 318 MET 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 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 C residue 300 ILE Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 20 THR 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 192 ILE 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 184 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 73 optimal weight: 0.0870 chunk 166 optimal weight: 0.3980 chunk 125 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 53 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 ASN ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** 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 = 0.3977 r_free = 0.3977 target = 0.192120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.148925 restraints weight = 20536.502| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.66 r_work: 0.3182 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 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 = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18166 Z= 0.152 Angle : 0.569 9.567 24641 Z= 0.299 Chirality : 0.043 0.298 2788 Planarity : 0.004 0.045 3083 Dihedral : 4.483 22.247 2400 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.16 % Allowed : 16.81 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.18), residues: 2147 helix: 2.16 (0.16), residues: 958 sheet: 0.33 (0.24), residues: 454 loop : -1.68 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 155 TYR 0.017 0.001 TYR B 311 PHE 0.020 0.001 PHE E 53 TRP 0.018 0.001 TRP D 226 HIS 0.005 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00347 (18162) covalent geometry : angle 0.56841 (24633) SS BOND : bond 0.00430 ( 4) SS BOND : angle 0.87347 ( 8) hydrogen bonds : bond 0.05135 ( 1048) hydrogen bonds : angle 4.58754 ( 3072) *********************** 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 422 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 359 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: H 21 SER cc_start: 0.9007 (t) cc_final: 0.8796 (m) REVERT: H 37 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8525 (t) REVERT: L 25 ARG cc_start: 0.8122 (mtp-110) cc_final: 0.7739 (mtp-110) REVERT: L 28 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8099 (mm-40) REVERT: A 38 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6719 (mm-30) REVERT: A 87 LEU cc_start: 0.7707 (tp) cc_final: 0.7479 (tp) REVERT: A 217 ASN cc_start: 0.8661 (m-40) cc_final: 0.8349 (m110) REVERT: B 157 ASN cc_start: 0.8531 (t0) cc_final: 0.8144 (t0) REVERT: B 266 GLU cc_start: 0.7826 (tt0) cc_final: 0.7553 (tt0) REVERT: B 291 MET cc_start: 0.7315 (mtp) cc_final: 0.6961 (mtp) REVERT: B 313 MET cc_start: 0.5753 (OUTLIER) cc_final: 0.5414 (mmm) REVERT: B 318 MET cc_start: 0.3285 (tmm) cc_final: 0.1769 (mmm) REVERT: C 112 MET cc_start: 0.8536 (mtp) cc_final: 0.8200 (mtp) REVERT: C 191 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7346 (mm-30) REVERT: C 292 LYS cc_start: 0.7442 (mmtp) cc_final: 0.7051 (mmtp) REVERT: C 313 MET cc_start: 0.4303 (tpp) cc_final: 0.4077 (tpp) REVERT: C 341 MET cc_start: 0.5143 (mmt) cc_final: 0.4847 (mmp) REVERT: D 190 ASP cc_start: 0.7526 (m-30) cc_final: 0.7001 (m-30) REVERT: D 220 GLU cc_start: 0.8024 (tt0) cc_final: 0.7647 (mt-10) REVERT: E 53 PHE cc_start: 0.6022 (t80) cc_final: 0.5740 (t80) REVERT: E 74 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.6855 (tp-100) REVERT: E 134 ASN cc_start: 0.6840 (p0) cc_final: 0.6489 (p0) REVERT: E 164 LYS cc_start: 0.7143 (mttt) cc_final: 0.6502 (mtpt) REVERT: E 200 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7107 (mp) outliers start: 63 outliers final: 45 residues processed: 393 average time/residue: 0.1379 time to fit residues: 83.2688 Evaluate side-chains 398 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 346 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 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 66 SER Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 89 CYS 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 F residue 99 SER 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 195 LEU 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 192 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 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 C residue 300 ILE 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 208 VAL 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 184 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 219 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 177 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 chunk 196 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 7 GLN ** 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** E 120 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.190609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.146815 restraints weight = 20740.732| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.59 r_work: 0.3166 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 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 = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1649 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= 0.183 Angle : 0.589 10.040 24641 Z= 0.309 Chirality : 0.043 0.167 2788 Planarity : 0.005 0.048 3083 Dihedral : 4.534 22.222 2400 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.96 % Allowed : 16.66 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.18), residues: 2147 helix: 2.08 (0.16), residues: 958 sheet: 0.30 (0.25), residues: 438 loop : -1.73 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 155 TYR 0.018 0.002 TYR B 311 PHE 0.016 0.001 PHE C 27 TRP 0.036 0.001 TRP D 226 HIS 0.005 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00430 (18162) covalent geometry : angle 0.58862 (24633) SS BOND : bond 0.00428 ( 4) SS BOND : angle 1.07800 ( 8) hydrogen bonds : bond 0.05313 ( 1048) hydrogen bonds : angle 4.62139 ( 3072) *********************** 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 442 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 363 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 21 SER cc_start: 0.9008 (t) cc_final: 0.8792 (m) REVERT: H 37 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8517 (t) REVERT: H 76 LYS cc_start: 0.7936 (ptmm) cc_final: 0.7645 (ptpt) REVERT: L 28 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8157 (mm-40) REVERT: A 38 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6710 (mm-30) REVERT: A 87 LEU cc_start: 0.7745 (tp) cc_final: 0.7498 (tp) REVERT: A 109 VAL cc_start: 0.7728 (OUTLIER) cc_final: 0.7526 (m) REVERT: A 217 ASN cc_start: 0.8660 (m-40) cc_final: 0.8378 (m110) REVERT: A 301 PHE cc_start: 0.7182 (m-80) cc_final: 0.6871 (m-80) REVERT: B 157 ASN cc_start: 0.8480 (t0) cc_final: 0.8156 (t0) REVERT: B 201 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6746 (pp20) REVERT: B 266 GLU cc_start: 0.7864 (tt0) cc_final: 0.7486 (tt0) REVERT: B 313 MET cc_start: 0.5822 (OUTLIER) cc_final: 0.5333 (mmm) REVERT: B 318 MET cc_start: 0.3288 (tmm) cc_final: 0.1751 (mmm) REVERT: C 112 MET cc_start: 0.8558 (mtp) cc_final: 0.8248 (mtp) REVERT: C 191 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7372 (mm-30) REVERT: C 292 LYS cc_start: 0.7413 (mmtp) cc_final: 0.7056 (mmtp) REVERT: C 313 MET cc_start: 0.4438 (tpp) cc_final: 0.4149 (tpp) REVERT: C 341 MET cc_start: 0.5179 (mmt) cc_final: 0.4847 (mmp) REVERT: D 10 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8210 (tttp) REVERT: D 190 ASP cc_start: 0.7530 (m-30) cc_final: 0.7028 (m-30) REVERT: D 220 GLU cc_start: 0.7978 (tt0) cc_final: 0.7648 (mt-10) REVERT: D 226 TRP cc_start: 0.9053 (m-10) cc_final: 0.8815 (m-10) REVERT: D 236 TYR cc_start: 0.8110 (t80) cc_final: 0.7544 (t80) REVERT: E 53 PHE cc_start: 0.5991 (t80) cc_final: 0.5551 (t80) REVERT: E 74 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.6819 (tp-100) REVERT: E 164 LYS cc_start: 0.7163 (mttt) cc_final: 0.6503 (mtpt) REVERT: E 200 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7041 (mp) REVERT: E 280 LEU cc_start: 0.8407 (tp) cc_final: 0.8159 (tp) outliers start: 79 outliers final: 58 residues processed: 407 average time/residue: 0.1320 time to fit residues: 83.2712 Evaluate side-chains 425 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 357 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 H residue 120 THR 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 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 92 SER Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain A residue 38 GLU 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 195 LEU 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 A residue 318 MET Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 192 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 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 191 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 300 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 132 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 208 VAL 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 200 LEU 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 23 optimal weight: 0.0270 chunk 92 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 206 optimal weight: 0.7980 chunk 154 optimal weight: 0.3980 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 4 optimal weight: 0.0870 chunk 195 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** 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 = 0.3988 r_free = 0.3988 target = 0.193142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.150358 restraints weight = 20615.164| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.77 r_work: 0.3181 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 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 = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1744 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= 0.137 Angle : 0.564 9.357 24641 Z= 0.296 Chirality : 0.042 0.150 2788 Planarity : 0.004 0.046 3083 Dihedral : 4.422 22.082 2400 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.31 % Allowed : 17.76 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.18), residues: 2147 helix: 2.24 (0.16), residues: 958 sheet: 0.38 (0.24), residues: 452 loop : -1.64 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 155 TYR 0.018 0.001 TYR B 311 PHE 0.016 0.001 PHE C 27 TRP 0.024 0.001 TRP D 226 HIS 0.005 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00305 (18162) covalent geometry : angle 0.56411 (24633) SS BOND : bond 0.00566 ( 4) SS BOND : angle 1.09855 ( 8) hydrogen bonds : bond 0.04934 ( 1048) hydrogen bonds : angle 4.49733 ( 3072) *********************** 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 424 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 358 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 21 SER cc_start: 0.9005 (t) cc_final: 0.8788 (m) REVERT: H 37 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8539 (t) REVERT: H 76 LYS cc_start: 0.7919 (ptmm) cc_final: 0.7613 (ptpt) REVERT: L 25 ARG cc_start: 0.8141 (mtp-110) cc_final: 0.7795 (mtp-110) REVERT: L 28 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8150 (mm-40) REVERT: F 39 GLN cc_start: 0.6148 (tt0) cc_final: 0.5742 (tt0) REVERT: F 82 GLN cc_start: 0.6370 (tm-30) cc_final: 0.6059 (tm-30) REVERT: F 113 MET cc_start: 0.8647 (mtt) cc_final: 0.8151 (mtt) REVERT: A 38 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6851 (mm-30) REVERT: A 87 LEU cc_start: 0.7692 (tp) cc_final: 0.7442 (tp) REVERT: A 109 VAL cc_start: 0.7754 (OUTLIER) cc_final: 0.7553 (m) REVERT: A 217 ASN cc_start: 0.8631 (m-40) cc_final: 0.8347 (m110) REVERT: A 222 ARG cc_start: 0.7031 (ttm-80) cc_final: 0.6272 (tpp80) REVERT: A 301 PHE cc_start: 0.7160 (m-80) cc_final: 0.6821 (m-80) REVERT: B 157 ASN cc_start: 0.8399 (t0) cc_final: 0.8056 (t0) REVERT: B 163 LYS cc_start: 0.7768 (mmmt) cc_final: 0.7450 (mmtm) REVERT: B 201 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6665 (pp20) REVERT: B 266 GLU cc_start: 0.7817 (tt0) cc_final: 0.7323 (tt0) REVERT: B 313 MET cc_start: 0.5640 (OUTLIER) cc_final: 0.5385 (mmm) REVERT: B 318 MET cc_start: 0.2798 (tmm) cc_final: 0.1461 (mmm) REVERT: C 112 MET cc_start: 0.8529 (mtp) cc_final: 0.8238 (mtp) REVERT: C 191 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7308 (mm-30) REVERT: C 313 MET cc_start: 0.4396 (tpp) cc_final: 0.4125 (tpp) REVERT: C 341 MET cc_start: 0.5101 (mmt) cc_final: 0.4787 (mmp) REVERT: D 10 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8082 (tttp) REVERT: D 190 ASP cc_start: 0.7568 (m-30) cc_final: 0.7059 (m-30) REVERT: D 220 GLU cc_start: 0.8078 (tt0) cc_final: 0.7725 (mt-10) REVERT: D 226 TRP cc_start: 0.9024 (m-10) cc_final: 0.8631 (m-10) REVERT: D 236 TYR cc_start: 0.8133 (t80) cc_final: 0.7592 (t80) REVERT: E 74 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6823 (tp-100) REVERT: E 164 LYS cc_start: 0.7143 (mttt) cc_final: 0.6506 (mtpt) REVERT: E 200 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7019 (mp) REVERT: E 280 LEU cc_start: 0.8356 (tp) cc_final: 0.8130 (tp) outliers start: 66 outliers final: 48 residues processed: 395 average time/residue: 0.1417 time to fit residues: 85.1949 Evaluate side-chains 404 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 346 time to evaluate : 0.715 ------------------------------------------------------------------------------- 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 66 SER 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 F residue 99 SER Chi-restraints excluded: chain A residue 38 GLU 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 195 LEU 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 45 THR 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 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 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 191 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 22 LYS Chi-restraints excluded: chain D residue 50 VAL 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 233 SER Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 200 LEU 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 163 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 chunk 164 optimal weight: 0.2980 chunk 58 optimal weight: 6.9990 chunk 27 optimal weight: 0.0270 chunk 39 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 133 optimal weight: 0.0570 chunk 67 optimal weight: 0.9990 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 7 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 HIS ** 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 = 0.4022 r_free = 0.4022 target = 0.196708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.154679 restraints weight = 20632.364| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.92 r_work: 0.3197 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 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 = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1884 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= 0.126 Angle : 0.561 9.507 24641 Z= 0.293 Chirality : 0.042 0.151 2788 Planarity : 0.004 0.046 3083 Dihedral : 4.323 21.543 2400 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.11 % Allowed : 18.36 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.19), residues: 2147 helix: 2.36 (0.16), residues: 958 sheet: 0.39 (0.24), residues: 469 loop : -1.61 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 269 TYR 0.016 0.001 TYR B 311 PHE 0.013 0.001 PHE E 107 TRP 0.025 0.001 TRP D 226 HIS 0.005 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00273 (18162) covalent geometry : angle 0.56068 (24633) SS BOND : bond 0.00557 ( 4) SS BOND : angle 1.44146 ( 8) hydrogen bonds : bond 0.04642 ( 1048) hydrogen bonds : angle 4.38508 ( 3072) *********************** 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 427 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 365 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 21 SER cc_start: 0.9004 (t) cc_final: 0.8775 (m) REVERT: H 37 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8563 (t) REVERT: H 76 LYS cc_start: 0.7897 (ptmm) cc_final: 0.7593 (ptpt) REVERT: L 28 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8044 (mm-40) REVERT: F 39 GLN cc_start: 0.6077 (tt0) cc_final: 0.5593 (tt0) REVERT: F 82 GLN cc_start: 0.6390 (tm-30) cc_final: 0.6086 (tm-30) REVERT: A 38 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6883 (mm-30) REVERT: A 87 LEU cc_start: 0.7572 (tp) cc_final: 0.7332 (tp) REVERT: A 100 GLU cc_start: 0.5765 (tt0) cc_final: 0.5169 (tp30) REVERT: A 222 ARG cc_start: 0.6859 (ttm-80) cc_final: 0.6552 (ttm-80) REVERT: A 277 ASP cc_start: 0.7688 (m-30) cc_final: 0.7460 (m-30) REVERT: B 157 ASN cc_start: 0.8344 (t0) cc_final: 0.8025 (t0) REVERT: B 163 LYS cc_start: 0.7732 (mmmt) cc_final: 0.7421 (mmtm) REVERT: B 201 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6482 (pp20) REVERT: B 266 GLU cc_start: 0.7797 (tt0) cc_final: 0.7151 (tt0) REVERT: B 313 MET cc_start: 0.5655 (OUTLIER) cc_final: 0.5404 (mmm) REVERT: B 318 MET cc_start: 0.2763 (tmm) cc_final: 0.1444 (mmm) REVERT: C 112 MET cc_start: 0.8478 (mtp) cc_final: 0.8238 (mtp) REVERT: C 191 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7319 (mm-30) REVERT: C 313 MET cc_start: 0.4429 (tpp) cc_final: 0.4163 (tpp) REVERT: C 341 MET cc_start: 0.5103 (mmt) cc_final: 0.4768 (mmp) REVERT: D 10 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7804 (tttp) REVERT: D 190 ASP cc_start: 0.7511 (m-30) cc_final: 0.7008 (m-30) REVERT: D 220 GLU cc_start: 0.8075 (tt0) cc_final: 0.7769 (mt-10) REVERT: D 226 TRP cc_start: 0.9036 (m-10) cc_final: 0.8683 (m-10) REVERT: D 236 TYR cc_start: 0.8138 (t80) cc_final: 0.7603 (t80) REVERT: E 74 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.6769 (tp-100) REVERT: E 164 LYS cc_start: 0.7091 (mttt) cc_final: 0.6269 (mtpt) REVERT: E 200 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6964 (mp) REVERT: E 280 LEU cc_start: 0.8335 (tp) cc_final: 0.8129 (tp) outliers start: 62 outliers final: 48 residues processed: 399 average time/residue: 0.1353 time to fit residues: 83.0031 Evaluate side-chains 407 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 350 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 H residue 120 THR 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 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 92 SER Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 99 SER 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 231 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain B residue 45 THR 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 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 142 LYS 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 60 THR Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 200 LEU 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 107 optimal weight: 0.2980 chunk 195 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 135 optimal weight: 0.9980 chunk 11 optimal weight: 0.0670 chunk 140 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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** ** E 120 HIS ** 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 = 0.4003 r_free = 0.4003 target = 0.194753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.152436 restraints weight = 20528.571| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.77 r_work: 0.3192 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 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 = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1918 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= 0.144 Angle : 0.570 9.479 24641 Z= 0.298 Chirality : 0.042 0.151 2788 Planarity : 0.004 0.047 3083 Dihedral : 4.356 21.728 2400 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.11 % Allowed : 18.46 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.18), residues: 2147 helix: 2.31 (0.16), residues: 958 sheet: 0.40 (0.24), residues: 469 loop : -1.63 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 202 TYR 0.018 0.001 TYR A 279 PHE 0.026 0.001 PHE A 113 TRP 0.025 0.001 TRP D 226 HIS 0.004 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00329 (18162) covalent geometry : angle 0.57000 (24633) SS BOND : bond 0.00394 ( 4) SS BOND : angle 1.43156 ( 8) hydrogen bonds : bond 0.04737 ( 1048) hydrogen bonds : angle 4.39166 ( 3072) ********************** 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: 62 poor density : 350 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 21 SER cc_start: 0.9007 (t) cc_final: 0.8789 (m) REVERT: H 37 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8568 (t) REVERT: H 76 LYS cc_start: 0.7910 (ptmm) cc_final: 0.7613 (ptpt) REVERT: L 28 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8069 (mm-40) REVERT: F 39 GLN cc_start: 0.6112 (tt0) cc_final: 0.5632 (tt0) REVERT: F 82 GLN cc_start: 0.6417 (tm-30) cc_final: 0.6108 (tm-30) REVERT: A 38 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6864 (mm-30) REVERT: A 87 LEU cc_start: 0.7568 (tp) cc_final: 0.7324 (tp) REVERT: A 155 ARG cc_start: 0.5736 (ttm110) cc_final: 0.5314 (ttm110) REVERT: A 222 ARG cc_start: 0.6946 (ttm-80) cc_final: 0.6205 (tpp80) REVERT: A 277 ASP cc_start: 0.7720 (m-30) cc_final: 0.7490 (m-30) REVERT: A 301 PHE cc_start: 0.7163 (m-80) cc_final: 0.6833 (m-80) REVERT: B 157 ASN cc_start: 0.8327 (t0) cc_final: 0.8059 (t0) REVERT: B 201 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6499 (pp20) REVERT: B 266 GLU cc_start: 0.7783 (tt0) cc_final: 0.7137 (tt0) REVERT: B 313 MET cc_start: 0.5647 (OUTLIER) cc_final: 0.5396 (mmm) REVERT: B 318 MET cc_start: 0.2727 (tmm) cc_final: 0.1418 (mmm) REVERT: C 112 MET cc_start: 0.8503 (mtp) cc_final: 0.8267 (mtp) REVERT: C 191 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7378 (mm-30) REVERT: C 313 MET cc_start: 0.4311 (tpp) cc_final: 0.4038 (tpp) REVERT: C 341 MET cc_start: 0.5120 (mmt) cc_final: 0.4804 (mmp) REVERT: D 10 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8010 (tttp) REVERT: D 190 ASP cc_start: 0.7514 (m-30) cc_final: 0.7010 (m-30) REVERT: D 202 ARG cc_start: 0.7426 (mtm-85) cc_final: 0.7207 (mpp-170) REVERT: D 220 GLU cc_start: 0.8076 (tt0) cc_final: 0.7773 (mt-10) REVERT: D 226 TRP cc_start: 0.9068 (m-10) cc_final: 0.8666 (m-10) REVERT: D 236 TYR cc_start: 0.8171 (t80) cc_final: 0.7633 (t80) REVERT: E 74 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6763 (tp-100) REVERT: E 164 LYS cc_start: 0.7194 (mttt) cc_final: 0.6319 (mtpt) REVERT: E 200 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6942 (mp) REVERT: E 280 LEU cc_start: 0.8350 (tp) cc_final: 0.8137 (tp) outliers start: 62 outliers final: 51 residues processed: 386 average time/residue: 0.1389 time to fit residues: 82.3070 Evaluate side-chains 405 residues out of total 1993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 345 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 H residue 120 THR 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 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 92 SER Chi-restraints excluded: chain F residue 27 PHE Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 99 SER 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 231 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 175 ASP 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 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 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 22 LYS 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 208 VAL Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 200 LEU 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 7 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 0.0970 chunk 179 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.191464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.148686 restraints weight = 20727.426| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.81 r_work: 0.3171 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 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 = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1887 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= 0.179 Angle : 0.595 9.793 24641 Z= 0.310 Chirality : 0.043 0.181 2788 Planarity : 0.005 0.046 3083 Dihedral : 4.440 21.775 2400 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.36 % Allowed : 18.67 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.18), residues: 2147 helix: 2.20 (0.16), residues: 958 sheet: 0.35 (0.24), residues: 458 loop : -1.69 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 202 TYR 0.018 0.002 TYR B 311 PHE 0.025 0.001 PHE A 113 TRP 0.026 0.001 TRP D 226 HIS 0.004 0.001 HIS D 257 Details of bonding type rmsd covalent geometry : bond 0.00423 (18162) covalent geometry : angle 0.59411 (24633) SS BOND : bond 0.00406 ( 4) SS BOND : angle 1.62927 ( 8) hydrogen bonds : bond 0.05006 ( 1048) hydrogen bonds : angle 4.47473 ( 3072) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4618.67 seconds wall clock time: 79 minutes 59.26 seconds (4799.26 seconds total)