Starting phenix.real_space_refine on Mon Jun 16 19:08:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmm_41394/06_2025/8tmm_41394.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmm_41394/06_2025/8tmm_41394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tmm_41394/06_2025/8tmm_41394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmm_41394/06_2025/8tmm_41394.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmm_41394/06_2025/8tmm_41394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmm_41394/06_2025/8tmm_41394.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1577 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 4 5.21 5 S 67 5.16 5 C 11579 2.51 5 N 2915 2.21 5 O 3313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17878 Number of models: 1 Model: "" Number of chains: 13 Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "G" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 794 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "A" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2804 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "B" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2925 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "C" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2805 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "D" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2925 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "E" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2925 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.08, per 1000 atoms: 0.62 Number of scatterers: 17878 At special positions: 0 Unit cell: (122.245, 133.938, 161.576, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 Mg 4 11.99 O 3313 8.00 N 2915 7.00 C 11579 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 24 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.52 Conformation dependent library (CDL) restraints added in 2.2 seconds 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4160 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 17 sheets defined 48.1% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'G' and resid 80 through 84 removed outlier: 4.028A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.501A pdb=" N ASP F 90 " --> pdb=" O ARG F 87 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 87 through 91' Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.579A pdb=" N VAL A 50 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Proline residue: A 52 - end of helix removed outlier: 3.759A pdb=" N ASP A 55 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 80 removed outlier: 3.705A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 165 through 202 removed outlier: 3.571A pdb=" N LEU A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 238 removed outlier: 3.764A pdb=" N VAL A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 3.660A pdb=" N GLU A 230 " --> pdb=" O TRP A 226 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 247 through 283 removed outlier: 3.503A pdb=" N PHE A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 313 Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 325 through 345 removed outlier: 3.639A pdb=" N PHE A 345 " --> pdb=" O MET A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 removed outlier: 3.529A pdb=" N SER B 56 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 81 removed outlier: 3.714A pdb=" N VAL B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 165 through 202 removed outlier: 3.713A pdb=" N LEU B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 239 removed outlier: 3.519A pdb=" N VAL B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Proline residue: B 227 - end of helix removed outlier: 3.827A pdb=" N VAL B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 299 removed outlier: 3.867A pdb=" N PHE B 251 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 293 " --> pdb=" O GLU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 311 removed outlier: 3.959A pdb=" N PHE B 306 " --> pdb=" O MET B 302 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 323 removed outlier: 3.890A pdb=" N LEU B 321 " --> pdb=" O MET B 318 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TRP B 323 " --> pdb=" O GLU B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 347 removed outlier: 3.611A pdb=" N LYS B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 50 through 56 removed outlier: 3.555A pdb=" N ARG C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 56 " --> pdb=" O PRO C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 50 through 56' Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.560A pdb=" N VAL C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 92 Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.891A pdb=" N ARG C 151 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 202 removed outlier: 3.859A pdb=" N LEU C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 238 Proline residue: C 227 - end of helix removed outlier: 3.868A pdb=" N GLU C 230 " --> pdb=" O TRP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 282 removed outlier: 3.667A pdb=" N PHE C 251 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 252 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL C 278 " --> pdb=" O GLY C 274 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N TYR C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 311 removed outlier: 4.115A pdb=" N ILE C 297 " --> pdb=" O VAL C 293 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) Proline residue: C 303 - end of helix Processing helix chain 'C' and resid 318 through 323 removed outlier: 4.197A pdb=" N ARG C 322 " --> pdb=" O MET C 318 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP C 323 " --> pdb=" O PRO C 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 318 through 323' Processing helix chain 'C' and resid 325 through 345 removed outlier: 3.823A pdb=" N PHE C 345 " --> pdb=" O MET C 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 56 removed outlier: 3.897A pdb=" N ASP D 55 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER D 56 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 80 removed outlier: 3.834A pdb=" N VAL D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 160 through 164 removed outlier: 3.844A pdb=" N LYS D 164 " --> pdb=" O ILE D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 202 Processing helix chain 'D' and resid 205 through 238 removed outlier: 3.901A pdb=" N GLN D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.855A pdb=" N GLU D 230 " --> pdb=" O TRP D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 312 removed outlier: 3.624A pdb=" N LEU D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE D 300 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 325 through 349 removed outlier: 4.133A pdb=" N VAL D 329 " --> pdb=" O TRP D 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 55 removed outlier: 3.619A pdb=" N PHE E 53 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG E 54 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 80 removed outlier: 3.735A pdb=" N VAL E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 165 through 202 removed outlier: 3.656A pdb=" N LEU E 169 " --> pdb=" O ARG E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 238 removed outlier: 3.510A pdb=" N VAL E 208 " --> pdb=" O GLU E 204 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TRP E 226 " --> pdb=" O ARG E 222 " (cutoff:3.500A) Proline residue: E 227 - end of helix Processing helix chain 'E' and resid 247 through 311 removed outlier: 3.727A pdb=" N ASP E 253 " --> pdb=" O PRO E 249 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL E 254 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) Proline residue: E 303 - end of helix removed outlier: 4.070A pdb=" N TYR E 311 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 349 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'H' and resid 45 through 51 removed outlier: 6.585A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TYR H 100 " --> pdb=" O MET H 113 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N MET H 113 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR H 102 " --> pdb=" O ASN H 111 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASN H 111 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 45 through 51 removed outlier: 6.585A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 6 through 8 removed outlier: 3.624A pdb=" N THR L 75 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER L 64 " --> pdb=" O THR L 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.573A pdb=" N THR L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.693A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 5 through 8 Processing sheet with id=AA8, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.702A pdb=" N LEU G 12 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.702A pdb=" N LEU G 12 " --> pdb=" O GLU G 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.756A pdb=" N GLY F 10 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER F 33 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.756A pdb=" N GLY F 10 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N CYS F 96 " --> pdb=" O TRP F 116 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TRP F 116 " --> pdb=" O CYS F 96 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG F 98 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 39 through 44 removed outlier: 3.937A pdb=" N GLU A 121 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 98 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 40 through 44 removed outlier: 4.636A pdb=" N GLU B 121 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP B 116 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 40 through 44 removed outlier: 3.690A pdb=" N ASN C 33 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C 31 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR C 44 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE C 29 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR C 60 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N MET C 138 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE C 62 " --> pdb=" O MET C 138 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLN C 140 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C 64 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 39 through 42 removed outlier: 6.779A pdb=" N THR D 60 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N MET D 138 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE D 62 " --> pdb=" O MET D 138 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLN D 140 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE D 64 " --> pdb=" O GLN D 140 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU D 123 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR D 114 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 40 through 44 removed outlier: 4.732A pdb=" N GLU E 121 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP E 116 " --> pdb=" O GLU E 121 " (cutoff:3.500A) 1069 hydrogen bonds defined for protein. 3027 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.30 Time building geometry restraints manager: 5.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5642 1.34 - 1.46: 4399 1.46 - 1.58: 8120 1.58 - 1.70: 0 1.70 - 1.82: 121 Bond restraints: 18282 Sorted by residual: bond pdb=" CG1 ILE C 192 " pdb=" CD1 ILE C 192 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.78e+00 bond pdb=" CB PHE D 306 " pdb=" CG PHE D 306 " ideal model delta sigma weight residual 1.502 1.468 0.034 2.30e-02 1.89e+03 2.22e+00 bond pdb=" CB GLN G 90 " pdb=" CG GLN G 90 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.74e+00 bond pdb=" CD GLU A 266 " pdb=" OE1 GLU A 266 " ideal model delta sigma weight residual 1.249 1.226 0.023 1.90e-02 2.77e+03 1.41e+00 bond pdb=" CG LYS D 292 " pdb=" CD LYS D 292 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.24e+00 ... (remaining 18277 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 24405 2.09 - 4.18: 331 4.18 - 6.26: 44 6.26 - 8.35: 7 8.35 - 10.44: 4 Bond angle restraints: 24791 Sorted by residual: angle pdb=" C LEU B 235 " pdb=" N TYR B 236 " pdb=" CA TYR B 236 " ideal model delta sigma weight residual 122.06 114.31 7.75 1.86e+00 2.89e-01 1.74e+01 angle pdb=" CA MET C 291 " pdb=" CB MET C 291 " pdb=" CG MET C 291 " ideal model delta sigma weight residual 114.10 120.61 -6.51 2.00e+00 2.50e-01 1.06e+01 angle pdb=" C PRO E 303 " pdb=" N LEU E 304 " pdb=" CA LEU E 304 " ideal model delta sigma weight residual 122.06 116.06 6.00 1.86e+00 2.89e-01 1.04e+01 angle pdb=" CB MET D 291 " pdb=" CG MET D 291 " pdb=" SD MET D 291 " ideal model delta sigma weight residual 112.70 103.64 9.06 3.00e+00 1.11e-01 9.13e+00 angle pdb=" CA LEU E 304 " pdb=" CB LEU E 304 " pdb=" CG LEU E 304 " ideal model delta sigma weight residual 116.30 126.74 -10.44 3.50e+00 8.16e-02 8.90e+00 ... (remaining 24786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 9687 18.00 - 36.00: 1053 36.00 - 54.00: 178 54.00 - 71.99: 27 71.99 - 89.99: 19 Dihedral angle restraints: 10964 sinusoidal: 4513 harmonic: 6451 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 174.84 -81.84 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS G 24 " pdb=" SG CYS G 24 " pdb=" SG CYS G 89 " pdb=" CB CYS G 89 " ideal model delta sinusoidal sigma weight residual 93.00 155.05 -62.05 1 1.00e+01 1.00e-02 5.10e+01 dihedral pdb=" CA TRP A 323 " pdb=" C TRP A 323 " pdb=" N LYS A 324 " pdb=" CA LYS A 324 " ideal model delta harmonic sigma weight residual 180.00 155.27 24.73 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 10961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1983 0.040 - 0.080: 589 0.080 - 0.120: 204 0.120 - 0.160: 26 0.160 - 0.200: 3 Chirality restraints: 2805 Sorted by residual: chirality pdb=" CA TYR C 327 " pdb=" N TYR C 327 " pdb=" C TYR C 327 " pdb=" CB TYR C 327 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ASP C 148 " pdb=" N ASP C 148 " pdb=" C ASP C 148 " pdb=" CB ASP C 148 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CG LEU C 184 " pdb=" CB LEU C 184 " pdb=" CD1 LEU C 184 " pdb=" CD2 LEU C 184 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 2802 not shown) Planarity restraints: 3103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 350 " -0.025 2.00e-02 2.50e+03 2.78e-02 1.93e+01 pdb=" CG TRP D 350 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP D 350 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP D 350 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 350 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP D 350 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 350 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 350 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 350 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 350 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 83 " 0.065 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO C 84 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 84 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 84 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 12 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO E 13 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 13 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 13 " 0.029 5.00e-02 4.00e+02 ... (remaining 3100 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 161 2.63 - 3.20: 16423 3.20 - 3.77: 27883 3.77 - 4.33: 37495 4.33 - 4.90: 62145 Nonbonded interactions: 144107 Sorted by model distance: nonbonded pdb=" OD1 ASN D 288 " pdb=" NZ LYS D 292 " model vdw 2.065 3.120 nonbonded pdb=" O LYS E 111 " pdb=" OH TYR E 181 " model vdw 2.097 3.040 nonbonded pdb=" OG SER L 66 " pdb=" OG1 THR L 73 " model vdw 2.112 3.040 nonbonded pdb=" OG1 THR A 287 " pdb=" OD1 ASN E 288 " model vdw 2.132 3.040 nonbonded pdb=" OG SER F 55 " pdb=" O PRO B 14 " model vdw 2.176 3.040 ... (remaining 144102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 350) selection = (chain 'B' and resid 17 through 350) selection = (chain 'C' and resid 17 through 350) selection = (chain 'D' and resid 17 through 350) selection = (chain 'E' and resid 17 through 350) } ncs_group { reference = (chain 'F' and resid 1 through 122) selection = chain 'H' } ncs_group { reference = chain 'G' selection = (chain 'L' and resid 2 through 107) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 40.710 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18286 Z= 0.148 Angle : 0.612 10.439 24799 Z= 0.324 Chirality : 0.043 0.200 2805 Planarity : 0.005 0.098 3103 Dihedral : 14.964 89.993 6792 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2163 helix: 1.60 (0.17), residues: 953 sheet: 0.68 (0.25), residues: 448 loop : -1.33 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP D 350 HIS 0.003 0.001 HIS C 212 PHE 0.014 0.001 PHE B 315 TYR 0.018 0.001 TYR C 171 ARG 0.006 0.000 ARG B 229 Details of bonding type rmsd hydrogen bonds : bond 0.12914 ( 1048) hydrogen bonds : angle 6.01205 ( 3027) SS BOND : bond 0.00192 ( 4) SS BOND : angle 1.43045 ( 8) covalent geometry : bond 0.00326 (18282) covalent geometry : angle 0.61161 (24791) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 1.868 Fit side-chains REVERT: F 13 GLN cc_start: 0.7589 (mm110) cc_final: 0.7328 (mm-40) REVERT: F 43 LYS cc_start: 0.8065 (mttm) cc_final: 0.7808 (ttmm) REVERT: F 89 GLU cc_start: 0.6568 (tm-30) cc_final: 0.5741 (tm-30) REVERT: F 100 TYR cc_start: 0.9100 (p90) cc_final: 0.8685 (p90) REVERT: F 114 ASP cc_start: 0.7534 (m-30) cc_final: 0.7118 (m-30) REVERT: A 71 ASP cc_start: 0.7785 (p0) cc_final: 0.7473 (p0) REVERT: A 111 LYS cc_start: 0.7470 (mtpt) cc_final: 0.7225 (mtmt) REVERT: A 124 SER cc_start: 0.9076 (p) cc_final: 0.8782 (p) REVERT: B 341 MET cc_start: 0.7729 (mpp) cc_final: 0.7430 (mpp) REVERT: C 115 TYR cc_start: 0.7066 (t80) cc_final: 0.6642 (t80) REVERT: C 256 ASP cc_start: 0.7232 (m-30) cc_final: 0.6661 (m-30) REVERT: C 341 MET cc_start: 0.4571 (mmt) cc_final: 0.4164 (mmt) REVERT: D 74 GLN cc_start: 0.7558 (tt0) cc_final: 0.7337 (tt0) REVERT: D 157 ASN cc_start: 0.7851 (t0) cc_final: 0.7477 (t0) REVERT: E 190 ASP cc_start: 0.7146 (m-30) cc_final: 0.6788 (m-30) REVERT: E 193 ASP cc_start: 0.6544 (m-30) cc_final: 0.6147 (m-30) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.2681 time to fit residues: 175.2672 Evaluate side-chains 389 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 0.0060 chunk 162 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 125 optimal weight: 0.0020 chunk 195 optimal weight: 0.6980 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 77 ASN A 120 HIS A 157 ASN C 140 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN D 104 ASN E 95 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.204844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.162525 restraints weight = 22034.664| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.87 r_work: 0.3307 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18286 Z= 0.155 Angle : 0.590 8.969 24799 Z= 0.315 Chirality : 0.043 0.186 2805 Planarity : 0.004 0.061 3103 Dihedral : 4.534 23.076 2417 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.35 % Allowed : 9.72 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.18), residues: 2163 helix: 1.93 (0.16), residues: 959 sheet: 0.77 (0.24), residues: 457 loop : -1.29 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 350 HIS 0.006 0.001 HIS C 257 PHE 0.022 0.001 PHE B 39 TYR 0.024 0.001 TYR F 103 ARG 0.005 0.000 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.05614 ( 1048) hydrogen bonds : angle 4.83217 ( 3027) SS BOND : bond 0.00320 ( 4) SS BOND : angle 1.54261 ( 8) covalent geometry : bond 0.00342 (18282) covalent geometry : angle 0.58961 (24791) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 405 time to evaluate : 2.000 Fit side-chains revert: symmetry clash REVERT: F 43 LYS cc_start: 0.8381 (mttm) cc_final: 0.8101 (ttmm) REVERT: F 89 GLU cc_start: 0.6892 (tm-30) cc_final: 0.5982 (tm-30) REVERT: A 54 ARG cc_start: 0.6397 (tmm160) cc_final: 0.5876 (tmm-80) REVERT: A 71 ASP cc_start: 0.7896 (p0) cc_final: 0.7648 (p0) REVERT: A 124 SER cc_start: 0.9306 (p) cc_final: 0.9067 (p) REVERT: B 186 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7813 (tp30) REVERT: C 139 PHE cc_start: 0.6260 (m-10) cc_final: 0.5563 (m-80) REVERT: C 198 GLU cc_start: 0.6936 (tp30) cc_final: 0.6588 (tp30) REVERT: C 244 GLU cc_start: 0.7592 (tp30) cc_final: 0.7331 (tp30) REVERT: C 334 MET cc_start: 0.5879 (ppp) cc_final: 0.3931 (mtt) REVERT: D 74 GLN cc_start: 0.7779 (tt0) cc_final: 0.7491 (tt0) REVERT: D 155 ARG cc_start: 0.5825 (mtt180) cc_final: 0.5553 (mtt-85) REVERT: D 157 ASN cc_start: 0.7711 (t0) cc_final: 0.7249 (t0) REVERT: D 198 GLU cc_start: 0.6597 (tp30) cc_final: 0.6332 (tp30) REVERT: D 288 ASN cc_start: 0.8419 (t0) cc_final: 0.8218 (t0) REVERT: E 46 ASP cc_start: 0.8036 (t0) cc_final: 0.7560 (t0) REVERT: E 90 ILE cc_start: 0.7828 (mt) cc_final: 0.7603 (mt) REVERT: E 190 ASP cc_start: 0.7633 (m-30) cc_final: 0.7244 (m-30) REVERT: E 193 ASP cc_start: 0.6949 (m-30) cc_final: 0.6541 (m-30) outliers start: 27 outliers final: 19 residues processed: 413 average time/residue: 0.2805 time to fit residues: 177.5152 Evaluate side-chains 408 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 389 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 97 optimal weight: 0.0980 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 120 optimal weight: 0.0000 chunk 140 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN C 126 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.203562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.160963 restraints weight = 21902.692| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.94 r_work: 0.3287 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18286 Z= 0.151 Angle : 0.567 8.265 24799 Z= 0.301 Chirality : 0.043 0.199 2805 Planarity : 0.004 0.049 3103 Dihedral : 4.503 23.409 2417 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.29 % Allowed : 13.46 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.18), residues: 2163 helix: 2.00 (0.16), residues: 960 sheet: 0.75 (0.24), residues: 467 loop : -1.35 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 36 HIS 0.006 0.001 HIS C 257 PHE 0.021 0.001 PHE B 39 TYR 0.022 0.001 TYR F 103 ARG 0.005 0.000 ARG E 96 Details of bonding type rmsd hydrogen bonds : bond 0.05299 ( 1048) hydrogen bonds : angle 4.65565 ( 3027) SS BOND : bond 0.00217 ( 4) SS BOND : angle 1.72361 ( 8) covalent geometry : bond 0.00338 (18282) covalent geometry : angle 0.56656 (24791) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 409 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.8371 (mttm) cc_final: 0.8099 (ttmm) REVERT: A 53 PHE cc_start: 0.7912 (m-80) cc_final: 0.7554 (m-80) REVERT: A 54 ARG cc_start: 0.6413 (tmm160) cc_final: 0.5874 (tmm-80) REVERT: A 71 ASP cc_start: 0.7861 (p0) cc_final: 0.7646 (p0) REVERT: A 152 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6483 (mt-10) REVERT: A 195 LEU cc_start: 0.8337 (tp) cc_final: 0.8113 (tp) REVERT: B 186 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7810 (tp30) REVERT: B 306 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.5829 (p90) REVERT: B 341 MET cc_start: 0.7641 (mpp) cc_final: 0.6974 (mpp) REVERT: C 28 GLU cc_start: 0.7719 (tp30) cc_final: 0.6850 (tm-30) REVERT: C 198 GLU cc_start: 0.6976 (tp30) cc_final: 0.6628 (tp30) REVERT: C 244 GLU cc_start: 0.7718 (tp30) cc_final: 0.7362 (tp30) REVERT: C 256 ASP cc_start: 0.6943 (m-30) cc_final: 0.6074 (m-30) REVERT: C 313 MET cc_start: 0.3636 (ttp) cc_final: 0.2796 (ttp) REVERT: D 74 GLN cc_start: 0.7711 (tt0) cc_final: 0.7372 (tt0) REVERT: D 157 ASN cc_start: 0.7590 (t0) cc_final: 0.7074 (t0) REVERT: D 198 GLU cc_start: 0.6629 (tp30) cc_final: 0.6372 (tp30) REVERT: D 288 ASN cc_start: 0.8401 (t0) cc_final: 0.8195 (t0) REVERT: E 24 ARG cc_start: 0.7920 (mtt-85) cc_final: 0.7340 (mtt180) REVERT: E 46 ASP cc_start: 0.8049 (t0) cc_final: 0.7589 (t0) REVERT: E 90 ILE cc_start: 0.7798 (mt) cc_final: 0.7557 (mt) REVERT: E 165 ARG cc_start: 0.7501 (mmp80) cc_final: 0.6979 (mtm180) REVERT: E 190 ASP cc_start: 0.7654 (m-30) cc_final: 0.7294 (m-30) REVERT: E 193 ASP cc_start: 0.6918 (m-30) cc_final: 0.6519 (m-30) REVERT: E 291 MET cc_start: 0.7243 (mmt) cc_final: 0.6946 (mmt) outliers start: 46 outliers final: 27 residues processed: 430 average time/residue: 0.3297 time to fit residues: 218.2699 Evaluate side-chains 425 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 396 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 139 optimal weight: 0.0980 chunk 175 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 210 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.203020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.160767 restraints weight = 21960.420| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 4.09 r_work: 0.3241 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18286 Z= 0.165 Angle : 0.575 7.816 24799 Z= 0.304 Chirality : 0.043 0.200 2805 Planarity : 0.004 0.048 3103 Dihedral : 4.500 23.503 2417 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.54 % Allowed : 14.86 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.18), residues: 2163 helix: 2.03 (0.16), residues: 957 sheet: 0.72 (0.24), residues: 466 loop : -1.33 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 36 HIS 0.006 0.001 HIS C 212 PHE 0.020 0.001 PHE B 39 TYR 0.028 0.001 TYR F 100 ARG 0.004 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.05246 ( 1048) hydrogen bonds : angle 4.63158 ( 3027) SS BOND : bond 0.00155 ( 4) SS BOND : angle 1.82223 ( 8) covalent geometry : bond 0.00377 (18282) covalent geometry : angle 0.57420 (24791) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 416 time to evaluate : 2.557 Fit side-chains revert: symmetry clash REVERT: L 90 GLN cc_start: 0.8070 (tt0) cc_final: 0.7842 (tt0) REVERT: F 43 LYS cc_start: 0.8384 (mttm) cc_final: 0.8108 (ttmm) REVERT: A 54 ARG cc_start: 0.6453 (tmm160) cc_final: 0.5912 (tmm-80) REVERT: A 87 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7972 (mm) REVERT: A 152 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6486 (mt-10) REVERT: B 186 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7781 (tp30) REVERT: B 306 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.5772 (p90) REVERT: B 341 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.6840 (mpp) REVERT: C 98 LYS cc_start: 0.5639 (tmmt) cc_final: 0.5349 (tmmt) REVERT: C 198 GLU cc_start: 0.6947 (tp30) cc_final: 0.6644 (tp30) REVERT: C 212 HIS cc_start: 0.7096 (m90) cc_final: 0.6839 (m90) REVERT: C 244 GLU cc_start: 0.7748 (tp30) cc_final: 0.7327 (tp30) REVERT: C 263 ASP cc_start: 0.7168 (m-30) cc_final: 0.6921 (m-30) REVERT: D 74 GLN cc_start: 0.7710 (tt0) cc_final: 0.7457 (tt0) REVERT: D 133 LYS cc_start: 0.7120 (mmtm) cc_final: 0.6874 (mmtm) REVERT: D 157 ASN cc_start: 0.7654 (t0) cc_final: 0.7221 (t0) REVERT: D 198 GLU cc_start: 0.6574 (tp30) cc_final: 0.6238 (tp30) REVERT: D 288 ASN cc_start: 0.8412 (t0) cc_final: 0.8142 (t0) REVERT: E 24 ARG cc_start: 0.7935 (mtt-85) cc_final: 0.7360 (mtt180) REVERT: E 46 ASP cc_start: 0.8073 (t0) cc_final: 0.7619 (t0) REVERT: E 90 ILE cc_start: 0.7867 (mt) cc_final: 0.7629 (mt) REVERT: E 165 ARG cc_start: 0.7650 (mmp80) cc_final: 0.7097 (mtm180) REVERT: E 190 ASP cc_start: 0.7687 (m-30) cc_final: 0.7348 (m-30) REVERT: E 193 ASP cc_start: 0.6980 (m-30) cc_final: 0.6584 (m-30) outliers start: 51 outliers final: 37 residues processed: 436 average time/residue: 0.3342 time to fit residues: 226.9163 Evaluate side-chains 438 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 397 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 192 optimal weight: 0.7980 chunk 125 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 130 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.206820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.163261 restraints weight = 22163.236| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 4.13 r_work: 0.3337 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18286 Z= 0.154 Angle : 0.567 7.315 24799 Z= 0.300 Chirality : 0.043 0.211 2805 Planarity : 0.004 0.049 3103 Dihedral : 4.478 23.747 2417 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.04 % Allowed : 16.80 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.18), residues: 2163 helix: 2.07 (0.16), residues: 958 sheet: 0.76 (0.24), residues: 462 loop : -1.31 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 47 HIS 0.007 0.001 HIS C 212 PHE 0.019 0.001 PHE B 39 TYR 0.024 0.001 TYR F 103 ARG 0.005 0.000 ARG E 162 Details of bonding type rmsd hydrogen bonds : bond 0.05083 ( 1048) hydrogen bonds : angle 4.55062 ( 3027) SS BOND : bond 0.00063 ( 4) SS BOND : angle 1.75984 ( 8) covalent geometry : bond 0.00347 (18282) covalent geometry : angle 0.56608 (24791) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 411 time to evaluate : 2.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.8426 (mttm) cc_final: 0.8161 (ttmm) REVERT: A 54 ARG cc_start: 0.6416 (tmm160) cc_final: 0.5890 (tmm-80) REVERT: A 87 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8072 (mm) REVERT: A 152 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6414 (mt-10) REVERT: B 186 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7774 (tp30) REVERT: B 306 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.5625 (p90) REVERT: B 341 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.6813 (mpp) REVERT: C 98 LYS cc_start: 0.5592 (tmmt) cc_final: 0.5282 (tmmt) REVERT: C 192 ILE cc_start: 0.8501 (mp) cc_final: 0.8294 (mp) REVERT: C 198 GLU cc_start: 0.7008 (tp30) cc_final: 0.6702 (tp30) REVERT: C 244 GLU cc_start: 0.7728 (tp30) cc_final: 0.7283 (tp30) REVERT: C 263 ASP cc_start: 0.7117 (m-30) cc_final: 0.6871 (m-30) REVERT: C 313 MET cc_start: 0.4086 (ttp) cc_final: 0.3338 (ttp) REVERT: D 74 GLN cc_start: 0.7717 (tt0) cc_final: 0.7422 (tt0) REVERT: D 157 ASN cc_start: 0.7670 (t0) cc_final: 0.7295 (t0) REVERT: D 198 GLU cc_start: 0.6615 (tp30) cc_final: 0.6345 (tp30) REVERT: D 202 ARG cc_start: 0.6845 (mpp80) cc_final: 0.6617 (mpp80) REVERT: D 288 ASN cc_start: 0.8480 (t0) cc_final: 0.8230 (t0) REVERT: E 24 ARG cc_start: 0.7882 (mtt-85) cc_final: 0.7285 (mtt180) REVERT: E 46 ASP cc_start: 0.8086 (t0) cc_final: 0.7646 (t0) REVERT: E 90 ILE cc_start: 0.7831 (mt) cc_final: 0.7604 (mt) REVERT: E 165 ARG cc_start: 0.7587 (mmp80) cc_final: 0.7001 (mtm180) REVERT: E 190 ASP cc_start: 0.7633 (m-30) cc_final: 0.7340 (m-30) REVERT: E 193 ASP cc_start: 0.6898 (m-30) cc_final: 0.6525 (m-30) REVERT: E 232 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8528 (mm) outliers start: 61 outliers final: 43 residues processed: 440 average time/residue: 0.2752 time to fit residues: 187.5168 Evaluate side-chains 450 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 402 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 104 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 134 optimal weight: 0.2980 chunk 154 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 198 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN E 257 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.202762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.160385 restraints weight = 22017.457| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 4.06 r_work: 0.3261 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 18286 Z= 0.164 Angle : 0.575 7.279 24799 Z= 0.304 Chirality : 0.043 0.209 2805 Planarity : 0.004 0.049 3103 Dihedral : 4.489 23.807 2417 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.14 % Allowed : 17.65 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.18), residues: 2163 helix: 2.05 (0.16), residues: 956 sheet: 0.73 (0.24), residues: 462 loop : -1.34 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 36 HIS 0.004 0.001 HIS A 68 PHE 0.019 0.001 PHE B 39 TYR 0.024 0.001 TYR F 103 ARG 0.006 0.000 ARG E 162 Details of bonding type rmsd hydrogen bonds : bond 0.05082 ( 1048) hydrogen bonds : angle 4.56755 ( 3027) SS BOND : bond 0.00092 ( 4) SS BOND : angle 1.83375 ( 8) covalent geometry : bond 0.00377 (18282) covalent geometry : angle 0.57377 (24791) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 408 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.8379 (mttm) cc_final: 0.8101 (ttmm) REVERT: A 54 ARG cc_start: 0.6432 (tmm160) cc_final: 0.5904 (tmm-80) REVERT: A 87 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8015 (mm) REVERT: A 152 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6373 (mt-10) REVERT: B 186 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7730 (tp30) REVERT: B 260 GLN cc_start: 0.8351 (mt0) cc_final: 0.8070 (mt0) REVERT: B 306 PHE cc_start: 0.6988 (OUTLIER) cc_final: 0.5440 (p90) REVERT: B 341 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.6763 (mpp) REVERT: C 98 LYS cc_start: 0.5597 (tmmt) cc_final: 0.5248 (tmmt) REVERT: C 112 MET cc_start: 0.4601 (tmm) cc_final: 0.4255 (tmm) REVERT: C 192 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8332 (mp) REVERT: C 198 GLU cc_start: 0.6978 (tp30) cc_final: 0.6663 (tp30) REVERT: C 212 HIS cc_start: 0.6863 (m90) cc_final: 0.6622 (m90) REVERT: C 244 GLU cc_start: 0.7775 (tp30) cc_final: 0.7303 (tp30) REVERT: C 313 MET cc_start: 0.4114 (ttp) cc_final: 0.3387 (ttp) REVERT: D 74 GLN cc_start: 0.7700 (tt0) cc_final: 0.7382 (tt0) REVERT: D 157 ASN cc_start: 0.7675 (t0) cc_final: 0.7318 (t0) REVERT: D 198 GLU cc_start: 0.6575 (tp30) cc_final: 0.6234 (tp30) REVERT: D 288 ASN cc_start: 0.8480 (t0) cc_final: 0.8225 (t0) REVERT: D 331 LEU cc_start: 0.5339 (OUTLIER) cc_final: 0.5055 (tt) REVERT: D 341 MET cc_start: 0.5427 (mmt) cc_final: 0.4993 (mmp) REVERT: E 24 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7323 (mtt180) REVERT: E 29 ILE cc_start: 0.7736 (mt) cc_final: 0.7424 (mt) REVERT: E 46 ASP cc_start: 0.8067 (t0) cc_final: 0.7548 (t0) REVERT: E 90 ILE cc_start: 0.7852 (mt) cc_final: 0.7618 (mt) REVERT: E 132 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8222 (t) REVERT: E 165 ARG cc_start: 0.7626 (mmp80) cc_final: 0.7067 (mtm180) REVERT: E 190 ASP cc_start: 0.7701 (m-30) cc_final: 0.7402 (m-30) REVERT: E 193 ASP cc_start: 0.6903 (m-30) cc_final: 0.6505 (m-30) REVERT: E 232 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8526 (mm) outliers start: 63 outliers final: 48 residues processed: 436 average time/residue: 0.2731 time to fit residues: 184.3572 Evaluate side-chains 461 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 405 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 160 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 299 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 151 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS A 140 GLN B 288 ASN C 260 GLN E 157 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.198080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.155968 restraints weight = 21841.380| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 4.04 r_work: 0.3193 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 18286 Z= 0.270 Angle : 0.669 8.475 24799 Z= 0.356 Chirality : 0.046 0.228 2805 Planarity : 0.005 0.065 3103 Dihedral : 4.868 24.089 2417 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.49 % Allowed : 18.25 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2163 helix: 1.68 (0.16), residues: 958 sheet: 0.38 (0.24), residues: 463 loop : -1.53 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 36 HIS 0.011 0.002 HIS A 68 PHE 0.016 0.002 PHE A 107 TYR 0.030 0.002 TYR F 103 ARG 0.008 0.001 ARG G 67 Details of bonding type rmsd hydrogen bonds : bond 0.05854 ( 1048) hydrogen bonds : angle 4.89791 ( 3027) SS BOND : bond 0.00127 ( 4) SS BOND : angle 2.27094 ( 8) covalent geometry : bond 0.00638 (18282) covalent geometry : angle 0.66744 (24791) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 420 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.8499 (mttm) cc_final: 0.8246 (ttmm) REVERT: A 54 ARG cc_start: 0.6481 (tmm160) cc_final: 0.5968 (tmm-80) REVERT: A 87 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7980 (mm) REVERT: A 152 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6399 (mt-10) REVERT: A 266 GLU cc_start: 0.8206 (mp0) cc_final: 0.7815 (mp0) REVERT: B 306 PHE cc_start: 0.6986 (OUTLIER) cc_final: 0.5575 (p90) REVERT: B 341 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.6320 (mpp) REVERT: C 115 TYR cc_start: 0.7058 (t80) cc_final: 0.6747 (t80) REVERT: C 139 PHE cc_start: 0.5818 (m-10) cc_final: 0.5000 (m-80) REVERT: C 163 LYS cc_start: 0.6995 (mptt) cc_final: 0.6313 (ptmt) REVERT: C 198 GLU cc_start: 0.6999 (tp30) cc_final: 0.6698 (tp30) REVERT: C 212 HIS cc_start: 0.6978 (m90) cc_final: 0.6759 (m90) REVERT: C 244 GLU cc_start: 0.7805 (tp30) cc_final: 0.7311 (tp30) REVERT: C 263 ASP cc_start: 0.7051 (m-30) cc_final: 0.6782 (m-30) REVERT: C 313 MET cc_start: 0.4178 (ttp) cc_final: 0.3561 (ttp) REVERT: D 28 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7196 (mm-30) REVERT: D 74 GLN cc_start: 0.7737 (tt0) cc_final: 0.7387 (tt0) REVERT: D 157 ASN cc_start: 0.7752 (t0) cc_final: 0.7456 (t0) REVERT: D 198 GLU cc_start: 0.6402 (tp30) cc_final: 0.6124 (tp30) REVERT: D 288 ASN cc_start: 0.8516 (t0) cc_final: 0.8268 (t0) REVERT: D 331 LEU cc_start: 0.5511 (OUTLIER) cc_final: 0.5228 (tt) REVERT: D 341 MET cc_start: 0.5437 (mmt) cc_final: 0.4990 (mmp) REVERT: E 29 ILE cc_start: 0.7786 (mt) cc_final: 0.7482 (mt) REVERT: E 46 ASP cc_start: 0.8225 (t0) cc_final: 0.7697 (t0) REVERT: E 90 ILE cc_start: 0.7980 (mt) cc_final: 0.7741 (mt) REVERT: E 162 ARG cc_start: 0.7121 (mtp180) cc_final: 0.6850 (mtm180) REVERT: E 165 ARG cc_start: 0.7771 (mmp80) cc_final: 0.7540 (mmp80) REVERT: E 232 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8656 (mm) outliers start: 70 outliers final: 46 residues processed: 454 average time/residue: 0.2878 time to fit residues: 200.9443 Evaluate side-chains 459 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 407 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 299 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 72 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 179 optimal weight: 0.5980 chunk 122 optimal weight: 7.9990 chunk 125 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 26 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN B 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.201645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.159267 restraints weight = 21681.442| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 4.03 r_work: 0.3249 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 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 = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 18286 Z= 0.151 Angle : 0.594 7.694 24799 Z= 0.314 Chirality : 0.043 0.218 2805 Planarity : 0.004 0.049 3103 Dihedral : 4.667 24.439 2417 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.79 % Allowed : 19.64 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2163 helix: 1.95 (0.16), residues: 955 sheet: 0.53 (0.24), residues: 460 loop : -1.45 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 36 HIS 0.005 0.001 HIS C 212 PHE 0.020 0.002 PHE B 39 TYR 0.026 0.001 TYR L 56 ARG 0.006 0.000 ARG E 162 Details of bonding type rmsd hydrogen bonds : bond 0.05200 ( 1048) hydrogen bonds : angle 4.65062 ( 3027) SS BOND : bond 0.00139 ( 4) SS BOND : angle 1.79018 ( 8) covalent geometry : bond 0.00339 (18282) covalent geometry : angle 0.59368 (24791) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 402 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.8359 (mttm) cc_final: 0.8113 (ttmm) REVERT: A 54 ARG cc_start: 0.6605 (tmm160) cc_final: 0.6043 (tmm-80) REVERT: A 87 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7998 (mm) REVERT: A 152 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6394 (mt-10) REVERT: B 186 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7751 (tp30) REVERT: B 260 GLN cc_start: 0.8338 (mt0) cc_final: 0.8030 (mt0) REVERT: B 306 PHE cc_start: 0.6912 (OUTLIER) cc_final: 0.5522 (p90) REVERT: B 341 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.6936 (mpp) REVERT: C 88 GLU cc_start: 0.8117 (pp20) cc_final: 0.7755 (pm20) REVERT: C 198 GLU cc_start: 0.6971 (tp30) cc_final: 0.6657 (tp30) REVERT: C 212 HIS cc_start: 0.6941 (m90) cc_final: 0.6715 (m90) REVERT: C 244 GLU cc_start: 0.7844 (tp30) cc_final: 0.7352 (tp30) REVERT: C 263 ASP cc_start: 0.7013 (m-30) cc_final: 0.6753 (m-30) REVERT: C 313 MET cc_start: 0.4036 (ttp) cc_final: 0.3310 (ttp) REVERT: D 28 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7222 (mm-30) REVERT: D 74 GLN cc_start: 0.7705 (tt0) cc_final: 0.7359 (tt0) REVERT: D 157 ASN cc_start: 0.7653 (t0) cc_final: 0.7327 (t0) REVERT: D 198 GLU cc_start: 0.6518 (tp30) cc_final: 0.6224 (tp30) REVERT: D 202 ARG cc_start: 0.6854 (mpp80) cc_final: 0.6617 (mpp80) REVERT: D 210 ARG cc_start: 0.8194 (mtp85) cc_final: 0.7925 (mtp85) REVERT: D 288 ASN cc_start: 0.8446 (t0) cc_final: 0.8203 (t0) REVERT: D 331 LEU cc_start: 0.5333 (OUTLIER) cc_final: 0.5081 (tt) REVERT: D 341 MET cc_start: 0.5451 (mmt) cc_final: 0.5023 (mmp) REVERT: E 24 ARG cc_start: 0.7981 (mtt-85) cc_final: 0.7377 (mtt180) REVERT: E 46 ASP cc_start: 0.8130 (t0) cc_final: 0.7674 (t0) REVERT: E 90 ILE cc_start: 0.7886 (mt) cc_final: 0.7630 (mt) REVERT: E 132 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8470 (t) REVERT: E 165 ARG cc_start: 0.7638 (mmp80) cc_final: 0.7276 (mtm180) REVERT: E 193 ASP cc_start: 0.6851 (m-30) cc_final: 0.6381 (m-30) REVERT: E 232 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8569 (mm) outliers start: 56 outliers final: 37 residues processed: 429 average time/residue: 0.2735 time to fit residues: 179.7251 Evaluate side-chains 441 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 397 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 299 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 89 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN E 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.196480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.154029 restraints weight = 22114.190| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 4.20 r_work: 0.3176 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.115 | | 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: 0.7630 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 18286 Z= 0.310 Angle : 0.707 11.216 24799 Z= 0.375 Chirality : 0.047 0.308 2805 Planarity : 0.005 0.065 3103 Dihedral : 4.917 24.512 2417 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.24 % Allowed : 19.54 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.18), residues: 2163 helix: 1.58 (0.16), residues: 957 sheet: 0.30 (0.24), residues: 461 loop : -1.64 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 36 HIS 0.010 0.002 HIS A 68 PHE 0.028 0.002 PHE D 251 TYR 0.056 0.002 TYR D 19 ARG 0.011 0.001 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.05963 ( 1048) hydrogen bonds : angle 4.98562 ( 3027) SS BOND : bond 0.00153 ( 4) SS BOND : angle 2.21778 ( 8) covalent geometry : bond 0.00730 (18282) covalent geometry : angle 0.70599 (24791) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 409 time to evaluate : 6.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 GLU cc_start: 0.7485 (tp30) cc_final: 0.7237 (tp30) REVERT: F 13 GLN cc_start: 0.8387 (mm110) cc_final: 0.8106 (mm-40) REVERT: F 43 LYS cc_start: 0.8518 (mttm) cc_final: 0.8259 (ttmm) REVERT: A 54 ARG cc_start: 0.6637 (tmm160) cc_final: 0.6090 (tmm-80) REVERT: A 87 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7988 (mm) REVERT: A 152 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6428 (mt-10) REVERT: B 306 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.5624 (p90) REVERT: B 341 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.6334 (mpp) REVERT: C 88 GLU cc_start: 0.8147 (pp20) cc_final: 0.7664 (pm20) REVERT: C 115 TYR cc_start: 0.7086 (t80) cc_final: 0.6786 (t80) REVERT: C 198 GLU cc_start: 0.6985 (tp30) cc_final: 0.6677 (tp30) REVERT: C 244 GLU cc_start: 0.7798 (tp30) cc_final: 0.7273 (tp30) REVERT: C 263 ASP cc_start: 0.7050 (m-30) cc_final: 0.6789 (m-30) REVERT: C 313 MET cc_start: 0.4271 (ttp) cc_final: 0.3656 (ttp) REVERT: D 28 GLU cc_start: 0.7614 (mm-30) cc_final: 0.5964 (mt-10) REVERT: D 74 GLN cc_start: 0.7750 (tt0) cc_final: 0.7388 (tt0) REVERT: D 157 ASN cc_start: 0.7714 (t0) cc_final: 0.7422 (t0) REVERT: D 198 GLU cc_start: 0.6338 (tp30) cc_final: 0.6086 (tp30) REVERT: D 331 LEU cc_start: 0.5481 (OUTLIER) cc_final: 0.5207 (tt) REVERT: D 341 MET cc_start: 0.5547 (mmt) cc_final: 0.5090 (mmp) REVERT: E 46 ASP cc_start: 0.8224 (t0) cc_final: 0.7757 (t0) REVERT: E 71 ASP cc_start: 0.7741 (p0) cc_final: 0.7483 (p0) REVERT: E 90 ILE cc_start: 0.8046 (mt) cc_final: 0.7777 (mt) REVERT: E 165 ARG cc_start: 0.7847 (mmp80) cc_final: 0.7488 (mtm180) REVERT: E 232 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8664 (mm) outliers start: 65 outliers final: 51 residues processed: 441 average time/residue: 0.3721 time to fit residues: 253.6316 Evaluate side-chains 458 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 401 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 299 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 189 optimal weight: 0.5980 chunk 5 optimal weight: 0.0570 chunk 34 optimal weight: 0.5980 chunk 154 optimal weight: 0.6980 chunk 202 optimal weight: 0.0870 chunk 207 optimal weight: 0.6980 chunk 153 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 GLN A 140 GLN B 260 GLN B 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.201446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.159130 restraints weight = 21766.537| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 4.13 r_work: 0.3259 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 18286 Z= 0.146 Angle : 0.609 11.135 24799 Z= 0.321 Chirality : 0.044 0.234 2805 Planarity : 0.004 0.049 3103 Dihedral : 4.715 24.730 2417 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.24 % Allowed : 20.74 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 2163 helix: 1.94 (0.16), residues: 954 sheet: 0.44 (0.25), residues: 464 loop : -1.50 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 36 HIS 0.010 0.001 HIS C 212 PHE 0.026 0.002 PHE D 251 TYR 0.055 0.002 TYR D 19 ARG 0.008 0.000 ARG E 162 Details of bonding type rmsd hydrogen bonds : bond 0.05168 ( 1048) hydrogen bonds : angle 4.70643 ( 3027) SS BOND : bond 0.00165 ( 4) SS BOND : angle 1.65794 ( 8) covalent geometry : bond 0.00322 (18282) covalent geometry : angle 0.60826 (24791) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 413 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.8339 (mttm) cc_final: 0.8089 (ttmm) REVERT: A 40 ARG cc_start: 0.7315 (ttt-90) cc_final: 0.6949 (ttp-110) REVERT: A 54 ARG cc_start: 0.6565 (tmm160) cc_final: 0.6001 (tmm-80) REVERT: A 87 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7972 (mm) REVERT: A 152 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6393 (mt-10) REVERT: B 186 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7753 (tp30) REVERT: B 197 GLU cc_start: 0.7485 (tp30) cc_final: 0.7207 (tp30) REVERT: B 306 PHE cc_start: 0.6953 (OUTLIER) cc_final: 0.5468 (p90) REVERT: B 341 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.6926 (mpp) REVERT: C 198 GLU cc_start: 0.7019 (tp30) cc_final: 0.6694 (tp30) REVERT: C 244 GLU cc_start: 0.7823 (tp30) cc_final: 0.7312 (tp30) REVERT: C 263 ASP cc_start: 0.6965 (m-30) cc_final: 0.6721 (m-30) REVERT: C 313 MET cc_start: 0.4048 (ttp) cc_final: 0.3296 (ttp) REVERT: D 28 GLU cc_start: 0.7543 (mm-30) cc_final: 0.5929 (mt-10) REVERT: D 74 GLN cc_start: 0.7682 (tt0) cc_final: 0.7326 (tt0) REVERT: D 75 ARG cc_start: 0.7986 (ttt180) cc_final: 0.7713 (ttt180) REVERT: D 157 ASN cc_start: 0.7569 (t0) cc_final: 0.7273 (t0) REVERT: D 198 GLU cc_start: 0.6460 (tp30) cc_final: 0.6159 (tp30) REVERT: D 202 ARG cc_start: 0.6898 (mpp80) cc_final: 0.6657 (mpp80) REVERT: D 210 ARG cc_start: 0.8164 (mtp85) cc_final: 0.7883 (mtp85) REVERT: D 288 ASN cc_start: 0.8428 (t0) cc_final: 0.8165 (t0) REVERT: D 331 LEU cc_start: 0.5298 (OUTLIER) cc_final: 0.5038 (tt) REVERT: D 341 MET cc_start: 0.5503 (mmt) cc_final: 0.5086 (mmp) REVERT: E 24 ARG cc_start: 0.7977 (mtt-85) cc_final: 0.7356 (mtt180) REVERT: E 46 ASP cc_start: 0.8125 (t0) cc_final: 0.7674 (t0) REVERT: E 90 ILE cc_start: 0.7840 (mt) cc_final: 0.7590 (mt) REVERT: E 132 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8528 (t) REVERT: E 165 ARG cc_start: 0.7683 (mmp80) cc_final: 0.7467 (mmp80) REVERT: E 181 TYR cc_start: 0.8433 (m-80) cc_final: 0.8039 (m-80) REVERT: E 193 ASP cc_start: 0.6728 (m-30) cc_final: 0.6362 (m-30) REVERT: E 204 GLU cc_start: 0.7840 (mp0) cc_final: 0.7585 (mp0) REVERT: E 232 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8525 (mm) outliers start: 45 outliers final: 34 residues processed: 433 average time/residue: 0.2864 time to fit residues: 190.6801 Evaluate side-chains 444 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 403 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 299 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 27 optimal weight: 0.0060 chunk 63 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 213 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 43 optimal weight: 0.0970 chunk 102 optimal weight: 0.5980 overall best weight: 0.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 90 GLN E 157 ASN E 217 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.203931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.162049 restraints weight = 21910.409| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 4.13 r_work: 0.3293 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 18286 Z= 0.131 Angle : 0.592 12.110 24799 Z= 0.310 Chirality : 0.043 0.236 2805 Planarity : 0.004 0.051 3103 Dihedral : 4.497 25.918 2417 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.34 % Allowed : 20.99 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.18), residues: 2163 helix: 2.08 (0.16), residues: 954 sheet: 0.66 (0.25), residues: 453 loop : -1.43 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP L 36 HIS 0.004 0.001 HIS C 257 PHE 0.016 0.001 PHE B 39 TYR 0.045 0.001 TYR D 19 ARG 0.005 0.000 ARG E 222 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 1048) hydrogen bonds : angle 4.52256 ( 3027) SS BOND : bond 0.00298 ( 4) SS BOND : angle 1.48895 ( 8) covalent geometry : bond 0.00287 (18282) covalent geometry : angle 0.59159 (24791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11426.69 seconds wall clock time: 202 minutes 18.83 seconds (12138.83 seconds total)