Starting phenix.real_space_refine on Fri Feb 6 08:21:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hhr_52174/02_2026/9hhr_52174.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hhr_52174/02_2026/9hhr_52174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hhr_52174/02_2026/9hhr_52174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hhr_52174/02_2026/9hhr_52174.map" model { file = "/net/cci-nas-00/data/ceres_data/9hhr_52174/02_2026/9hhr_52174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hhr_52174/02_2026/9hhr_52174.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.049 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 9709 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: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 9831 2.51 5 N 2577 2.21 5 O 2997 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15492 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3364 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 26, 'TRANS': 399} Chain: "B" Number of atoms: 3364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3364 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 26, 'TRANS': 399} Chain: "C" Number of atoms: 3364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3364 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 26, 'TRANS': 399} Chain: "D" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "E" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 829 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "F" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 829 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 829 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "L" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Time building chain proxies: 3.62, per 1000 atoms: 0.23 Number of scatterers: 15492 At special positions: 0 Unit cell: (136.08, 136.08, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2997 8.00 N 2577 7.00 C 9831 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 158 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 224 " distance=2.03 Simple disulfide: pdb=" SG CYS A 219 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 158 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 219 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 158 " distance=2.03 Simple disulfide: pdb=" SG CYS C 177 " - pdb=" SG CYS C 224 " distance=2.03 Simple disulfide: pdb=" SG CYS C 219 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 607.2 milliseconds 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 35 sheets defined 15.9% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 88 through 101 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.756A pdb=" N ALA A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG A 249 " --> pdb=" O PHE A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 294 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 383 through 400 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.698A pdb=" N SER B 28 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 100 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 172 through 179 removed outlier: 3.504A pdb=" N SER B 179 " --> pdb=" O GLY B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.715A pdb=" N LEU B 198 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 249 removed outlier: 3.754A pdb=" N ARG B 249 " --> pdb=" O PHE B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 294 removed outlier: 3.546A pdb=" N ILE B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.693A pdb=" N TYR B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 383 through 400 Processing helix chain 'C' and resid 88 through 101 removed outlier: 3.558A pdb=" N SER C 95 " --> pdb=" O GLN C 91 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN C 101 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 172 through 179 Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.663A pdb=" N ARG C 249 " --> pdb=" O PHE C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 294 removed outlier: 4.255A pdb=" N ASP C 268 " --> pdb=" O GLN C 264 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 278 " --> pdb=" O ASP C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.651A pdb=" N TYR C 304 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 305 " --> pdb=" O ASP C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 383 through 400 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.502A pdb=" N ASP E 82 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU E 83 " --> pdb=" O SER E 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 79 through 83' Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'L' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 206 removed outlier: 7.222A pdb=" N TRP A 236 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N MET A 239 " --> pdb=" O TRP A 227 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N TRP A 227 " --> pdb=" O MET A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 removed outlier: 4.246A pdb=" N ALA A 61 " --> pdb=" O PHE A 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA7, first strand: chain 'A' and resid 339 through 340 removed outlier: 3.768A pdb=" N GLU A 367 " --> pdb=" O ARG A 375 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 2 through 7 Processing sheet with id=AA9, first strand: chain 'B' and resid 15 through 16 Processing sheet with id=AB1, first strand: chain 'B' and resid 213 through 214 removed outlier: 7.482A pdb=" N TRP B 236 " --> pdb=" O PRO B 46 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N MET B 239 " --> pdb=" O TRP B 227 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N TRP B 227 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.502A pdb=" N THR B 66 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.502A pdb=" N THR B 66 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B 61 " --> pdb=" O PHE B 85 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 423 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 260 through 261 Processing sheet with id=AB5, first strand: chain 'B' and resid 339 through 340 removed outlier: 3.522A pdb=" N GLU B 367 " --> pdb=" O ARG B 375 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 2 through 7 Processing sheet with id=AB7, first strand: chain 'C' and resid 15 through 16 removed outlier: 5.969A pdb=" N GLY C 345 " --> pdb=" O THR C 352 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N THR C 352 " --> pdb=" O GLY C 345 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE C 347 " --> pdb=" O THR C 350 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 37 through 40 Processing sheet with id=AB9, first strand: chain 'C' and resid 181 through 184 removed outlier: 7.215A pdb=" N TRP C 236 " --> pdb=" O PRO C 46 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N MET C 239 " --> pdb=" O TRP C 227 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N TRP C 227 " --> pdb=" O MET C 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 152 through 153 Processing sheet with id=AC2, first strand: chain 'C' and resid 152 through 153 removed outlier: 4.040A pdb=" N ALA C 61 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 423 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 260 through 261 Processing sheet with id=AC4, first strand: chain 'C' and resid 339 through 340 removed outlier: 3.681A pdb=" N GLU C 367 " --> pdb=" O ARG C 375 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 3 through 5 removed outlier: 3.564A pdb=" N LEU D 81 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE D 79 " --> pdb=" O CYS D 22 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.648A pdb=" N GLY D 50 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ARG D 39 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TRP D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 19 through 23 removed outlier: 3.580A pdb=" N THR E 63 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 46 through 49 removed outlier: 6.650A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR E 49 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 3 through 5 removed outlier: 3.576A pdb=" N CYS F 22 " --> pdb=" O PHE F 79 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE F 79 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.523A pdb=" N THR F 116 " --> pdb=" O TYR F 94 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY F 50 " --> pdb=" O TRP F 37 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ARG F 39 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N TRP F 48 " --> pdb=" O ARG F 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 16 through 18 removed outlier: 6.370A pdb=" N GLN F 16 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER F 85 " --> pdb=" O GLN F 16 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.866A pdb=" N VAL G 19 " --> pdb=" O ILE G 75 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.775A pdb=" N THR G 53 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR G 49 " --> pdb=" O THR G 53 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N TYR G 49 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 19 through 23 removed outlier: 3.695A pdb=" N VAL H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.832A pdb=" N THR H 53 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR H 49 " --> pdb=" O THR H 53 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS H 45 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TYR H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 3 through 7 removed outlier: 3.649A pdb=" N THR L 21 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLN L 16 " --> pdb=" O SER L 85 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER L 85 " --> pdb=" O GLN L 16 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.648A pdb=" N TRP L 35 " --> pdb=" O TYR L 51 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N TYR L 51 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) 653 hydrogen bonds defined for protein. 1695 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.04 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4297 1.33 - 1.45: 3224 1.45 - 1.57: 8298 1.57 - 1.69: 0 1.69 - 1.82: 126 Bond restraints: 15945 Sorted by residual: bond pdb=" N ARG F 104 " pdb=" CA ARG F 104 " ideal model delta sigma weight residual 1.458 1.515 -0.057 6.30e-03 2.52e+04 8.17e+01 bond pdb=" CA SER C 197 " pdb=" CB SER C 197 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.40e-02 5.10e+03 1.54e+01 bond pdb=" N ARG L 104 " pdb=" CA ARG L 104 " ideal model delta sigma weight residual 1.456 1.500 -0.044 1.16e-02 7.43e+03 1.44e+01 bond pdb=" N TYR E 94 " pdb=" CA TYR E 94 " ideal model delta sigma weight residual 1.457 1.510 -0.053 1.41e-02 5.03e+03 1.43e+01 bond pdb=" N TYR F 106 " pdb=" CA TYR F 106 " ideal model delta sigma weight residual 1.454 1.498 -0.044 1.17e-02 7.31e+03 1.40e+01 ... (remaining 15940 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 21253 2.32 - 4.64: 366 4.64 - 6.96: 62 6.96 - 9.28: 16 9.28 - 11.60: 2 Bond angle restraints: 21699 Sorted by residual: angle pdb=" N SER C 197 " pdb=" CA SER C 197 " pdb=" C SER C 197 " ideal model delta sigma weight residual 112.59 104.09 8.50 1.22e+00 6.72e-01 4.86e+01 angle pdb=" C SER A 197 " pdb=" N LEU A 198 " pdb=" CA LEU A 198 " ideal model delta sigma weight residual 121.50 111.74 9.76 1.43e+00 4.89e-01 4.66e+01 angle pdb=" CA ASP A 243 " pdb=" CB ASP A 243 " pdb=" CG ASP A 243 " ideal model delta sigma weight residual 112.60 119.23 -6.63 1.00e+00 1.00e+00 4.40e+01 angle pdb=" CA PRO E 95 " pdb=" N PRO E 95 " pdb=" CD PRO E 95 " ideal model delta sigma weight residual 112.00 102.86 9.14 1.40e+00 5.10e-01 4.26e+01 angle pdb=" C MET D 109 " pdb=" N ASP D 110 " pdb=" CA ASP D 110 " ideal model delta sigma weight residual 120.44 128.86 -8.42 1.36e+00 5.41e-01 3.83e+01 ... (remaining 21694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7900 17.96 - 35.92: 1036 35.92 - 53.87: 319 53.87 - 71.83: 62 71.83 - 89.79: 19 Dihedral angle restraints: 9336 sinusoidal: 3675 harmonic: 5661 Sorted by residual: dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS A 92 " pdb=" CB CYS A 92 " ideal model delta sinusoidal sigma weight residual 93.00 179.67 -86.67 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CB CYS C 59 " pdb=" SG CYS C 59 " pdb=" SG CYS C 92 " pdb=" CB CYS C 92 " ideal model delta sinusoidal sigma weight residual 93.00 178.45 -85.45 1 1.00e+01 1.00e-02 8.84e+01 dihedral pdb=" C TYR E 94 " pdb=" N TYR E 94 " pdb=" CA TYR E 94 " pdb=" CB TYR E 94 " ideal model delta harmonic sigma weight residual -122.60 -142.23 19.63 0 2.50e+00 1.60e-01 6.16e+01 ... (remaining 9333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 2284 0.137 - 0.274: 18 0.274 - 0.411: 1 0.411 - 0.547: 0 0.547 - 0.684: 1 Chirality restraints: 2304 Sorted by residual: chirality pdb=" CA TYR E 94 " pdb=" N TYR E 94 " pdb=" C TYR E 94 " pdb=" CB TYR E 94 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" CA VAL C 43 " pdb=" N VAL C 43 " pdb=" C VAL C 43 " pdb=" CB VAL C 43 " both_signs ideal model delta sigma weight residual False 2.44 2.82 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA TYR H 94 " pdb=" N TYR H 94 " pdb=" C TYR H 94 " pdb=" CB TYR H 94 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2301 not shown) Planarity restraints: 2784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 92 " -0.031 2.00e-02 2.50e+03 6.03e-02 3.63e+01 pdb=" C SER E 92 " 0.104 2.00e-02 2.50e+03 pdb=" O SER E 92 " -0.038 2.00e-02 2.50e+03 pdb=" N SER E 93 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 93 " -0.026 2.00e-02 2.50e+03 5.39e-02 2.90e+01 pdb=" C SER H 93 " 0.093 2.00e-02 2.50e+03 pdb=" O SER H 93 " -0.034 2.00e-02 2.50e+03 pdb=" N TYR H 94 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 103 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C GLY F 103 " -0.077 2.00e-02 2.50e+03 pdb=" O GLY F 103 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG F 104 " 0.026 2.00e-02 2.50e+03 ... (remaining 2781 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1674 2.75 - 3.29: 14383 3.29 - 3.82: 26105 3.82 - 4.36: 31272 4.36 - 4.90: 54777 Nonbonded interactions: 128211 Sorted by model distance: nonbonded pdb=" OE2 GLU A 213 " pdb=" OG SER A 233 " model vdw 2.212 3.040 nonbonded pdb=" OE2 GLU C 213 " pdb=" OG SER C 233 " model vdw 2.220 3.040 nonbonded pdb=" O HIS B 33 " pdb=" ND1 HIS B 33 " model vdw 2.238 3.120 nonbonded pdb=" N GLU C 191 " pdb=" OE1 GLU C 191 " model vdw 2.247 3.120 nonbonded pdb=" O SER E 52 " pdb=" OG SER E 52 " model vdw 2.257 3.040 ... (remaining 128206 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' } 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=1.00 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: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.120 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1438 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 15969 Z= 0.234 Angle : 0.729 11.602 21747 Z= 0.438 Chirality : 0.048 0.684 2304 Planarity : 0.006 0.088 2784 Dihedral : 17.885 89.788 5652 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.98 % Allowed : 5.77 % Favored : 93.25 % Rotamer: Outliers : 4.30 % Allowed : 28.63 % Favored : 67.07 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.18), residues: 1941 helix: -0.39 (0.31), residues: 270 sheet: -1.04 (0.21), residues: 588 loop : -1.26 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 332 TYR 0.056 0.002 TYR E 94 PHE 0.024 0.001 PHE H 87 TRP 0.030 0.001 TRP D 37 HIS 0.010 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00358 (15945) covalent geometry : angle 0.72730 (21699) SS BOND : bond 0.00174 ( 24) SS BOND : angle 1.25433 ( 48) hydrogen bonds : bond 0.19173 ( 594) hydrogen bonds : angle 8.18321 ( 1695) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 182 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: D 106 TYR cc_start: 0.5932 (OUTLIER) cc_final: 0.5452 (m-80) outliers start: 74 outliers final: 57 residues processed: 253 average time/residue: 0.4731 time to fit residues: 136.1783 Evaluate side-chains 223 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 55 ASP Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 24 CYS Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 350 THR Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 164 SER Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 320 ASN Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain C residue 401 LYS Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 HIS ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS ** F 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.196386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134716 restraints weight = 18064.182| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.19 r_work: 0.3477 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 15969 Z= 0.206 Angle : 0.661 14.420 21747 Z= 0.349 Chirality : 0.045 0.171 2304 Planarity : 0.006 0.161 2784 Dihedral : 7.378 56.143 2200 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.49 % Favored : 93.10 % Rotamer: Outliers : 5.57 % Allowed : 25.78 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.18), residues: 1941 helix: 0.27 (0.31), residues: 267 sheet: -1.09 (0.20), residues: 612 loop : -1.14 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 332 TYR 0.034 0.002 TYR E 94 PHE 0.019 0.002 PHE L 79 TRP 0.020 0.002 TRP A 32 HIS 0.006 0.001 HIS F 36 Details of bonding type rmsd covalent geometry : bond 0.00503 (15945) covalent geometry : angle 0.65445 (21699) SS BOND : bond 0.00359 ( 24) SS BOND : angle 2.03886 ( 48) hydrogen bonds : bond 0.04428 ( 594) hydrogen bonds : angle 5.98345 ( 1695) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 186 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 11 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7189 (mttt) REVERT: A 164 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.8009 (m) REVERT: A 346 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7073 (mpp) REVERT: B 1 LYS cc_start: 0.7481 (ttpt) cc_final: 0.7038 (ttpt) REVERT: B 174 LYS cc_start: 0.7762 (mmtm) cc_final: 0.6753 (ptmm) REVERT: B 200 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.6776 (mttt) REVERT: C 13 ASN cc_start: 0.7306 (OUTLIER) cc_final: 0.6645 (m110) REVERT: C 33 HIS cc_start: 0.7537 (m-70) cc_final: 0.7032 (t-90) REVERT: C 217 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7790 (mtpp) REVERT: D 106 TYR cc_start: 0.5551 (OUTLIER) cc_final: 0.5211 (p90) REVERT: F 49 MET cc_start: 0.6397 (ptp) cc_final: 0.6192 (mpp) REVERT: F 98 ARG cc_start: 0.7074 (ttp-170) cc_final: 0.6859 (ttp-170) REVERT: F 105 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6911 (m-30) REVERT: F 107 TYR cc_start: 0.7423 (m-10) cc_final: 0.6928 (m-10) REVERT: H 4 MET cc_start: 0.4672 (mmp) cc_final: 0.3484 (tpp) REVERT: H 93 SER cc_start: 0.7950 (t) cc_final: 0.7612 (t) outliers start: 96 outliers final: 43 residues processed: 258 average time/residue: 0.4962 time to fit residues: 144.3803 Evaluate side-chains 217 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 181 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 113 optimal weight: 0.0970 chunk 90 optimal weight: 6.9990 chunk 138 optimal weight: 0.3980 chunk 189 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 146 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 HIS B 411 GLN C 49 HIS D 73 HIS F 77 ASN H 38 GLN L 40 GLN L 73 HIS ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.195235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.134486 restraints weight = 18245.611| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.19 r_work: 0.3451 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 15969 Z= 0.214 Angle : 0.660 16.571 21747 Z= 0.346 Chirality : 0.045 0.166 2304 Planarity : 0.006 0.170 2784 Dihedral : 6.434 58.265 2146 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.39 % Favored : 93.25 % Rotamer: Outliers : 6.85 % Allowed : 24.16 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.18), residues: 1941 helix: 0.06 (0.30), residues: 285 sheet: -1.10 (0.19), residues: 651 loop : -1.22 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 98 TYR 0.034 0.002 TYR E 94 PHE 0.019 0.002 PHE L 79 TRP 0.019 0.002 TRP F 37 HIS 0.007 0.001 HIS F 36 Details of bonding type rmsd covalent geometry : bond 0.00525 (15945) covalent geometry : angle 0.65411 (21699) SS BOND : bond 0.00370 ( 24) SS BOND : angle 1.95625 ( 48) hydrogen bonds : bond 0.04327 ( 594) hydrogen bonds : angle 5.78232 ( 1695) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 173 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7225 (mttt) REVERT: A 164 SER cc_start: 0.8498 (OUTLIER) cc_final: 0.8083 (m) REVERT: B 126 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8568 (mp) REVERT: B 174 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.6687 (ptmm) REVERT: C 13 ASN cc_start: 0.7332 (OUTLIER) cc_final: 0.6713 (m110) REVERT: C 217 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7873 (mtpp) REVERT: C 222 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8597 (tp40) REVERT: C 346 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.6734 (mpp) REVERT: C 406 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6717 (mm-30) REVERT: F 37 TRP cc_start: 0.8264 (m100) cc_final: 0.7798 (m100) REVERT: H 4 MET cc_start: 0.5360 (mmp) cc_final: 0.3803 (tpp) REVERT: H 17 ASP cc_start: 0.2590 (OUTLIER) cc_final: 0.2285 (p0) outliers start: 118 outliers final: 56 residues processed: 266 average time/residue: 0.5028 time to fit residues: 151.0005 Evaluate side-chains 232 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 166 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 29 ASP Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 346 MET Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 63 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 184 optimal weight: 9.9990 chunk 94 optimal weight: 0.5980 chunk 173 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 HIS D 73 HIS L 73 HIS ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.197995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136592 restraints weight = 18208.732| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.22 r_work: 0.3475 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15969 Z= 0.134 Angle : 0.595 17.537 21747 Z= 0.311 Chirality : 0.044 0.307 2304 Planarity : 0.006 0.172 2784 Dihedral : 5.815 55.033 2138 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.92 % Favored : 93.71 % Rotamer: Outliers : 5.34 % Allowed : 25.73 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.19), residues: 1941 helix: 0.93 (0.32), residues: 267 sheet: -0.98 (0.19), residues: 645 loop : -1.21 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.023 0.002 TYR E 94 PHE 0.017 0.002 PHE E 87 TRP 0.020 0.001 TRP D 37 HIS 0.007 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00317 (15945) covalent geometry : angle 0.59109 (21699) SS BOND : bond 0.00249 ( 24) SS BOND : angle 1.52404 ( 48) hydrogen bonds : bond 0.03538 ( 594) hydrogen bonds : angle 5.40744 ( 1695) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 175 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 11 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7162 (mttt) REVERT: A 164 SER cc_start: 0.8439 (OUTLIER) cc_final: 0.8000 (m) REVERT: B 47 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.6995 (pttp) REVERT: B 174 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.6682 (ptmm) REVERT: B 346 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7280 (mpp) REVERT: C 13 ASN cc_start: 0.7293 (OUTLIER) cc_final: 0.6667 (m110) REVERT: C 33 HIS cc_start: 0.7653 (OUTLIER) cc_final: 0.7055 (t-90) REVERT: C 217 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7805 (mtpp) REVERT: C 406 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6722 (mm-30) REVERT: F 37 TRP cc_start: 0.8172 (m100) cc_final: 0.7857 (m100) REVERT: H 4 MET cc_start: 0.5337 (mmp) cc_final: 0.3901 (tpp) REVERT: H 17 ASP cc_start: 0.2646 (OUTLIER) cc_final: 0.2352 (p0) outliers start: 92 outliers final: 52 residues processed: 244 average time/residue: 0.5145 time to fit residues: 140.8083 Evaluate side-chains 223 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 161 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 109 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 112 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 61 optimal weight: 0.2980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 HIS D 73 HIS L 73 HIS ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.196629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135380 restraints weight = 18231.522| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.21 r_work: 0.3485 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15969 Z= 0.160 Angle : 0.617 17.630 21747 Z= 0.323 Chirality : 0.044 0.217 2304 Planarity : 0.006 0.173 2784 Dihedral : 5.799 50.172 2137 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.23 % Favored : 93.41 % Rotamer: Outliers : 5.69 % Allowed : 25.44 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.19), residues: 1941 helix: 0.92 (0.32), residues: 267 sheet: -1.07 (0.19), residues: 660 loop : -1.13 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 332 TYR 0.028 0.002 TYR E 94 PHE 0.022 0.002 PHE C 85 TRP 0.022 0.001 TRP L 37 HIS 0.007 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00391 (15945) covalent geometry : angle 0.61065 (21699) SS BOND : bond 0.00275 ( 24) SS BOND : angle 1.90719 ( 48) hydrogen bonds : bond 0.03697 ( 594) hydrogen bonds : angle 5.34236 ( 1695) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 173 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 11 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7221 (mttt) REVERT: A 346 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7039 (mpp) REVERT: B 126 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8547 (mp) REVERT: B 174 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.6731 (ptmm) REVERT: B 266 SER cc_start: 0.8266 (t) cc_final: 0.7975 (p) REVERT: B 346 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7324 (mpp) REVERT: C 13 ASN cc_start: 0.7378 (OUTLIER) cc_final: 0.6725 (m110) REVERT: C 33 HIS cc_start: 0.7644 (OUTLIER) cc_final: 0.7043 (t-90) REVERT: C 217 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7852 (mtpp) REVERT: C 406 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6757 (mm-30) REVERT: F 37 TRP cc_start: 0.8271 (m100) cc_final: 0.7998 (m100) REVERT: H 4 MET cc_start: 0.5443 (mmp) cc_final: 0.2443 (tpt) REVERT: H 17 ASP cc_start: 0.2652 (OUTLIER) cc_final: 0.2391 (p0) REVERT: L 77 ASN cc_start: 0.7027 (t0) cc_final: 0.6648 (t160) outliers start: 98 outliers final: 61 residues processed: 246 average time/residue: 0.4666 time to fit residues: 129.2673 Evaluate side-chains 234 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 163 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LYS Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 123 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 80 optimal weight: 0.0170 chunk 187 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 172 optimal weight: 0.7980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 HIS D 73 HIS L 73 HIS ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.198668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138821 restraints weight = 18216.482| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.44 r_work: 0.3464 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15969 Z= 0.120 Angle : 0.568 12.528 21747 Z= 0.300 Chirality : 0.043 0.173 2304 Planarity : 0.006 0.156 2784 Dihedral : 5.535 46.355 2137 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.87 % Favored : 93.77 % Rotamer: Outliers : 4.76 % Allowed : 26.42 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.19), residues: 1941 helix: 1.23 (0.32), residues: 267 sheet: -0.94 (0.19), residues: 651 loop : -1.11 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 332 TYR 0.024 0.001 TYR E 94 PHE 0.021 0.002 PHE E 87 TRP 0.025 0.001 TRP D 37 HIS 0.008 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00282 (15945) covalent geometry : angle 0.56452 (21699) SS BOND : bond 0.00229 ( 24) SS BOND : angle 1.45876 ( 48) hydrogen bonds : bond 0.03279 ( 594) hydrogen bonds : angle 5.10582 ( 1695) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 172 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 351 THR cc_start: 0.7739 (m) cc_final: 0.7369 (t) REVERT: B 47 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7111 (pttp) REVERT: B 126 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8540 (mp) REVERT: B 174 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.6717 (ptmm) REVERT: B 346 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7316 (mpp) REVERT: C 13 ASN cc_start: 0.7295 (OUTLIER) cc_final: 0.6677 (m110) REVERT: C 33 HIS cc_start: 0.7679 (OUTLIER) cc_final: 0.7041 (t-90) REVERT: C 217 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7337 (mtmm) REVERT: C 351 THR cc_start: 0.7783 (m) cc_final: 0.7302 (t) REVERT: D 37 TRP cc_start: 0.8328 (m100) cc_final: 0.7968 (m100) REVERT: F 37 TRP cc_start: 0.8170 (m100) cc_final: 0.7854 (m100) REVERT: H 4 MET cc_start: 0.5373 (mmp) cc_final: 0.2515 (tpt) REVERT: L 77 ASN cc_start: 0.6939 (t0) cc_final: 0.6531 (t160) outliers start: 82 outliers final: 56 residues processed: 236 average time/residue: 0.4602 time to fit residues: 122.3150 Evaluate side-chains 222 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 159 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 242 LYS Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 105 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 109 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 84 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 132 optimal weight: 0.2980 chunk 170 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 163 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 HIS C 22 HIS D 40 GLN D 73 HIS F 73 HIS G 38 GLN L 73 HIS ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.200057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139983 restraints weight = 18110.378| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.33 r_work: 0.3520 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 15969 Z= 0.111 Angle : 0.582 20.577 21747 Z= 0.302 Chirality : 0.042 0.184 2304 Planarity : 0.006 0.181 2784 Dihedral : 5.359 46.959 2133 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.77 % Favored : 93.87 % Rotamer: Outliers : 4.82 % Allowed : 26.42 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.19), residues: 1941 helix: 1.41 (0.32), residues: 267 sheet: -0.83 (0.20), residues: 621 loop : -1.07 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 98 TYR 0.026 0.001 TYR E 94 PHE 0.023 0.001 PHE E 87 TRP 0.026 0.001 TRP L 37 HIS 0.009 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00259 (15945) covalent geometry : angle 0.57659 (21699) SS BOND : bond 0.00235 ( 24) SS BOND : angle 1.74592 ( 48) hydrogen bonds : bond 0.03143 ( 594) hydrogen bonds : angle 4.92793 ( 1695) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 180 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 351 THR cc_start: 0.7705 (m) cc_final: 0.7373 (t) REVERT: B 47 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7062 (pttp) REVERT: B 174 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.6613 (ptmm) REVERT: B 346 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7295 (mpp) REVERT: C 13 ASN cc_start: 0.7266 (OUTLIER) cc_final: 0.6646 (m110) REVERT: C 33 HIS cc_start: 0.7666 (OUTLIER) cc_final: 0.7024 (t-90) REVERT: C 97 GLU cc_start: 0.7486 (mp0) cc_final: 0.7258 (mp0) REVERT: C 206 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7011 (ttt-90) REVERT: C 351 THR cc_start: 0.7688 (m) cc_final: 0.7253 (t) REVERT: C 406 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6731 (mm-30) REVERT: H 4 MET cc_start: 0.5415 (mmp) cc_final: 0.2456 (tpt) REVERT: L 77 ASN cc_start: 0.6866 (t0) cc_final: 0.6470 (t160) outliers start: 83 outliers final: 50 residues processed: 242 average time/residue: 0.4676 time to fit residues: 127.6568 Evaluate side-chains 223 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 166 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 409 HIS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 103 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 118 optimal weight: 0.0000 chunk 172 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 HIS C 22 HIS D 73 HIS D 77 ASN L 73 HIS ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.200034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139624 restraints weight = 18271.562| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.20 r_work: 0.3528 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15969 Z= 0.114 Angle : 0.574 16.377 21747 Z= 0.299 Chirality : 0.043 0.157 2304 Planarity : 0.006 0.166 2784 Dihedral : 5.244 47.459 2128 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.13 % Favored : 93.56 % Rotamer: Outliers : 4.41 % Allowed : 27.00 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.19), residues: 1941 helix: 1.44 (0.32), residues: 267 sheet: -0.74 (0.20), residues: 594 loop : -1.12 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 71 TYR 0.024 0.001 TYR E 94 PHE 0.030 0.002 PHE B 85 TRP 0.029 0.001 TRP L 37 HIS 0.009 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00263 (15945) covalent geometry : angle 0.56781 (21699) SS BOND : bond 0.00229 ( 24) SS BOND : angle 1.89462 ( 48) hydrogen bonds : bond 0.03155 ( 594) hydrogen bonds : angle 4.89274 ( 1695) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 173 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 351 THR cc_start: 0.7717 (m) cc_final: 0.7423 (t) REVERT: B 47 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7182 (pttp) REVERT: B 174 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.6672 (ptmm) REVERT: B 346 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7220 (mpp) REVERT: C 13 ASN cc_start: 0.7266 (OUTLIER) cc_final: 0.6645 (m110) REVERT: C 33 HIS cc_start: 0.7661 (OUTLIER) cc_final: 0.7051 (t-90) REVERT: C 206 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7054 (ttt-90) REVERT: C 351 THR cc_start: 0.7660 (m) cc_final: 0.7214 (t) REVERT: D 37 TRP cc_start: 0.8352 (m100) cc_final: 0.7885 (m100) REVERT: H 4 MET cc_start: 0.5404 (mmp) cc_final: 0.2510 (tpt) REVERT: L 30 THR cc_start: 0.7012 (m) cc_final: 0.6793 (p) REVERT: L 77 ASN cc_start: 0.6905 (t0) cc_final: 0.6510 (t160) outliers start: 76 outliers final: 56 residues processed: 231 average time/residue: 0.5341 time to fit residues: 138.8534 Evaluate side-chains 228 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 166 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 409 HIS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 72 optimal weight: 1.9990 chunk 176 optimal weight: 20.0000 chunk 114 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 183 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 HIS D 73 HIS D 77 ASN L 73 HIS ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.199388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139722 restraints weight = 18164.567| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.30 r_work: 0.3512 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15969 Z= 0.127 Angle : 0.581 14.727 21747 Z= 0.304 Chirality : 0.043 0.148 2304 Planarity : 0.006 0.162 2784 Dihedral : 5.307 47.685 2128 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.08 % Favored : 93.61 % Rotamer: Outliers : 4.30 % Allowed : 27.12 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.19), residues: 1941 helix: 1.37 (0.32), residues: 267 sheet: -0.78 (0.20), residues: 621 loop : -1.04 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 71 TYR 0.025 0.001 TYR E 94 PHE 0.033 0.002 PHE B 85 TRP 0.037 0.002 TRP L 37 HIS 0.008 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00302 (15945) covalent geometry : angle 0.57517 (21699) SS BOND : bond 0.00211 ( 24) SS BOND : angle 1.87964 ( 48) hydrogen bonds : bond 0.03281 ( 594) hydrogen bonds : angle 4.92413 ( 1695) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 170 time to evaluate : 0.648 Fit side-chains REVERT: A 217 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7439 (ptmm) REVERT: A 351 THR cc_start: 0.7758 (m) cc_final: 0.7470 (t) REVERT: B 47 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7136 (pttp) REVERT: B 174 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.6661 (ptmm) REVERT: B 346 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7205 (mpp) REVERT: C 13 ASN cc_start: 0.7297 (OUTLIER) cc_final: 0.6679 (m110) REVERT: C 33 HIS cc_start: 0.7657 (OUTLIER) cc_final: 0.7021 (t-90) REVERT: C 206 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7043 (ttt-90) REVERT: C 351 THR cc_start: 0.7709 (m) cc_final: 0.7245 (t) REVERT: H 4 MET cc_start: 0.5404 (mmp) cc_final: 0.2426 (tpt) REVERT: L 30 THR cc_start: 0.6963 (m) cc_final: 0.6734 (p) REVERT: L 77 ASN cc_start: 0.6869 (t0) cc_final: 0.6472 (t160) outliers start: 74 outliers final: 58 residues processed: 223 average time/residue: 0.5178 time to fit residues: 130.2276 Evaluate side-chains 229 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 164 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 409 HIS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 206 ARG Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 111 optimal weight: 0.3980 chunk 11 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 162 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 HIS D 73 HIS D 77 ASN L 73 HIS ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.198103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.138295 restraints weight = 18230.286| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.25 r_work: 0.3477 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15969 Z= 0.152 Angle : 0.624 25.889 21747 Z= 0.320 Chirality : 0.044 0.193 2304 Planarity : 0.006 0.198 2784 Dihedral : 5.489 49.326 2128 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.29 % Favored : 93.41 % Rotamer: Outliers : 4.41 % Allowed : 27.35 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.19), residues: 1941 helix: 1.22 (0.32), residues: 267 sheet: -0.82 (0.19), residues: 651 loop : -1.07 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 71 TYR 0.029 0.002 TYR E 94 PHE 0.034 0.002 PHE B 85 TRP 0.042 0.002 TRP F 37 HIS 0.008 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00369 (15945) covalent geometry : angle 0.61801 (21699) SS BOND : bond 0.00300 ( 24) SS BOND : angle 1.86332 ( 48) hydrogen bonds : bond 0.03530 ( 594) hydrogen bonds : angle 5.03040 ( 1695) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3882 Ramachandran restraints generated. 1941 Oldfield, 0 Emsley, 1941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 174 time to evaluate : 0.625 Fit side-chains REVERT: A 217 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7438 (ptmm) REVERT: A 351 THR cc_start: 0.7766 (m) cc_final: 0.7461 (t) REVERT: B 174 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.6746 (ptmm) REVERT: B 346 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7210 (mpp) REVERT: C 13 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.6718 (m110) REVERT: C 33 HIS cc_start: 0.7658 (OUTLIER) cc_final: 0.7046 (t-90) REVERT: H 4 MET cc_start: 0.5391 (mmp) cc_final: 0.2411 (tpt) REVERT: L 30 THR cc_start: 0.7026 (OUTLIER) cc_final: 0.6791 (p) REVERT: L 77 ASN cc_start: 0.6907 (t0) cc_final: 0.6511 (t160) outliers start: 76 outliers final: 59 residues processed: 229 average time/residue: 0.4974 time to fit residues: 128.9569 Evaluate side-chains 235 residues out of total 1722 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 170 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LYS Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 32 TRP Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain B residue 13 ASN Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 409 HIS Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 130 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 140 optimal weight: 0.0170 chunk 139 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 146 optimal weight: 8.9990 chunk 102 optimal weight: 0.1980 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 HIS ** D 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN D 82 GLN ** L 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.197053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137209 restraints weight = 18050.080| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.27 r_work: 0.3468 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 15969 Z= 0.170 Angle : 0.635 23.410 21747 Z= 0.328 Chirality : 0.044 0.175 2304 Planarity : 0.006 0.189 2784 Dihedral : 5.618 50.869 2128 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.49 % Favored : 93.20 % Rotamer: Outliers : 4.24 % Allowed : 27.53 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.19), residues: 1941 helix: 1.07 (0.31), residues: 267 sheet: -0.82 (0.19), residues: 651 loop : -1.09 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 71 TYR 0.029 0.002 TYR E 94 PHE 0.031 0.002 PHE A 109 TRP 0.049 0.002 TRP L 37 HIS 0.007 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00414 (15945) covalent geometry : angle 0.62961 (21699) SS BOND : bond 0.00273 ( 24) SS BOND : angle 1.93297 ( 48) hydrogen bonds : bond 0.03682 ( 594) hydrogen bonds : angle 5.12636 ( 1695) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7129.53 seconds wall clock time: 121 minutes 57.23 seconds (7317.23 seconds total)