Starting phenix.real_space_refine on Mon May 19 20:54:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmm_41394/05_2025/8tmm_41394.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmm_41394/05_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_41394/05_2025/8tmm_41394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmm_41394/05_2025/8tmm_41394.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmm_41394/05_2025/8tmm_41394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmm_41394/05_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-5687/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: 11.48, per 1000 atoms: 0.64 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: 5.01 Conformation dependent library (CDL) restraints added in 2.4 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: 2.14 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: 6.78 Time building geometry restraints manager: 5.82 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 44.440 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.090 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:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.920 ------------------------------------------------------------------------------- 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 : 1.847 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: 0.2637 time to fit residues: 172.1571 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 : 2.057 ------------------------------------------------------------------------------- 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: 4.20 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 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: 0.7500 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 : 1.875 Fit side-chains revert: symmetry clash REVERT: F 43 LYS cc_start: 0.8386 (mttm) cc_final: 0.8106 (ttmm) REVERT: F 89 GLU cc_start: 0.6890 (tm-30) cc_final: 0.5979 (tm-30) REVERT: A 54 ARG cc_start: 0.6398 (tmm160) cc_final: 0.5878 (tmm-80) REVERT: A 71 ASP cc_start: 0.7896 (p0) cc_final: 0.7647 (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: 0.6265 (m-10) cc_final: 0.5564 (m-80) REVERT: C 198 GLU cc_start: 0.6939 (tp30) cc_final: 0.6591 (tp30) REVERT: C 244 GLU cc_start: 0.7596 (tp30) cc_final: 0.7334 (tp30) REVERT: C 334 MET cc_start: 0.5895 (ppp) cc_final: 0.3946 (mtt) REVERT: D 74 GLN cc_start: 0.7780 (tt0) cc_final: 0.7493 (tt0) REVERT: D 155 ARG cc_start: 0.5831 (mtt180) cc_final: 0.5560 (mtt-85) REVERT: D 157 ASN cc_start: 0.7717 (t0) cc_final: 0.7254 (t0) REVERT: D 198 GLU cc_start: 0.6600 (tp30) cc_final: 0.6337 (tp30) REVERT: D 288 ASN cc_start: 0.8422 (t0) cc_final: 0.8220 (t0) REVERT: E 46 ASP cc_start: 0.8034 (t0) cc_final: 0.7560 (t0) REVERT: E 90 ILE cc_start: 0.7829 (mt) cc_final: 0.7604 (mt) REVERT: E 190 ASP cc_start: 0.7634 (m-30) cc_final: 0.7243 (m-30) REVERT: E 193 ASP cc_start: 0.6952 (m-30) cc_final: 0.6544 (m-30) outliers start: 27 outliers final: 19 residues processed: 413 average time/residue: 0.2740 time to fit residues: 173.5776 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 : 1.832 ------------------------------------------------------------------------------- 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: 2.9990 chunk 73 optimal weight: 3.9990 chunk 208 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 120 optimal weight: 0.0040 chunk 140 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 38 optimal weight: 0.0470 chunk 202 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.3290 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.205844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.163672 restraints weight = 21912.588| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 3.86 r_work: 0.3306 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18286 Z= 0.135 Angle : 0.556 8.357 24799 Z= 0.295 Chirality : 0.042 0.203 2805 Planarity : 0.004 0.050 3103 Dihedral : 4.456 23.348 2417 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.04 % Allowed : 13.26 % Favored : 84.70 % 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: 1.02 (0.18), residues: 2163 helix: 2.05 (0.16), residues: 960 sheet: 0.83 (0.24), residues: 463 loop : -1.32 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 36 HIS 0.006 0.001 HIS C 257 PHE 0.022 0.001 PHE B 39 TYR 0.021 0.001 TYR F 103 ARG 0.005 0.000 ARG E 96 Details of bonding type rmsd hydrogen bonds : bond 0.05179 ( 1048) hydrogen bonds : angle 4.60297 ( 3027) SS BOND : bond 0.00271 ( 4) SS BOND : angle 1.55025 ( 8) covalent geometry : bond 0.00288 (18282) covalent geometry : angle 0.55495 (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 452 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 411 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.8364 (mttm) cc_final: 0.8091 (ttmm) REVERT: A 53 PHE cc_start: 0.7900 (m-80) cc_final: 0.7562 (m-80) REVERT: A 54 ARG cc_start: 0.6408 (tmm160) cc_final: 0.5871 (tmm-80) REVERT: A 71 ASP cc_start: 0.7875 (p0) cc_final: 0.7669 (p0) REVERT: A 152 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6390 (mt-10) REVERT: B 186 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7780 (tp30) REVERT: B 306 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.5968 (p90) REVERT: B 341 MET cc_start: 0.7627 (mpp) cc_final: 0.6966 (mpp) REVERT: C 198 GLU cc_start: 0.6976 (tp30) cc_final: 0.6623 (tp30) REVERT: C 244 GLU cc_start: 0.7706 (tp30) cc_final: 0.7348 (tp30) REVERT: C 341 MET cc_start: 0.4009 (mmt) cc_final: 0.3597 (mmt) REVERT: D 74 GLN cc_start: 0.7743 (tt0) cc_final: 0.7409 (tt0) REVERT: D 157 ASN cc_start: 0.7553 (t0) cc_final: 0.7045 (t0) REVERT: D 198 GLU cc_start: 0.6505 (tp30) cc_final: 0.6277 (tp30) REVERT: D 202 ARG cc_start: 0.6775 (mpp80) cc_final: 0.6507 (mpp80) REVERT: D 288 ASN cc_start: 0.8411 (t0) cc_final: 0.8201 (t0) REVERT: E 24 ARG cc_start: 0.7894 (mtt-85) cc_final: 0.7332 (mtt180) REVERT: E 46 ASP cc_start: 0.8024 (t0) cc_final: 0.7561 (t0) REVERT: E 90 ILE cc_start: 0.7749 (mt) cc_final: 0.7509 (mt) REVERT: E 190 ASP cc_start: 0.7607 (m-30) cc_final: 0.7210 (m-30) REVERT: E 193 ASP cc_start: 0.6887 (m-30) cc_final: 0.6489 (m-30) outliers start: 41 outliers final: 26 residues processed: 428 average time/residue: 0.2892 time to fit residues: 192.6001 Evaluate side-chains 435 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 407 time to evaluate : 2.008 ------------------------------------------------------------------------------- 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 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 18 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 138 MET 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 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: 0.6980 chunk 175 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.202081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.159168 restraints weight = 21974.022| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 3.92 r_work: 0.3264 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- 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: 0.7528 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18286 Z= 0.182 Angle : 0.583 7.774 24799 Z= 0.309 Chirality : 0.043 0.205 2805 Planarity : 0.004 0.049 3103 Dihedral : 4.504 23.481 2417 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.64 % Allowed : 15.05 % Favored : 82.30 % 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: 0.95 (0.18), residues: 2163 helix: 2.02 (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 0.024 0.001 TRP L 36 HIS 0.006 0.001 HIS C 212 PHE 0.019 0.001 PHE B 39 TYR 0.026 0.001 TYR F 100 ARG 0.004 0.000 ARG G 67 Details of bonding type rmsd hydrogen bonds : bond 0.05308 ( 1048) hydrogen bonds : angle 4.63511 ( 3027) SS BOND : bond 0.00155 ( 4) SS BOND : angle 1.93323 ( 8) covalent geometry : bond 0.00423 (18282) covalent geometry : angle 0.58246 (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 472 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 419 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 90 GLN cc_start: 0.8113 (tt0) cc_final: 0.7887 (tt0) REVERT: F 43 LYS cc_start: 0.8409 (mttm) cc_final: 0.8135 (ttmm) REVERT: A 54 ARG cc_start: 0.6449 (tmm160) cc_final: 0.5902 (tmm-80) REVERT: A 87 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7944 (mm) REVERT: A 152 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6436 (mt-10) REVERT: A 204 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7698 (pm20) REVERT: B 186 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7736 (tp30) REVERT: B 306 PHE cc_start: 0.7140 (OUTLIER) cc_final: 0.5742 (p90) REVERT: B 341 MET cc_start: 0.7675 (mpp) cc_final: 0.6828 (mpp) REVERT: C 98 LYS cc_start: 0.5602 (tmmt) cc_final: 0.5333 (tmmt) REVERT: C 198 GLU cc_start: 0.6957 (tp30) cc_final: 0.6657 (tp30) REVERT: C 212 HIS cc_start: 0.7048 (m90) cc_final: 0.6796 (m90) REVERT: C 244 GLU cc_start: 0.7749 (tp30) cc_final: 0.7330 (tp30) REVERT: D 74 GLN cc_start: 0.7706 (tt0) cc_final: 0.7451 (tt0) REVERT: D 133 LYS cc_start: 0.7128 (mmtm) cc_final: 0.6880 (mmtm) REVERT: D 157 ASN cc_start: 0.7592 (t0) cc_final: 0.7157 (t0) REVERT: D 198 GLU cc_start: 0.6565 (tp30) cc_final: 0.6230 (tp30) REVERT: E 24 ARG cc_start: 0.7915 (mtt-85) cc_final: 0.7339 (mtt180) REVERT: E 46 ASP cc_start: 0.7984 (t0) cc_final: 0.7555 (t0) REVERT: E 90 ILE cc_start: 0.7848 (mt) cc_final: 0.7622 (mt) REVERT: E 165 ARG cc_start: 0.7644 (mmp80) cc_final: 0.7246 (mtm180) REVERT: E 190 ASP cc_start: 0.7651 (m-30) cc_final: 0.7312 (m-30) REVERT: E 193 ASP cc_start: 0.6939 (m-30) cc_final: 0.6533 (m-30) outliers start: 53 outliers final: 37 residues processed: 442 average time/residue: 0.2728 time to fit residues: 185.6528 Evaluate side-chains 440 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 399 time to evaluate : 2.047 ------------------------------------------------------------------------------- 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 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 111 LYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 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 281 SER Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 138 MET 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 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: 2.9990 chunk 177 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 171 optimal weight: 0.5980 chunk 202 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.202013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.159556 restraints weight = 22126.142| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 4.19 r_work: 0.3244 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 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 = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18286 Z= 0.177 Angle : 0.582 7.337 24799 Z= 0.308 Chirality : 0.043 0.210 2805 Planarity : 0.004 0.048 3103 Dihedral : 4.531 23.782 2417 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.14 % Allowed : 16.80 % Favored : 80.06 % 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: 0.94 (0.18), residues: 2163 helix: 2.02 (0.16), residues: 958 sheet: 0.72 (0.24), residues: 462 loop : -1.36 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 47 HIS 0.007 0.001 HIS C 212 PHE 0.019 0.001 PHE B 39 TYR 0.026 0.002 TYR F 103 ARG 0.005 0.000 ARG E 162 Details of bonding type rmsd hydrogen bonds : bond 0.05256 ( 1048) hydrogen bonds : angle 4.61571 ( 3027) SS BOND : bond 0.00051 ( 4) SS BOND : angle 1.85978 ( 8) covalent geometry : bond 0.00408 (18282) covalent geometry : angle 0.58066 (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: 63 poor density : 409 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.8361 (mttm) cc_final: 0.8088 (ttmm) REVERT: A 54 ARG cc_start: 0.6431 (tmm160) cc_final: 0.5893 (tmm-80) REVERT: A 87 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7906 (mm) REVERT: A 152 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6412 (mt-10) REVERT: A 204 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7507 (pm20) REVERT: B 306 PHE cc_start: 0.7122 (OUTLIER) cc_final: 0.5623 (p90) REVERT: B 341 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.6187 (mpp) REVERT: C 98 LYS cc_start: 0.5566 (tmmt) cc_final: 0.5280 (tmmt) REVERT: C 192 ILE cc_start: 0.8479 (mp) cc_final: 0.8254 (mp) REVERT: C 198 GLU cc_start: 0.6962 (tp30) cc_final: 0.6651 (tp30) REVERT: C 244 GLU cc_start: 0.7752 (tp30) cc_final: 0.7306 (tp30) REVERT: C 313 MET cc_start: 0.4069 (ttp) cc_final: 0.3326 (ttp) REVERT: D 74 GLN cc_start: 0.7696 (tt0) cc_final: 0.7400 (tt0) REVERT: D 157 ASN cc_start: 0.7634 (t0) cc_final: 0.7275 (t0) REVERT: D 198 GLU cc_start: 0.6560 (tp30) cc_final: 0.6226 (tp30) REVERT: E 24 ARG cc_start: 0.7933 (mtt-85) cc_final: 0.7341 (mtt180) REVERT: E 46 ASP cc_start: 0.8152 (t0) cc_final: 0.7706 (t0) REVERT: E 90 ILE cc_start: 0.7838 (mt) cc_final: 0.7601 (mt) REVERT: E 165 ARG cc_start: 0.7620 (mmp80) cc_final: 0.7173 (mtm180) REVERT: E 190 ASP cc_start: 0.7690 (m-30) cc_final: 0.7374 (m-30) REVERT: E 193 ASP cc_start: 0.6939 (m-30) cc_final: 0.6518 (m-30) REVERT: E 232 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8537 (mm) outliers start: 63 outliers final: 44 residues processed: 439 average time/residue: 0.2737 time to fit residues: 185.8055 Evaluate side-chains 453 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 403 time to evaluate : 1.905 ------------------------------------------------------------------------------- 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 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 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 195 LEU Chi-restraints excluded: chain A residue 204 GLU 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 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 138 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 131 LEU 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: 5.9990 chunk 136 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 134 optimal weight: 0.0060 chunk 154 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.198838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.156225 restraints weight = 22002.709| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.87 r_work: 0.3231 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 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 = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 18286 Z= 0.239 Angle : 0.628 7.734 24799 Z= 0.334 Chirality : 0.045 0.219 2805 Planarity : 0.005 0.054 3103 Dihedral : 4.707 23.965 2417 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.39 % Allowed : 17.85 % Favored : 78.76 % 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: 0.68 (0.18), residues: 2163 helix: 1.83 (0.16), residues: 958 sheet: 0.53 (0.24), residues: 464 loop : -1.49 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 36 HIS 0.006 0.001 HIS B 94 PHE 0.019 0.002 PHE B 39 TYR 0.028 0.002 TYR F 103 ARG 0.009 0.000 ARG E 162 Details of bonding type rmsd hydrogen bonds : bond 0.05600 ( 1048) hydrogen bonds : angle 4.77646 ( 3027) SS BOND : bond 0.00084 ( 4) SS BOND : angle 2.13386 ( 8) covalent geometry : bond 0.00563 (18282) covalent geometry : angle 0.62688 (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 483 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 415 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.8441 (mttm) cc_final: 0.8163 (ttmm) REVERT: F 100 TYR cc_start: 0.9106 (p90) cc_final: 0.8789 (p90) REVERT: A 54 ARG cc_start: 0.6450 (tmm160) cc_final: 0.5931 (tmm-80) REVERT: A 87 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7970 (mm) REVERT: A 152 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6460 (mt-10) REVERT: A 204 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7653 (pm20) REVERT: B 306 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.5423 (p90) REVERT: B 341 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.6209 (mpp) REVERT: C 98 LYS cc_start: 0.5575 (tmmt) cc_final: 0.5251 (tmmt) REVERT: C 139 PHE cc_start: 0.6104 (m-10) cc_final: 0.5186 (m-80) REVERT: C 198 GLU cc_start: 0.7002 (tp30) cc_final: 0.6698 (tp30) REVERT: C 212 HIS cc_start: 0.6986 (m90) cc_final: 0.6769 (m90) REVERT: C 244 GLU cc_start: 0.7783 (tp30) cc_final: 0.7333 (tp30) REVERT: C 313 MET cc_start: 0.3945 (ttp) cc_final: 0.3266 (ttp) REVERT: D 74 GLN cc_start: 0.7733 (tt0) cc_final: 0.7397 (tt0) REVERT: D 157 ASN cc_start: 0.7725 (t0) cc_final: 0.7410 (t0) REVERT: D 198 GLU cc_start: 0.6419 (tp30) cc_final: 0.6121 (tp30) REVERT: D 331 LEU cc_start: 0.5557 (OUTLIER) cc_final: 0.5259 (tt) REVERT: D 341 MET cc_start: 0.5403 (mmt) cc_final: 0.4970 (mmp) REVERT: E 29 ILE cc_start: 0.7763 (mt) cc_final: 0.7452 (mt) REVERT: E 46 ASP cc_start: 0.8098 (t0) cc_final: 0.7586 (t0) REVERT: E 90 ILE cc_start: 0.7924 (mt) cc_final: 0.7679 (mt) REVERT: E 132 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8444 (t) REVERT: E 165 ARG cc_start: 0.7725 (mmp80) cc_final: 0.7296 (mtm180) REVERT: E 190 ASP cc_start: 0.7705 (m-30) cc_final: 0.7442 (m-30) REVERT: E 193 ASP cc_start: 0.6917 (m-30) cc_final: 0.6429 (m-30) REVERT: E 232 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8625 (mm) outliers start: 68 outliers final: 45 residues processed: 444 average time/residue: 0.2600 time to fit residues: 178.7419 Evaluate side-chains 462 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 409 time to evaluate : 1.858 ------------------------------------------------------------------------------- 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 F residue 123 THR Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 GLU 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 138 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 232 LEU 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: 4.9990 chunk 112 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.200721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.158048 restraints weight = 21762.539| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 4.02 r_work: 0.3237 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18286 Z= 0.178 Angle : 0.593 7.308 24799 Z= 0.314 Chirality : 0.044 0.216 2805 Planarity : 0.004 0.049 3103 Dihedral : 4.662 24.275 2417 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.44 % Allowed : 18.74 % Favored : 77.82 % 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: 0.76 (0.18), residues: 2163 helix: 1.91 (0.16), residues: 957 sheet: 0.58 (0.25), residues: 459 loop : -1.44 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 36 HIS 0.005 0.001 HIS C 212 PHE 0.019 0.001 PHE B 39 TYR 0.025 0.002 TYR F 103 ARG 0.004 0.000 ARG E 162 Details of bonding type rmsd hydrogen bonds : bond 0.05311 ( 1048) hydrogen bonds : angle 4.66623 ( 3027) SS BOND : bond 0.00072 ( 4) SS BOND : angle 1.89543 ( 8) covalent geometry : bond 0.00410 (18282) covalent geometry : angle 0.59171 (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 482 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 413 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.8280 (mttm) cc_final: 0.8023 (ttmm) REVERT: A 54 ARG cc_start: 0.6632 (tmm160) cc_final: 0.6073 (tmm-80) REVERT: A 87 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8037 (mm) REVERT: A 152 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6433 (mt-10) REVERT: A 204 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7484 (pm20) REVERT: B 306 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.5425 (p90) REVERT: B 341 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.6429 (mpp) REVERT: C 98 LYS cc_start: 0.5605 (tmmt) cc_final: 0.5273 (tmmt) REVERT: C 139 PHE cc_start: 0.6168 (m-10) cc_final: 0.5220 (m-80) REVERT: C 198 GLU cc_start: 0.7018 (tp30) cc_final: 0.6690 (tp30) REVERT: C 244 GLU cc_start: 0.7772 (tp30) cc_final: 0.7279 (tp30) REVERT: C 313 MET cc_start: 0.3990 (ttp) cc_final: 0.3332 (ttp) REVERT: D 74 GLN cc_start: 0.7736 (tt0) cc_final: 0.7382 (tt0) REVERT: D 157 ASN cc_start: 0.7695 (t0) cc_final: 0.7379 (t0) REVERT: D 198 GLU cc_start: 0.6571 (tp30) cc_final: 0.6288 (tp30) REVERT: D 202 ARG cc_start: 0.6883 (mpp80) cc_final: 0.6646 (mpp80) REVERT: D 331 LEU cc_start: 0.5594 (OUTLIER) cc_final: 0.5298 (tt) REVERT: D 341 MET cc_start: 0.5499 (mmt) cc_final: 0.5057 (mmp) REVERT: E 24 ARG cc_start: 0.7989 (mtt-85) cc_final: 0.7388 (mtt180) REVERT: E 29 ILE cc_start: 0.7796 (mt) cc_final: 0.7481 (mt) REVERT: E 46 ASP cc_start: 0.8104 (t0) cc_final: 0.7572 (t0) REVERT: E 90 ILE cc_start: 0.7922 (mt) cc_final: 0.7693 (mt) REVERT: E 132 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8462 (t) REVERT: E 165 ARG cc_start: 0.7708 (mmp80) cc_final: 0.7317 (mtm180) REVERT: E 190 ASP cc_start: 0.7716 (m-30) cc_final: 0.7481 (m-30) REVERT: E 193 ASP cc_start: 0.6817 (m-30) cc_final: 0.6431 (m-30) REVERT: E 232 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8608 (mm) outliers start: 69 outliers final: 49 residues processed: 444 average time/residue: 0.2725 time to fit residues: 185.2407 Evaluate side-chains 462 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 405 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 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 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 72 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 125 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS B 260 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.202556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.160191 restraints weight = 21621.551| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.94 r_work: 0.3247 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 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 = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18286 Z= 0.163 Angle : 0.594 7.639 24799 Z= 0.315 Chirality : 0.044 0.218 2805 Planarity : 0.004 0.047 3103 Dihedral : 4.604 24.282 2417 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.34 % Allowed : 19.44 % 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: 0.81 (0.18), residues: 2163 helix: 1.95 (0.16), residues: 957 sheet: 0.57 (0.25), residues: 462 loop : -1.42 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP L 36 HIS 0.004 0.001 HIS C 257 PHE 0.018 0.001 PHE B 39 TYR 0.052 0.002 TYR D 19 ARG 0.004 0.000 ARG E 222 Details of bonding type rmsd hydrogen bonds : bond 0.05193 ( 1048) hydrogen bonds : angle 4.65311 ( 3027) SS BOND : bond 0.00100 ( 4) SS BOND : angle 1.83743 ( 8) covalent geometry : bond 0.00374 (18282) covalent geometry : angle 0.59292 (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 480 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 413 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 43 LYS cc_start: 0.8280 (mttm) cc_final: 0.8030 (ttmm) REVERT: A 54 ARG cc_start: 0.6632 (tmm160) cc_final: 0.6079 (tmm-80) REVERT: A 87 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8046 (mm) REVERT: A 152 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6418 (mt-10) REVERT: A 204 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7533 (pm20) REVERT: B 306 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.5403 (p90) REVERT: B 341 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.6888 (mpp) REVERT: C 98 LYS cc_start: 0.5604 (tmmt) cc_final: 0.5270 (tmmt) REVERT: C 139 PHE cc_start: 0.6154 (m-10) cc_final: 0.5212 (m-80) REVERT: C 198 GLU cc_start: 0.7011 (tp30) cc_final: 0.6686 (tp30) REVERT: C 244 GLU cc_start: 0.7835 (tp30) cc_final: 0.7343 (tp30) REVERT: C 313 MET cc_start: 0.3983 (ttp) cc_final: 0.3243 (ttp) REVERT: D 28 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7248 (mm-30) REVERT: D 74 GLN cc_start: 0.7720 (tt0) cc_final: 0.7374 (tt0) REVERT: D 98 LYS cc_start: 0.7570 (pttt) cc_final: 0.7300 (pptt) REVERT: D 157 ASN cc_start: 0.7699 (t0) cc_final: 0.7381 (t0) REVERT: D 198 GLU cc_start: 0.6566 (tp30) cc_final: 0.6285 (tp30) REVERT: D 202 ARG cc_start: 0.6857 (mpp80) cc_final: 0.6625 (mpp80) REVERT: D 331 LEU cc_start: 0.5492 (OUTLIER) cc_final: 0.5189 (tt) REVERT: D 341 MET cc_start: 0.5514 (mmt) cc_final: 0.5078 (mmp) REVERT: E 24 ARG cc_start: 0.7984 (mtt-85) cc_final: 0.7389 (mtt180) REVERT: E 46 ASP cc_start: 0.8104 (t0) cc_final: 0.7652 (t0) REVERT: E 90 ILE cc_start: 0.7918 (mt) cc_final: 0.7674 (mt) REVERT: E 132 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8447 (t) REVERT: E 162 ARG cc_start: 0.7093 (mtp180) cc_final: 0.6730 (mtm180) REVERT: E 165 ARG cc_start: 0.7687 (mmp80) cc_final: 0.7302 (mtm180) REVERT: E 190 ASP cc_start: 0.7703 (m-30) cc_final: 0.7460 (m-30) REVERT: E 193 ASP cc_start: 0.6799 (m-30) cc_final: 0.6419 (m-30) REVERT: E 232 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8542 (mm) REVERT: E 334 MET cc_start: 0.4810 (mmt) cc_final: 0.4556 (mmt) outliers start: 67 outliers final: 51 residues processed: 445 average time/residue: 0.2851 time to fit residues: 197.1992 Evaluate side-chains 469 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 410 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 213 GLN Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 32 MET 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 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 232 LEU 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: 4.9990 chunk 23 optimal weight: 0.7980 chunk 170 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 192 optimal weight: 0.0870 overall best weight: 0.8960 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.200356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.157840 restraints weight = 21987.007| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 4.15 r_work: 0.3220 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 18286 Z= 0.197 Angle : 0.617 7.882 24799 Z= 0.327 Chirality : 0.044 0.227 2805 Planarity : 0.004 0.047 3103 Dihedral : 4.667 24.374 2417 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.19 % Allowed : 19.99 % Favored : 76.82 % 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: 0.70 (0.18), residues: 2163 helix: 1.88 (0.16), residues: 957 sheet: 0.54 (0.25), residues: 451 loop : -1.49 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 36 HIS 0.005 0.001 HIS C 212 PHE 0.026 0.002 PHE D 251 TYR 0.041 0.002 TYR D 19 ARG 0.005 0.000 ARG E 222 Details of bonding type rmsd hydrogen bonds : bond 0.05349 ( 1048) hydrogen bonds : angle 4.72140 ( 3027) SS BOND : bond 0.00060 ( 4) SS BOND : angle 1.97978 ( 8) covalent geometry : bond 0.00463 (18282) covalent geometry : angle 0.61565 (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 471 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 407 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 GLN cc_start: 0.8326 (mm110) cc_final: 0.8030 (mm-40) REVERT: F 43 LYS cc_start: 0.8394 (mttm) cc_final: 0.8150 (ttmm) REVERT: A 87 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7997 (mm) REVERT: A 152 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6454 (mt-10) REVERT: A 204 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7343 (pm20) REVERT: B 197 GLU cc_start: 0.7576 (tp30) cc_final: 0.7320 (tp30) REVERT: B 306 PHE cc_start: 0.6967 (OUTLIER) cc_final: 0.5535 (p90) REVERT: B 341 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.6404 (mpp) REVERT: C 139 PHE cc_start: 0.5929 (m-10) cc_final: 0.4966 (m-80) REVERT: C 163 LYS cc_start: 0.6988 (mptt) cc_final: 0.6312 (ptmt) REVERT: C 198 GLU cc_start: 0.6993 (tp30) cc_final: 0.6679 (tp30) REVERT: C 244 GLU cc_start: 0.7806 (tp30) cc_final: 0.7282 (tp30) REVERT: C 263 ASP cc_start: 0.7002 (m-30) cc_final: 0.6754 (m-30) REVERT: C 313 MET cc_start: 0.4060 (ttp) cc_final: 0.3331 (ttp) REVERT: D 28 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7302 (mm-30) REVERT: D 74 GLN cc_start: 0.7725 (tt0) cc_final: 0.7375 (tt0) REVERT: D 98 LYS cc_start: 0.7637 (pttt) cc_final: 0.7392 (pptt) REVERT: D 157 ASN cc_start: 0.7668 (t0) cc_final: 0.7359 (t0) REVERT: D 198 GLU cc_start: 0.6551 (tp30) cc_final: 0.6272 (tp30) REVERT: D 202 ARG cc_start: 0.6812 (mpp80) cc_final: 0.6570 (mpp80) REVERT: D 331 LEU cc_start: 0.5510 (OUTLIER) cc_final: 0.5231 (tt) REVERT: D 341 MET cc_start: 0.5435 (mmt) cc_final: 0.4999 (mmp) REVERT: E 24 ARG cc_start: 0.7988 (mtt-85) cc_final: 0.7376 (mtt180) REVERT: E 46 ASP cc_start: 0.8132 (t0) cc_final: 0.7672 (t0) REVERT: E 90 ILE cc_start: 0.7963 (mt) cc_final: 0.7708 (mt) REVERT: E 132 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8514 (t) REVERT: E 162 ARG cc_start: 0.7119 (mtp180) cc_final: 0.6875 (mtm180) REVERT: E 190 ASP cc_start: 0.7770 (m-30) cc_final: 0.7565 (m-30) REVERT: E 193 ASP cc_start: 0.6821 (m-30) cc_final: 0.6392 (m-30) REVERT: E 204 GLU cc_start: 0.7890 (mp0) cc_final: 0.7580 (mp0) REVERT: E 232 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8591 (mm) outliers start: 64 outliers final: 49 residues processed: 435 average time/residue: 0.2700 time to fit residues: 180.9792 Evaluate side-chains 460 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 403 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain A residue 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 195 LEU Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 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 138 MET Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 32 MET 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 112 MET Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 189 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 chunk 154 optimal weight: 0.1980 chunk 202 optimal weight: 0.0970 chunk 207 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 208 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 GLN G 90 GLN A 140 GLN B 288 ASN ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.204613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.162746 restraints weight = 21619.628| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 4.00 r_work: 0.3283 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18286 Z= 0.139 Angle : 0.589 9.553 24799 Z= 0.310 Chirality : 0.043 0.228 2805 Planarity : 0.004 0.047 3103 Dihedral : 4.540 24.505 2417 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.44 % Allowed : 21.04 % Favored : 76.52 % 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: 0.90 (0.18), residues: 2163 helix: 2.05 (0.16), residues: 958 sheet: 0.64 (0.25), residues: 456 loop : -1.40 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 36 HIS 0.005 0.001 HIS C 212 PHE 0.018 0.001 PHE B 39 TYR 0.037 0.001 TYR D 19 ARG 0.010 0.000 ARG E 165 Details of bonding type rmsd hydrogen bonds : bond 0.04925 ( 1048) hydrogen bonds : angle 4.57134 ( 3027) SS BOND : bond 0.00195 ( 4) SS BOND : angle 1.61065 ( 8) covalent geometry : bond 0.00309 (18282) covalent geometry : angle 0.58818 (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 472 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 423 time to evaluate : 2.055 Fit side-chains revert: symmetry clash REVERT: H 46 GLU cc_start: 0.6604 (tt0) cc_final: 0.6341 (tt0) REVERT: F 43 LYS cc_start: 0.8257 (mttm) cc_final: 0.8005 (ttmm) REVERT: F 100 TYR cc_start: 0.9143 (p90) cc_final: 0.8869 (p90) REVERT: A 53 PHE cc_start: 0.7948 (m-80) cc_final: 0.7670 (m-80) REVERT: A 54 ARG cc_start: 0.6602 (tmm160) cc_final: 0.6043 (tmm-80) REVERT: A 87 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8008 (mm) REVERT: A 95 GLN cc_start: 0.8504 (tt0) cc_final: 0.8266 (tt0) REVERT: A 152 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6383 (mt-10) REVERT: B 186 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7752 (tp30) REVERT: B 306 PHE cc_start: 0.6900 (OUTLIER) cc_final: 0.5448 (p90) REVERT: B 341 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.6870 (mpp) REVERT: C 98 LYS cc_start: 0.5573 (tmmt) cc_final: 0.5233 (tmmt) REVERT: C 115 TYR cc_start: 0.7006 (t80) cc_final: 0.6575 (t80) REVERT: C 139 PHE cc_start: 0.5921 (m-10) cc_final: 0.4974 (m-80) REVERT: C 198 GLU cc_start: 0.7003 (tp30) cc_final: 0.6707 (tp30) REVERT: C 244 GLU cc_start: 0.7742 (tp30) cc_final: 0.7222 (tp30) REVERT: C 263 ASP cc_start: 0.6967 (m-30) cc_final: 0.6729 (m-30) REVERT: C 313 MET cc_start: 0.4086 (ttp) cc_final: 0.3382 (ttp) REVERT: D 28 GLU cc_start: 0.7550 (mm-30) cc_final: 0.5902 (mt-10) REVERT: D 74 GLN cc_start: 0.7694 (tt0) cc_final: 0.7343 (tt0) REVERT: D 75 ARG cc_start: 0.7936 (ttt180) cc_final: 0.7677 (ttt180) REVERT: D 93 VAL cc_start: 0.8830 (t) cc_final: 0.8558 (t) REVERT: D 98 LYS cc_start: 0.7628 (pttt) cc_final: 0.7404 (pptt) REVERT: D 157 ASN cc_start: 0.7600 (t0) cc_final: 0.7279 (t0) REVERT: D 198 GLU cc_start: 0.6535 (tp30) cc_final: 0.6215 (tp30) REVERT: D 202 ARG cc_start: 0.6703 (mpp80) cc_final: 0.6429 (mpp80) REVERT: D 210 ARG cc_start: 0.8193 (mtp85) cc_final: 0.7919 (mtp85) REVERT: D 331 LEU cc_start: 0.5363 (OUTLIER) cc_final: 0.5089 (tt) REVERT: D 341 MET cc_start: 0.5656 (mmt) cc_final: 0.5202 (mmp) REVERT: E 24 ARG cc_start: 0.7921 (mtt-85) cc_final: 0.7300 (mtt180) REVERT: E 46 ASP cc_start: 0.8099 (t0) cc_final: 0.7655 (t0) REVERT: E 90 ILE cc_start: 0.7865 (mt) cc_final: 0.7634 (mt) REVERT: E 132 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8399 (t) REVERT: E 163 LYS cc_start: 0.8517 (tppt) cc_final: 0.8261 (tppt) REVERT: E 181 TYR cc_start: 0.8401 (m-80) cc_final: 0.8001 (m-80) REVERT: E 190 ASP cc_start: 0.7728 (m-30) cc_final: 0.7526 (m-30) REVERT: E 193 ASP cc_start: 0.6701 (m-30) cc_final: 0.6334 (m-30) REVERT: E 204 GLU cc_start: 0.7829 (mp0) cc_final: 0.7491 (mp0) REVERT: E 232 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8466 (mm) REVERT: E 334 MET cc_start: 0.4757 (mmt) cc_final: 0.4469 (mmt) outliers start: 49 outliers final: 37 residues processed: 444 average time/residue: 0.2822 time to fit residues: 191.6179 Evaluate side-chains 455 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 411 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain G residue 6 THR Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 90 GLN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 77 ASN Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain A residue 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 192 ILE Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 138 MET 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 27 optimal weight: 0.0870 chunk 63 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 134 optimal weight: 0.0170 chunk 142 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 213 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 43 optimal weight: 0.0870 chunk 102 optimal weight: 0.5980 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 90 GLN B 288 ASN ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.203631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.161689 restraints weight = 21739.157| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 3.96 r_work: 0.3296 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 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 = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18286 Z= 0.138 Angle : 0.593 8.605 24799 Z= 0.312 Chirality : 0.043 0.227 2805 Planarity : 0.004 0.047 3103 Dihedral : 4.500 24.412 2417 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.44 % Allowed : 21.09 % Favored : 76.47 % 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: 0.94 (0.18), residues: 2163 helix: 2.07 (0.16), residues: 958 sheet: 0.69 (0.25), residues: 455 loop : -1.38 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 36 HIS 0.004 0.001 HIS A 68 PHE 0.036 0.001 PHE D 251 TYR 0.034 0.001 TYR D 19 ARG 0.008 0.000 ARG E 165 Details of bonding type rmsd hydrogen bonds : bond 0.04878 ( 1048) hydrogen bonds : angle 4.54773 ( 3027) SS BOND : bond 0.00185 ( 4) SS BOND : angle 1.36057 ( 8) covalent geometry : bond 0.00303 (18282) covalent geometry : angle 0.59299 (24791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9979.77 seconds wall clock time: 173 minutes 14.08 seconds (10394.08 seconds total)