Starting phenix.real_space_refine on Mon Jun 16 16:08:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmk_41392/06_2025/8tmk_41392.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmk_41392/06_2025/8tmk_41392.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/8tmk_41392/06_2025/8tmk_41392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmk_41392/06_2025/8tmk_41392.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmk_41392/06_2025/8tmk_41392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmk_41392/06_2025/8tmk_41392.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= 0.039 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 3 5.21 5 S 65 5.16 5 C 11504 2.51 5 N 2894 2.21 5 O 3291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17757 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 971 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 809 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} 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: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2797 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain: "B" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2899 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "C" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2812 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 13, 'TRANS': 322} 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: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2797 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 13, 'TRANS': 320} 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: "D" 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: 11.46, per 1000 atoms: 0.65 Number of scatterers: 17757 At special positions: 0 Unit cell: (124.371, 141.379, 143.505, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 Mg 3 11.99 O 3291 8.00 N 2894 7.00 C 11504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " 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 25 " - pdb=" SG CYS F 99 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.08 Conformation dependent library (CDL) restraints added in 2.1 seconds 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4134 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 16 sheets defined 48.6% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'H' and resid 31 through 34 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.970A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.992A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.885A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 34 Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.579A pdb=" N SER A 49 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 51 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Proline residue: A 52 - end of helix removed outlier: 3.608A pdb=" N ASP A 55 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 81 removed outlier: 3.855A 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 156 Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 165 through 202 removed outlier: 3.632A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 237 Proline residue: A 227 - end of helix removed outlier: 3.837A pdb=" N GLU A 230 " --> pdb=" O TRP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 247 through 273 removed outlier: 3.546A pdb=" N PHE A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 283 Processing helix chain 'A' and resid 286 through 312 Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 325 through 349 Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.988A pdb=" N VAL B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 51 " --> pdb=" O VAL B 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 51' Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 69 through 80 removed outlier: 3.554A pdb=" N VAL B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.526A pdb=" N LYS B 164 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 202 removed outlier: 3.670A pdb=" N LEU B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU B 201 " --> pdb=" O GLU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 237 Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 312 removed outlier: 3.756A pdb=" N PHE B 251 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 325 through 346 Processing helix chain 'C' and resid 46 through 50 removed outlier: 3.647A pdb=" N SER C 49 " --> pdb=" O ASP C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 81 removed outlier: 3.903A 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 157 Processing helix chain 'C' and resid 165 through 202 Processing helix chain 'C' and resid 204 through 237 removed outlier: 3.573A pdb=" N GLN C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Proline residue: C 227 - end of helix removed outlier: 3.685A pdb=" N GLU C 230 " --> pdb=" O TRP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 281 removed outlier: 3.545A pdb=" N PHE C 251 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 300 removed outlier: 3.638A pdb=" N ILE C 300 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 312 Processing helix chain 'C' and resid 325 through 349 Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.503A pdb=" N SER D 49 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU D 51 " --> pdb=" O GLU D 48 " (cutoff:3.500A) Proline residue: D 52 - end of helix Processing helix chain 'D' and resid 69 through 80 removed outlier: 3.627A pdb=" N VAL D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 165 through 202 removed outlier: 3.526A pdb=" N LEU D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU D 198 " --> pdb=" O VAL D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 239 removed outlier: 3.509A pdb=" N VAL D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.745A pdb=" N VAL D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 removed outlier: 3.795A pdb=" N GLU D 244 " --> pdb=" O PRO D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 311 Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 326 through 348 Processing helix chain 'E' and resid 47 through 51 removed outlier: 3.572A pdb=" N VAL E 50 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 81 removed outlier: 3.506A 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: 3.601A pdb=" N LEU E 169 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR E 181 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE E 182 " --> pdb=" O VAL E 178 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL E 183 " --> pdb=" O ASP E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 237 removed outlier: 3.711A pdb=" N VAL E 208 " --> pdb=" O GLU E 204 " (cutoff:3.500A) Proline residue: E 227 - end of helix Processing helix chain 'E' and resid 247 through 251 Processing helix chain 'E' and resid 252 through 311 Proline residue: E 303 - end of helix Processing helix chain 'E' and resid 326 through 347 Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 61 through 63 removed outlier: 6.620A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS H 99 " --> pdb=" O TRP H 119 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TRP H 119 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG H 101 " --> pdb=" O ASP H 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 61 through 63 removed outlier: 6.620A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AA5, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.886A pdb=" N LEU L 12 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.490A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.529A 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 removed outlier: 3.537A pdb=" N VAL G 20 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.605A pdb=" N TYR G 88 " --> pdb=" O TYR G 37 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR G 37 " --> pdb=" O TYR G 88 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 6 through 10 Processing sheet with id=AB1, first strand: chain 'F' and resid 60 through 63 removed outlier: 3.919A pdb=" N SER F 60 " --> pdb=" O SER F 55 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER F 53 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE F 37 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER F 36 " --> pdb=" O SER F 102 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 60 through 63 removed outlier: 3.919A pdb=" N SER F 60 " --> pdb=" O SER F 55 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER F 53 " --> pdb=" O ILE F 37 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE F 37 " --> pdb=" O SER F 53 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER F 36 " --> pdb=" O SER F 102 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 39 through 44 removed outlier: 3.657A pdb=" N SER A 128 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 44 removed outlier: 3.721A pdb=" N ILE C 29 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU C 121 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP C 116 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU C 123 " --> pdb=" O THR C 114 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 39 through 44 Processing sheet with id=AB7, first strand: chain 'E' and resid 28 through 33 removed outlier: 6.056A pdb=" N THR E 60 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N MET E 138 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE E 62 " --> pdb=" O MET E 138 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU E 123 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR E 114 " --> pdb=" O GLU E 123 " (cutoff:3.500A) 1078 hydrogen bonds defined for protein. 3072 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.38 Time building geometry restraints manager: 4.89 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: 5542 1.34 - 1.46: 3002 1.46 - 1.57: 9498 1.57 - 1.69: 1 1.69 - 1.81: 117 Bond restraints: 18160 Sorted by residual: bond pdb=" CG PRO B 227 " pdb=" CD PRO B 227 " ideal model delta sigma weight residual 1.503 1.381 0.122 3.40e-02 8.65e+02 1.29e+01 bond pdb=" CB PRO B 227 " pdb=" CG PRO B 227 " ideal model delta sigma weight residual 1.492 1.605 -0.113 5.00e-02 4.00e+02 5.13e+00 bond pdb=" N PRO B 227 " pdb=" CD PRO B 227 " ideal model delta sigma weight residual 1.473 1.497 -0.024 1.40e-02 5.10e+03 2.94e+00 bond pdb=" CG LEU B 184 " pdb=" CD1 LEU B 184 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.78e+00 bond pdb=" N PRO B 227 " pdb=" CA PRO B 227 " ideal model delta sigma weight residual 1.471 1.451 0.020 1.32e-02 5.74e+03 2.22e+00 ... (remaining 18155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 24337 2.51 - 5.02: 258 5.02 - 7.53: 30 7.53 - 10.04: 5 10.04 - 12.55: 1 Bond angle restraints: 24631 Sorted by residual: angle pdb=" CA PRO B 227 " pdb=" N PRO B 227 " pdb=" CD PRO B 227 " ideal model delta sigma weight residual 112.00 99.45 12.55 1.40e+00 5.10e-01 8.03e+01 angle pdb=" N PRO B 227 " pdb=" CD PRO B 227 " pdb=" CG PRO B 227 " ideal model delta sigma weight residual 103.20 93.18 10.02 1.50e+00 4.44e-01 4.46e+01 angle pdb=" C LEU C 235 " pdb=" N TYR C 236 " pdb=" CA TYR C 236 " ideal model delta sigma weight residual 122.53 113.80 8.73 1.92e+00 2.71e-01 2.07e+01 angle pdb=" C VAL D 343 " pdb=" N TYR D 344 " pdb=" CA TYR D 344 " ideal model delta sigma weight residual 121.58 114.53 7.05 1.95e+00 2.63e-01 1.31e+01 angle pdb=" C ASP B 179 " pdb=" N ASP B 180 " pdb=" CA ASP B 180 " ideal model delta sigma weight residual 121.14 115.15 5.99 1.75e+00 3.27e-01 1.17e+01 ... (remaining 24626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9694 17.96 - 35.92: 967 35.92 - 53.89: 170 53.89 - 71.85: 25 71.85 - 89.81: 24 Dihedral angle restraints: 10880 sinusoidal: 4470 harmonic: 6410 Sorted by residual: dihedral pdb=" CB CYS L 24 " pdb=" SG CYS L 24 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 161.29 -68.29 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CA LYS C 349 " pdb=" C LYS C 349 " pdb=" N TRP C 350 " pdb=" CA TRP C 350 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+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 93.00 127.98 -34.98 1 1.00e+01 1.00e-02 1.73e+01 ... (remaining 10877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1765 0.036 - 0.072: 710 0.072 - 0.108: 250 0.108 - 0.143: 55 0.143 - 0.179: 11 Chirality restraints: 2791 Sorted by residual: chirality pdb=" CB ILE G 3 " pdb=" CA ILE G 3 " pdb=" CG1 ILE G 3 " pdb=" CG2 ILE G 3 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CA ILE C 64 " pdb=" N ILE C 64 " pdb=" C ILE C 64 " pdb=" CB ILE C 64 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CB VAL E 239 " pdb=" CA VAL E 239 " pdb=" CG1 VAL E 239 " pdb=" CG2 VAL E 239 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 2788 not shown) Planarity restraints: 3081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 226 " 0.097 5.00e-02 4.00e+02 1.37e-01 3.00e+01 pdb=" N PRO B 227 " -0.236 5.00e-02 4.00e+02 pdb=" CA PRO B 227 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO B 227 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 96 " 0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO E 97 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO E 97 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 97 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 16 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO F 17 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO F 17 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 17 " -0.029 5.00e-02 4.00e+02 ... (remaining 3078 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 330 2.68 - 3.24: 17522 3.24 - 3.79: 28227 3.79 - 4.35: 36826 4.35 - 4.90: 61538 Nonbonded interactions: 144443 Sorted by model distance: nonbonded pdb=" OD1 ASN B 314 " pdb="MG MG B 401 " model vdw 2.128 2.170 nonbonded pdb=" OD1 ASN B 288 " pdb=" OG1 THR C 287 " model vdw 2.129 3.040 nonbonded pdb=" OG SER B 281 " pdb=" O LEU C 280 " model vdw 2.134 3.040 nonbonded pdb=" OD1 ASN D 288 " pdb=" OG1 THR E 287 " model vdw 2.168 3.040 nonbonded pdb=" O ARG E 54 " pdb=" NZ LYS E 133 " model vdw 2.188 3.120 ... (remaining 144438 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' 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' } ncs_group { reference = chain 'F' selection = (chain 'H' and resid 4 through 126) } ncs_group { reference = chain 'G' selection = (chain 'L' and resid 2 through 107) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.170 Process input model: 41.390 Find NCS groups from input model: 0.860 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 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 : 0.005 0.122 18164 Z= 0.193 Angle : 0.660 12.548 24639 Z= 0.350 Chirality : 0.045 0.179 2791 Planarity : 0.005 0.137 3081 Dihedral : 14.866 89.810 6734 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 0.05 % Allowed : 0.35 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.18), residues: 2148 helix: 1.78 (0.16), residues: 974 sheet: 0.71 (0.25), residues: 427 loop : -1.54 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 350 HIS 0.003 0.001 HIS E 68 PHE 0.024 0.002 PHE B 315 TYR 0.023 0.002 TYR D 344 ARG 0.011 0.001 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.11047 ( 1053) hydrogen bonds : angle 5.84488 ( 3072) SS BOND : bond 0.00234 ( 4) SS BOND : angle 1.22949 ( 8) covalent geometry : bond 0.00456 (18160) covalent geometry : angle 0.65996 (24631) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 395 time to evaluate : 2.008 Fit side-chains REVERT: L 46 LYS cc_start: 0.8352 (ttmm) cc_final: 0.8090 (ttmm) REVERT: L 108 LYS cc_start: 0.3329 (mmtt) cc_final: 0.2671 (mmtt) REVERT: A 270 ASP cc_start: 0.6625 (m-30) cc_final: 0.6326 (m-30) REVERT: B 160 ILE cc_start: 0.8421 (mt) cc_final: 0.8217 (mt) REVERT: C 193 ASP cc_start: 0.8231 (t70) cc_final: 0.8020 (t70) REVERT: C 230 GLU cc_start: 0.6788 (tt0) cc_final: 0.6532 (tt0) REVERT: D 186 GLU cc_start: 0.7810 (tt0) cc_final: 0.7460 (tt0) REVERT: D 243 ILE cc_start: 0.8659 (mm) cc_final: 0.8239 (mm) REVERT: E 267 THR cc_start: 0.8194 (p) cc_final: 0.7977 (t) outliers start: 1 outliers final: 1 residues processed: 396 average time/residue: 0.2887 time to fit residues: 174.2869 Evaluate side-chains 364 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 157 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 166 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 192 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 ASN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.185614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.145587 restraints weight = 20979.921| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.16 r_work: 0.3018 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18164 Z= 0.194 Angle : 0.628 8.797 24639 Z= 0.326 Chirality : 0.045 0.220 2791 Planarity : 0.005 0.065 3081 Dihedral : 4.552 30.334 2403 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.40 % Allowed : 9.63 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.18), residues: 2148 helix: 1.98 (0.16), residues: 981 sheet: 0.65 (0.24), residues: 446 loop : -1.47 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 350 HIS 0.005 0.001 HIS A 83 PHE 0.017 0.001 PHE B 315 TYR 0.023 0.002 TYR D 279 ARG 0.006 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.05845 ( 1053) hydrogen bonds : angle 4.82591 ( 3072) SS BOND : bond 0.00163 ( 4) SS BOND : angle 1.19759 ( 8) covalent geometry : bond 0.00452 (18160) covalent geometry : angle 0.62782 (24631) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 371 time to evaluate : 1.814 Fit side-chains REVERT: H 9 GLU cc_start: 0.8355 (pt0) cc_final: 0.8120 (pt0) REVERT: L 108 LYS cc_start: 0.4191 (mmtt) cc_final: 0.3262 (mmtt) REVERT: A 216 ARG cc_start: 0.7866 (mmm-85) cc_final: 0.7305 (mtp85) REVERT: A 270 ASP cc_start: 0.7462 (m-30) cc_final: 0.7008 (m-30) REVERT: A 292 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7809 (mmtm) REVERT: D 121 GLU cc_start: 0.6992 (pm20) cc_final: 0.6628 (pm20) REVERT: D 186 GLU cc_start: 0.8452 (tt0) cc_final: 0.8249 (tt0) REVERT: D 243 ILE cc_start: 0.8812 (mm) cc_final: 0.8481 (mm) REVERT: E 30 GLU cc_start: 0.6100 (pm20) cc_final: 0.5862 (pm20) REVERT: E 96 ARG cc_start: 0.7339 (ttp80) cc_final: 0.6832 (ttp80) REVERT: E 155 ARG cc_start: 0.6181 (mtp-110) cc_final: 0.5761 (mtp-110) outliers start: 28 outliers final: 22 residues processed: 385 average time/residue: 0.2806 time to fit residues: 164.1888 Evaluate side-chains 380 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 358 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 279 TYR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 310 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 177 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN E 213 GLN ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.188417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.148268 restraints weight = 20791.688| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.94 r_work: 0.3065 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18164 Z= 0.179 Angle : 0.599 7.985 24639 Z= 0.311 Chirality : 0.044 0.215 2791 Planarity : 0.004 0.051 3081 Dihedral : 4.452 19.104 2401 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.21 % Allowed : 12.64 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.18), residues: 2148 helix: 2.09 (0.16), residues: 980 sheet: 0.67 (0.25), residues: 426 loop : -1.44 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 350 HIS 0.005 0.001 HIS B 257 PHE 0.018 0.001 PHE B 315 TYR 0.019 0.001 TYR H 106 ARG 0.011 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.05556 ( 1053) hydrogen bonds : angle 4.65549 ( 3072) SS BOND : bond 0.00134 ( 4) SS BOND : angle 0.93888 ( 8) covalent geometry : bond 0.00416 (18160) covalent geometry : angle 0.59850 (24631) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 385 time to evaluate : 1.828 Fit side-chains REVERT: H 9 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8068 (pt0) REVERT: L 108 LYS cc_start: 0.3989 (mmtt) cc_final: 0.3147 (mmtt) REVERT: F 49 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8270 (tm-30) REVERT: A 39 PHE cc_start: 0.7268 (p90) cc_final: 0.6906 (p90) REVERT: A 216 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7334 (mtp85) REVERT: A 267 THR cc_start: 0.8809 (t) cc_final: 0.8405 (m) REVERT: A 270 ASP cc_start: 0.7177 (m-30) cc_final: 0.6691 (m-30) REVERT: A 275 LEU cc_start: 0.8072 (mt) cc_final: 0.7648 (mt) REVERT: D 186 GLU cc_start: 0.8388 (tt0) cc_final: 0.8128 (tt0) REVERT: D 243 ILE cc_start: 0.8798 (mm) cc_final: 0.8496 (mm) REVERT: D 260 GLN cc_start: 0.7946 (mt0) cc_final: 0.7606 (tt0) REVERT: E 30 GLU cc_start: 0.6217 (pm20) cc_final: 0.5900 (pm20) REVERT: E 96 ARG cc_start: 0.7007 (ttp80) cc_final: 0.6297 (ttt180) REVERT: E 141 GLU cc_start: 0.5910 (tt0) cc_final: 0.5701 (tt0) REVERT: E 155 ARG cc_start: 0.6169 (mtp-110) cc_final: 0.5779 (mtp180) REVERT: E 198 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6604 (mt-10) REVERT: E 341 MET cc_start: 0.6361 (mtt) cc_final: 0.5944 (mtp) outliers start: 44 outliers final: 36 residues processed: 405 average time/residue: 0.2866 time to fit residues: 177.1893 Evaluate side-chains 402 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 365 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 310 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 24 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 189 optimal weight: 0.3980 chunk 91 optimal weight: 0.1980 chunk 74 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 150 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** E 288 ASN ** 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 = 0.3931 r_free = 0.3931 target = 0.188458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.147678 restraints weight = 20824.397| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.79 r_work: 0.3079 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18164 Z= 0.157 Angle : 0.578 8.679 24639 Z= 0.300 Chirality : 0.043 0.225 2791 Planarity : 0.004 0.065 3081 Dihedral : 4.380 18.124 2401 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.76 % Allowed : 14.34 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.18), residues: 2148 helix: 2.18 (0.16), residues: 981 sheet: 0.67 (0.25), residues: 428 loop : -1.43 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 350 HIS 0.004 0.001 HIS D 212 PHE 0.017 0.001 PHE F 71 TYR 0.017 0.001 TYR H 106 ARG 0.006 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.05350 ( 1053) hydrogen bonds : angle 4.55735 ( 3072) SS BOND : bond 0.00145 ( 4) SS BOND : angle 0.73041 ( 8) covalent geometry : bond 0.00357 (18160) covalent geometry : angle 0.57802 (24631) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 373 time to evaluate : 1.943 Fit side-chains REVERT: H 9 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8138 (pt0) REVERT: L 108 LYS cc_start: 0.4064 (mmtt) cc_final: 0.3305 (mmtt) REVERT: F 49 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8229 (tm-30) REVERT: A 39 PHE cc_start: 0.7290 (p90) cc_final: 0.6926 (p90) REVERT: A 126 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7238 (tp40) REVERT: A 216 ARG cc_start: 0.7859 (mmm-85) cc_final: 0.7297 (mtp85) REVERT: A 267 THR cc_start: 0.8829 (t) cc_final: 0.8385 (m) REVERT: A 270 ASP cc_start: 0.7146 (m-30) cc_final: 0.6634 (m-30) REVERT: A 275 LEU cc_start: 0.8168 (mt) cc_final: 0.7783 (mt) REVERT: B 334 MET cc_start: 0.6604 (OUTLIER) cc_final: 0.6349 (ttt) REVERT: C 91 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7764 (mm) REVERT: C 291 MET cc_start: 0.7981 (tpp) cc_final: 0.7779 (tpp) REVERT: D 155 ARG cc_start: 0.8664 (mtt180) cc_final: 0.8386 (mtt180) REVERT: D 164 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8510 (mttp) REVERT: D 198 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6351 (tt0) REVERT: D 243 ILE cc_start: 0.8792 (mm) cc_final: 0.8503 (mm) REVERT: D 260 GLN cc_start: 0.7957 (mt0) cc_final: 0.7680 (tt0) REVERT: D 344 TYR cc_start: 0.5415 (OUTLIER) cc_final: 0.2642 (p90) REVERT: E 30 GLU cc_start: 0.6225 (pm20) cc_final: 0.5913 (pm20) REVERT: E 141 GLU cc_start: 0.5999 (tt0) cc_final: 0.5793 (tt0) REVERT: E 155 ARG cc_start: 0.6164 (mtp-110) cc_final: 0.5768 (mtp-110) REVERT: E 184 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7657 (mp) REVERT: E 341 MET cc_start: 0.6333 (mtt) cc_final: 0.5999 (mtp) outliers start: 55 outliers final: 41 residues processed: 403 average time/residue: 0.2721 time to fit residues: 169.4902 Evaluate side-chains 406 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 360 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 310 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 94 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 99 optimal weight: 0.2980 chunk 170 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 GLN A 260 GLN ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.185927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.146260 restraints weight = 21039.927| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.10 r_work: 0.3018 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18164 Z= 0.185 Angle : 0.597 8.781 24639 Z= 0.309 Chirality : 0.044 0.245 2791 Planarity : 0.004 0.049 3081 Dihedral : 4.416 17.829 2401 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.41 % Allowed : 14.99 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.18), residues: 2148 helix: 2.10 (0.16), residues: 981 sheet: 0.62 (0.25), residues: 427 loop : -1.45 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 350 HIS 0.004 0.001 HIS B 257 PHE 0.018 0.001 PHE F 71 TYR 0.020 0.001 TYR H 106 ARG 0.007 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.05479 ( 1053) hydrogen bonds : angle 4.56017 ( 3072) SS BOND : bond 0.00148 ( 4) SS BOND : angle 0.84221 ( 8) covalent geometry : bond 0.00434 (18160) covalent geometry : angle 0.59680 (24631) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 365 time to evaluate : 2.114 Fit side-chains REVERT: H 9 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8101 (pt0) REVERT: L 108 LYS cc_start: 0.4234 (mmtt) cc_final: 0.3412 (mmtt) REVERT: F 49 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8257 (tm-30) REVERT: A 39 PHE cc_start: 0.7293 (p90) cc_final: 0.6974 (p90) REVERT: A 126 GLN cc_start: 0.7959 (tm130) cc_final: 0.7290 (tp40) REVERT: A 216 ARG cc_start: 0.7924 (mmm-85) cc_final: 0.7364 (mtp85) REVERT: A 267 THR cc_start: 0.8892 (t) cc_final: 0.8452 (m) REVERT: A 270 ASP cc_start: 0.7335 (m-30) cc_final: 0.6886 (m-30) REVERT: B 334 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.6371 (ttt) REVERT: C 204 GLU cc_start: 0.5244 (OUTLIER) cc_final: 0.4671 (mm-30) REVERT: D 122 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8472 (pp) REVERT: D 164 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8498 (mttp) REVERT: D 198 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6434 (tt0) REVERT: D 243 ILE cc_start: 0.8807 (mm) cc_final: 0.8503 (mm) REVERT: D 344 TYR cc_start: 0.5466 (OUTLIER) cc_final: 0.2237 (p90) REVERT: D 345 PHE cc_start: 0.6272 (OUTLIER) cc_final: 0.5933 (m-10) REVERT: E 30 GLU cc_start: 0.6277 (pm20) cc_final: 0.5967 (pm20) REVERT: E 141 GLU cc_start: 0.6036 (tt0) cc_final: 0.5813 (tt0) REVERT: E 155 ARG cc_start: 0.6211 (mtp-110) cc_final: 0.5813 (mtp-110) REVERT: E 184 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7704 (mp) REVERT: E 206 GLU cc_start: 0.6750 (pm20) cc_final: 0.6274 (pm20) REVERT: E 291 MET cc_start: 0.8657 (mmm) cc_final: 0.8296 (tpt) REVERT: E 341 MET cc_start: 0.6344 (mtt) cc_final: 0.5959 (mtp) outliers start: 68 outliers final: 51 residues processed: 403 average time/residue: 0.2813 time to fit residues: 173.8619 Evaluate side-chains 410 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 352 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 345 PHE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 310 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 23 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 167 optimal weight: 0.9980 chunk 161 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** E 288 ASN ** 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 = 0.3885 r_free = 0.3885 target = 0.183795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.144837 restraints weight = 20928.365| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.28 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18164 Z= 0.198 Angle : 0.609 8.498 24639 Z= 0.316 Chirality : 0.044 0.251 2791 Planarity : 0.005 0.074 3081 Dihedral : 4.474 18.054 2401 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.51 % Allowed : 15.90 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.18), residues: 2148 helix: 2.02 (0.16), residues: 980 sheet: 0.54 (0.25), residues: 437 loop : -1.48 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 350 HIS 0.003 0.001 HIS B 257 PHE 0.017 0.001 PHE C 301 TYR 0.021 0.002 TYR H 106 ARG 0.011 0.001 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.05557 ( 1053) hydrogen bonds : angle 4.58799 ( 3072) SS BOND : bond 0.00155 ( 4) SS BOND : angle 0.84567 ( 8) covalent geometry : bond 0.00466 (18160) covalent geometry : angle 0.60918 (24631) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 362 time to evaluate : 2.364 Fit side-chains REVERT: H 9 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7783 (pt0) REVERT: L 108 LYS cc_start: 0.3509 (mmtt) cc_final: 0.2953 (mmtt) REVERT: F 49 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8182 (tm-30) REVERT: A 39 PHE cc_start: 0.7473 (p90) cc_final: 0.7229 (p90) REVERT: A 126 GLN cc_start: 0.7845 (tm130) cc_final: 0.7595 (tm-30) REVERT: A 216 ARG cc_start: 0.7624 (mmm-85) cc_final: 0.7221 (mtp85) REVERT: A 267 THR cc_start: 0.8934 (t) cc_final: 0.8394 (m) REVERT: A 270 ASP cc_start: 0.6747 (m-30) cc_final: 0.6368 (m-30) REVERT: C 22 LYS cc_start: 0.7904 (pptt) cc_final: 0.7699 (pptt) REVERT: C 204 GLU cc_start: 0.5166 (OUTLIER) cc_final: 0.4932 (mm-30) REVERT: D 122 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8485 (pp) REVERT: D 198 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6451 (tt0) REVERT: D 243 ILE cc_start: 0.8670 (mm) cc_final: 0.8344 (mm) REVERT: D 344 TYR cc_start: 0.5662 (OUTLIER) cc_final: 0.2885 (p90) REVERT: D 345 PHE cc_start: 0.6755 (OUTLIER) cc_final: 0.6453 (m-10) REVERT: E 100 GLU cc_start: 0.6115 (mt-10) cc_final: 0.5554 (mt-10) REVERT: E 155 ARG cc_start: 0.6212 (mtp-110) cc_final: 0.5928 (mtp-110) REVERT: E 184 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7825 (mp) REVERT: E 341 MET cc_start: 0.6496 (mtt) cc_final: 0.6272 (mtp) outliers start: 70 outliers final: 57 residues processed: 397 average time/residue: 0.3066 time to fit residues: 190.0874 Evaluate side-chains 419 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 356 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 345 PHE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 310 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 52 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 58 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 36 optimal weight: 0.0050 chunk 166 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** E 288 ASN ** 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 = 0.3902 r_free = 0.3902 target = 0.185692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.145062 restraints weight = 20968.743| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.11 r_work: 0.3051 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18164 Z= 0.148 Angle : 0.581 8.526 24639 Z= 0.298 Chirality : 0.043 0.271 2791 Planarity : 0.004 0.049 3081 Dihedral : 4.338 17.093 2401 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.16 % Allowed : 17.00 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.18), residues: 2148 helix: 2.15 (0.16), residues: 980 sheet: 0.60 (0.25), residues: 423 loop : -1.39 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 350 HIS 0.004 0.001 HIS H 38 PHE 0.014 0.001 PHE C 301 TYR 0.016 0.001 TYR H 106 ARG 0.008 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.05195 ( 1053) hydrogen bonds : angle 4.48210 ( 3072) SS BOND : bond 0.00309 ( 4) SS BOND : angle 1.02952 ( 8) covalent geometry : bond 0.00334 (18160) covalent geometry : angle 0.58094 (24631) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 370 time to evaluate : 1.968 Fit side-chains REVERT: H 9 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8122 (pt0) REVERT: L 108 LYS cc_start: 0.4066 (mmtt) cc_final: 0.3184 (mmtt) REVERT: F 30 PHE cc_start: 0.8532 (p90) cc_final: 0.8269 (p90) REVERT: F 49 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8213 (tm-30) REVERT: A 189 ASP cc_start: 0.8779 (t0) cc_final: 0.8445 (t0) REVERT: A 216 ARG cc_start: 0.7875 (mmm-85) cc_final: 0.7307 (mtp85) REVERT: A 267 THR cc_start: 0.8913 (t) cc_final: 0.8363 (m) REVERT: A 270 ASP cc_start: 0.7238 (m-30) cc_final: 0.6775 (m-30) REVERT: A 318 MET cc_start: 0.8198 (tmm) cc_final: 0.7887 (tmm) REVERT: B 232 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8456 (mm) REVERT: C 22 LYS cc_start: 0.7994 (pptt) cc_final: 0.7748 (pptt) REVERT: C 91 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7979 (mm) REVERT: C 204 GLU cc_start: 0.5176 (OUTLIER) cc_final: 0.4682 (mp0) REVERT: D 122 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8357 (pp) REVERT: D 198 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6306 (tt0) REVERT: D 243 ILE cc_start: 0.8745 (mm) cc_final: 0.8477 (mm) REVERT: D 276 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8130 (mt) REVERT: D 344 TYR cc_start: 0.5595 (OUTLIER) cc_final: 0.2594 (p90) REVERT: D 345 PHE cc_start: 0.6444 (OUTLIER) cc_final: 0.6106 (m-10) REVERT: E 100 GLU cc_start: 0.6273 (mt-10) cc_final: 0.5643 (mt-10) REVERT: E 155 ARG cc_start: 0.6162 (mtp-110) cc_final: 0.5765 (mtp-110) REVERT: E 184 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7703 (mp) REVERT: E 341 MET cc_start: 0.6268 (mtt) cc_final: 0.5859 (mtp) outliers start: 63 outliers final: 45 residues processed: 403 average time/residue: 0.2794 time to fit residues: 174.5848 Evaluate side-chains 403 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 349 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 345 PHE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 310 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 44 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 201 optimal weight: 0.3980 chunk 62 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** E 288 ASN ** 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 = 0.3931 r_free = 0.3931 target = 0.188339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.148639 restraints weight = 20757.360| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.96 r_work: 0.3068 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18164 Z= 0.163 Angle : 0.602 8.788 24639 Z= 0.308 Chirality : 0.044 0.285 2791 Planarity : 0.004 0.073 3081 Dihedral : 4.358 16.792 2401 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.16 % Allowed : 17.70 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.18), residues: 2148 helix: 2.11 (0.16), residues: 980 sheet: 0.60 (0.25), residues: 422 loop : -1.43 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 350 HIS 0.003 0.001 HIS B 257 PHE 0.027 0.001 PHE A 39 TYR 0.018 0.001 TYR H 106 ARG 0.015 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.05239 ( 1053) hydrogen bonds : angle 4.47581 ( 3072) SS BOND : bond 0.00164 ( 4) SS BOND : angle 1.14344 ( 8) covalent geometry : bond 0.00376 (18160) covalent geometry : angle 0.60220 (24631) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 357 time to evaluate : 1.957 Fit side-chains REVERT: H 9 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8044 (pt0) REVERT: L 108 LYS cc_start: 0.4104 (mmtt) cc_final: 0.3229 (mmtt) REVERT: F 30 PHE cc_start: 0.8523 (p90) cc_final: 0.8248 (p90) REVERT: F 49 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8254 (tm-30) REVERT: A 40 ARG cc_start: 0.6704 (ttt-90) cc_final: 0.6491 (tmt170) REVERT: A 267 THR cc_start: 0.8895 (t) cc_final: 0.8525 (t) REVERT: A 270 ASP cc_start: 0.7227 (m-30) cc_final: 0.6787 (m-30) REVERT: A 291 MET cc_start: 0.8499 (mmm) cc_final: 0.7781 (mmt) REVERT: A 318 MET cc_start: 0.8137 (tmm) cc_final: 0.7828 (tmm) REVERT: B 232 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8512 (mm) REVERT: C 22 LYS cc_start: 0.8006 (pptt) cc_final: 0.7716 (pptt) REVERT: C 204 GLU cc_start: 0.5220 (OUTLIER) cc_final: 0.4742 (mp0) REVERT: D 122 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8364 (pp) REVERT: D 198 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6353 (tt0) REVERT: D 243 ILE cc_start: 0.8751 (mm) cc_final: 0.8480 (mm) REVERT: D 276 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8135 (mt) REVERT: D 344 TYR cc_start: 0.5543 (OUTLIER) cc_final: 0.2550 (p90) REVERT: D 345 PHE cc_start: 0.6493 (OUTLIER) cc_final: 0.6157 (m-10) REVERT: E 100 GLU cc_start: 0.6302 (mt-10) cc_final: 0.5665 (mt-10) REVERT: E 155 ARG cc_start: 0.6163 (mtp-110) cc_final: 0.5779 (mtp-110) REVERT: E 184 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7709 (mp) REVERT: E 341 MET cc_start: 0.6288 (mtt) cc_final: 0.5869 (mtp) outliers start: 63 outliers final: 51 residues processed: 391 average time/residue: 0.2692 time to fit residues: 163.1326 Evaluate side-chains 407 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 348 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 345 PHE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 310 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 66 optimal weight: 0.0020 chunk 206 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 HIS ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.184921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.145526 restraints weight = 21071.734| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.36 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18164 Z= 0.170 Angle : 0.611 8.874 24639 Z= 0.313 Chirality : 0.044 0.310 2791 Planarity : 0.004 0.052 3081 Dihedral : 4.370 16.878 2401 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.16 % Allowed : 18.56 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.18), residues: 2148 helix: 2.08 (0.16), residues: 980 sheet: 0.61 (0.25), residues: 421 loop : -1.41 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 350 HIS 0.004 0.001 HIS B 257 PHE 0.024 0.001 PHE A 39 TYR 0.019 0.001 TYR H 106 ARG 0.011 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.05278 ( 1053) hydrogen bonds : angle 4.49621 ( 3072) SS BOND : bond 0.00162 ( 4) SS BOND : angle 1.12260 ( 8) covalent geometry : bond 0.00397 (18160) covalent geometry : angle 0.61057 (24631) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 356 time to evaluate : 1.947 Fit side-chains REVERT: H 9 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7755 (pt0) REVERT: L 108 LYS cc_start: 0.3465 (mmtt) cc_final: 0.2821 (mmtt) REVERT: F 30 PHE cc_start: 0.8479 (p90) cc_final: 0.8261 (p90) REVERT: F 49 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8226 (tm-30) REVERT: A 267 THR cc_start: 0.8899 (t) cc_final: 0.8567 (t) REVERT: A 270 ASP cc_start: 0.6729 (m-30) cc_final: 0.6405 (m-30) REVERT: A 313 MET cc_start: 0.6501 (mmm) cc_final: 0.6081 (mmm) REVERT: B 232 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8579 (mm) REVERT: C 22 LYS cc_start: 0.7882 (pptt) cc_final: 0.7637 (pptt) REVERT: C 91 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8197 (mm) REVERT: D 122 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8391 (pp) REVERT: D 198 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6433 (tt0) REVERT: D 243 ILE cc_start: 0.8601 (mm) cc_final: 0.8311 (mm) REVERT: D 276 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8039 (mt) REVERT: D 344 TYR cc_start: 0.5734 (OUTLIER) cc_final: 0.3178 (p90) REVERT: D 345 PHE cc_start: 0.6693 (OUTLIER) cc_final: 0.6402 (m-10) REVERT: E 100 GLU cc_start: 0.6169 (mt-10) cc_final: 0.5606 (mt-10) REVERT: E 155 ARG cc_start: 0.6191 (mtp-110) cc_final: 0.5908 (mtp-110) REVERT: E 184 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7847 (mp) outliers start: 63 outliers final: 51 residues processed: 390 average time/residue: 0.2782 time to fit residues: 168.8916 Evaluate side-chains 412 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 353 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 345 PHE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 310 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.3980 chunk 133 optimal weight: 0.6980 chunk 171 optimal weight: 0.7980 chunk 211 optimal weight: 5.9990 chunk 138 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** E 288 ASN ** 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 = 0.3890 r_free = 0.3890 target = 0.184572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.145727 restraints weight = 20876.647| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 3.32 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18164 Z= 0.172 Angle : 0.626 9.936 24639 Z= 0.320 Chirality : 0.045 0.319 2791 Planarity : 0.004 0.054 3081 Dihedral : 4.402 19.392 2401 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.06 % Allowed : 19.01 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2148 helix: 2.05 (0.16), residues: 980 sheet: 0.60 (0.25), residues: 422 loop : -1.44 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 350 HIS 0.004 0.001 HIS B 257 PHE 0.024 0.001 PHE A 39 TYR 0.019 0.001 TYR H 106 ARG 0.010 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.05285 ( 1053) hydrogen bonds : angle 4.50161 ( 3072) SS BOND : bond 0.00163 ( 4) SS BOND : angle 1.11373 ( 8) covalent geometry : bond 0.00402 (18160) covalent geometry : angle 0.62613 (24631) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 357 time to evaluate : 1.838 Fit side-chains REVERT: H 9 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7758 (pt0) REVERT: L 108 LYS cc_start: 0.3489 (mmtt) cc_final: 0.2838 (mmtt) REVERT: F 30 PHE cc_start: 0.8480 (p90) cc_final: 0.8257 (p90) REVERT: F 49 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8218 (tm-30) REVERT: A 267 THR cc_start: 0.8875 (t) cc_final: 0.8535 (t) REVERT: A 270 ASP cc_start: 0.6746 (m-30) cc_final: 0.6412 (m-30) REVERT: A 313 MET cc_start: 0.6466 (mmm) cc_final: 0.6048 (mmm) REVERT: B 232 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8598 (mm) REVERT: C 22 LYS cc_start: 0.7898 (pptt) cc_final: 0.7639 (pptt) REVERT: C 91 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8145 (mm) REVERT: D 122 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8399 (pp) REVERT: D 198 GLU cc_start: 0.6727 (mt-10) cc_final: 0.6429 (tt0) REVERT: D 243 ILE cc_start: 0.8612 (mm) cc_final: 0.8316 (mm) REVERT: D 276 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8046 (mt) REVERT: D 291 MET cc_start: 0.7566 (mtt) cc_final: 0.7169 (ttt) REVERT: D 344 TYR cc_start: 0.5748 (OUTLIER) cc_final: 0.3187 (p90) REVERT: D 345 PHE cc_start: 0.6647 (OUTLIER) cc_final: 0.6380 (m-10) REVERT: E 100 GLU cc_start: 0.6165 (mt-10) cc_final: 0.5607 (mt-10) REVERT: E 155 ARG cc_start: 0.6214 (mtp-110) cc_final: 0.5930 (mtp-110) outliers start: 61 outliers final: 49 residues processed: 387 average time/residue: 0.2763 time to fit residues: 166.0224 Evaluate side-chains 407 residues out of total 1994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 351 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 GLU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 345 PHE Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 310 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 188 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 202 optimal weight: 0.5980 chunk 186 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN ** E 288 ASN ** 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 = 0.3894 r_free = 0.3894 target = 0.184952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.146388 restraints weight = 20917.674| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.31 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18164 Z= 0.177 Angle : 0.629 8.466 24639 Z= 0.322 Chirality : 0.045 0.319 2791 Planarity : 0.004 0.054 3081 Dihedral : 4.410 19.511 2401 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.01 % Allowed : 18.96 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2148 helix: 1.99 (0.16), residues: 979 sheet: 0.59 (0.25), residues: 421 loop : -1.41 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 350 HIS 0.004 0.001 HIS B 257 PHE 0.024 0.001 PHE A 39 TYR 0.019 0.001 TYR H 106 ARG 0.009 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.05356 ( 1053) hydrogen bonds : angle 4.53313 ( 3072) SS BOND : bond 0.00176 ( 4) SS BOND : angle 1.13791 ( 8) covalent geometry : bond 0.00416 (18160) covalent geometry : angle 0.62926 (24631) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8661.75 seconds wall clock time: 150 minutes 31.18 seconds (9031.18 seconds total)