Starting phenix.real_space_refine on Tue Mar 3 18:58:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f4i_31453/03_2026/7f4i_31453.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f4i_31453/03_2026/7f4i_31453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f4i_31453/03_2026/7f4i_31453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f4i_31453/03_2026/7f4i_31453.map" model { file = "/net/cci-nas-00/data/ceres_data/7f4i_31453/03_2026/7f4i_31453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f4i_31453/03_2026/7f4i_31453.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 55 5.16 5 C 5099 2.51 5 N 1407 2.21 5 O 1469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8031 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 427 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "A" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1936 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 963 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2577 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2053 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 259} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 74 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'NLE:plan-1': 1, 'ASP:plan': 1, '4J2:plan-2': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.87, per 1000 atoms: 0.23 Number of scatterers: 8031 At special positions: 0 Unit cell: (85.68, 128.52, 93.177, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 55 16.00 O 1469 8.00 N 1407 7.00 C 5099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 267 " - pdb=" SG CYS R 273 " 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: 0.69 Conformation dependent library (CDL) restraints added in 324.5 milliseconds 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 4J2 U 4 " Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 43.8% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'G' and resid 11 through 24 removed outlier: 3.804A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.572A pdb=" N LYS A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.605A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 279 removed outlier: 4.403A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.373A pdb=" N THR A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.767A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.961A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'R' and resid 43 through 65 Processing helix chain 'R' and resid 66 through 70 Processing helix chain 'R' and resid 71 through 102 Processing helix chain 'R' and resid 109 through 147 removed outlier: 4.407A pdb=" N GLN R 115 " --> pdb=" O ALA R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 156 Processing helix chain 'R' and resid 157 through 182 Processing helix chain 'R' and resid 185 through 226 removed outlier: 4.071A pdb=" N LEU R 189 " --> pdb=" O HIS R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 267 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 270 through 272 No H-bonds generated for 'chain 'R' and resid 270 through 272' Processing helix chain 'R' and resid 273 through 278 Processing helix chain 'R' and resid 279 through 299 Proline residue: R 295 - end of helix Processing helix chain 'R' and resid 302 through 311 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.316A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AA3, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.937A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.678A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.572A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.061A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.580A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.742A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.684A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.618A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1233 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: 1.31 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2507 1.34 - 1.47: 2037 1.47 - 1.60: 3568 1.60 - 1.73: 0 1.73 - 1.86: 75 Bond restraints: 8187 Sorted by residual: bond pdb=" C 4J2 U 4 " pdb=" N ARG U 5 " ideal model delta sigma weight residual 1.329 1.455 -0.126 1.40e-02 5.10e+03 8.13e+01 bond pdb=" CA ASN B 340 " pdb=" C ASN B 340 " ideal model delta sigma weight residual 1.521 1.481 0.040 1.23e-02 6.61e+03 1.04e+01 bond pdb=" CE2 4J2 U 4 " pdb=" CZ1 4J2 U 4 " ideal model delta sigma weight residual 1.419 1.364 0.055 2.00e-02 2.50e+03 7.69e+00 bond pdb=" CA 4J2 U 4 " pdb=" C 4J2 U 4 " ideal model delta sigma weight residual 1.525 1.476 0.049 2.10e-02 2.27e+03 5.53e+00 bond pdb=" CA SER B 343 " pdb=" CB SER B 343 " ideal model delta sigma weight residual 1.530 1.488 0.042 2.00e-02 2.50e+03 4.46e+00 ... (remaining 8182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.36: 11084 7.36 - 14.72: 4 14.72 - 22.08: 1 22.08 - 29.45: 1 29.45 - 36.81: 2 Bond angle restraints: 11092 Sorted by residual: angle pdb=" O 4J2 U 4 " pdb=" C 4J2 U 4 " pdb=" N ARG U 5 " ideal model delta sigma weight residual 123.00 86.19 36.81 1.60e+00 3.91e-01 5.29e+02 angle pdb=" CA 4J2 U 4 " pdb=" C 4J2 U 4 " pdb=" N ARG U 5 " ideal model delta sigma weight residual 116.20 148.84 -32.64 2.00e+00 2.50e-01 2.66e+02 angle pdb=" C 4J2 U 4 " pdb=" N ARG U 5 " pdb=" CA ARG U 5 " ideal model delta sigma weight residual 121.70 144.60 -22.90 1.80e+00 3.09e-01 1.62e+02 angle pdb=" C HIS U 3 " pdb=" N 4J2 U 4 " pdb=" CA 4J2 U 4 " ideal model delta sigma weight residual 121.70 103.47 18.23 1.80e+00 3.09e-01 1.03e+02 angle pdb=" O ASN B 340 " pdb=" C ASN B 340 " pdb=" N GLY B 341 " ideal model delta sigma weight residual 123.25 117.60 5.65 1.14e+00 7.69e-01 2.46e+01 ... (remaining 11087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4554 17.65 - 35.30: 272 35.30 - 52.95: 36 52.95 - 70.60: 5 70.60 - 88.25: 6 Dihedral angle restraints: 4873 sinusoidal: 1878 harmonic: 2995 Sorted by residual: dihedral pdb=" CA ILE R 40 " pdb=" C ILE R 40 " pdb=" N SER R 41 " pdb=" CA SER R 41 " ideal model delta harmonic sigma weight residual -180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLY B 53 " pdb=" C GLY B 53 " pdb=" N HIS B 54 " pdb=" CA HIS B 54 " ideal model delta harmonic sigma weight residual 180.00 152.53 27.47 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ASP B 195 " pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta harmonic sigma weight residual -180.00 -152.92 -27.08 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 4870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 757 0.049 - 0.098: 385 0.098 - 0.147: 112 0.147 - 0.196: 20 0.196 - 0.245: 1 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CA ARG U 5 " pdb=" N ARG U 5 " pdb=" C ARG U 5 " pdb=" CB ARG U 5 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ASP N 109 " pdb=" N ASP N 109 " pdb=" C ASP N 109 " pdb=" CB ASP N 109 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.76e-01 chirality pdb=" CB ILE R 144 " pdb=" CA ILE R 144 " pdb=" CG1 ILE R 144 " pdb=" CG2 ILE R 144 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 1272 not shown) Planarity restraints: 1406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 340 " -0.043 2.00e-02 2.50e+03 8.29e-02 6.87e+01 pdb=" C ASN B 340 " 0.143 2.00e-02 2.50e+03 pdb=" O ASN B 340 " -0.053 2.00e-02 2.50e+03 pdb=" N GLY B 341 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA 4J2 U 4 " 0.045 2.00e-02 2.50e+03 6.37e-02 4.06e+01 pdb=" C 4J2 U 4 " -0.110 2.00e-02 2.50e+03 pdb=" O 4J2 U 4 " 0.025 2.00e-02 2.50e+03 pdb=" N ARG U 5 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS U 3 " -0.030 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" C HIS U 3 " 0.099 2.00e-02 2.50e+03 pdb=" O HIS U 3 " -0.035 2.00e-02 2.50e+03 pdb=" N 4J2 U 4 " -0.034 2.00e-02 2.50e+03 ... (remaining 1403 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 333 2.72 - 3.26: 8217 3.26 - 3.81: 12867 3.81 - 4.35: 16759 4.35 - 4.90: 28254 Nonbonded interactions: 66430 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.169 3.040 nonbonded pdb=" OD1 ASN N 84 " pdb=" OG SER N 85 " model vdw 2.227 3.040 nonbonded pdb=" NH2 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.360 3.120 nonbonded pdb=" OG SER B 227 " pdb=" OD1 ASP B 247 " model vdw 2.378 3.040 nonbonded pdb=" OE2 GLU R 94 " pdb="CA CA R 501 " model vdw 2.389 2.510 ... (remaining 66425 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.810 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.009 0.126 8188 Z= 0.500 Angle : 1.215 36.806 11094 Z= 0.711 Chirality : 0.060 0.245 1275 Planarity : 0.011 0.147 1406 Dihedral : 11.957 88.253 2930 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.25), residues: 1010 helix: -0.05 (0.23), residues: 403 sheet: 0.59 (0.36), residues: 211 loop : -0.80 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.057 0.006 ARG A 385 TYR 0.038 0.006 TYR B 111 PHE 0.028 0.005 PHE R 76 TRP 0.065 0.009 TRP B 63 HIS 0.018 0.005 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00916 ( 8187) covalent geometry : angle 1.21463 (11092) SS BOND : bond 0.00384 ( 1) SS BOND : angle 0.21076 ( 2) hydrogen bonds : bond 0.15064 ( 438) hydrogen bonds : angle 6.62921 ( 1233) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 GLU cc_start: 0.9240 (tp30) cc_final: 0.9038 (tp30) REVERT: G 21 MET cc_start: 0.9286 (mmm) cc_final: 0.8997 (mtp) REVERT: G 38 MET cc_start: 0.9111 (ptt) cc_final: 0.8884 (ptp) REVERT: G 48 ASP cc_start: 0.8694 (t0) cc_final: 0.8479 (t0) REVERT: A 25 MET cc_start: 0.7593 (tmm) cc_final: 0.7387 (tmm) REVERT: A 271 ASN cc_start: 0.9029 (m-40) cc_final: 0.8785 (m110) REVERT: A 330 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8799 (mp0) REVERT: N 18 LEU cc_start: 0.8431 (mt) cc_final: 0.7956 (mp) REVERT: N 46 GLU cc_start: 0.8071 (pt0) cc_final: 0.7626 (pt0) REVERT: N 99 CYS cc_start: 0.8432 (m) cc_final: 0.8100 (m) REVERT: N 124 VAL cc_start: 0.9271 (t) cc_final: 0.8802 (t) REVERT: B 10 GLU cc_start: 0.9498 (tt0) cc_final: 0.9123 (tp30) REVERT: B 15 LYS cc_start: 0.9571 (ttmt) cc_final: 0.9332 (tptp) REVERT: B 43 ILE cc_start: 0.9256 (mm) cc_final: 0.9024 (mt) REVERT: B 156 GLN cc_start: 0.8613 (mt0) cc_final: 0.8386 (mt0) REVERT: B 175 GLN cc_start: 0.8388 (pt0) cc_final: 0.8115 (pt0) REVERT: B 209 LYS cc_start: 0.8686 (mttt) cc_final: 0.8164 (mtmt) REVERT: B 280 LYS cc_start: 0.9311 (ttmm) cc_final: 0.8904 (ttmt) REVERT: B 337 LYS cc_start: 0.8356 (mttt) cc_final: 0.8092 (mttt) REVERT: R 290 ASN cc_start: 0.8101 (t0) cc_final: 0.7783 (t0) REVERT: R 294 ASP cc_start: 0.8734 (m-30) cc_final: 0.8385 (m-30) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1212 time to fit residues: 32.1233 Evaluate side-chains 137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS N 3 GLN N 120 GLN B 259 GLN R 70 HIS R 219 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.083876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.061941 restraints weight = 20406.183| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.58 r_work: 0.2861 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8188 Z= 0.136 Angle : 0.622 7.489 11094 Z= 0.331 Chirality : 0.043 0.201 1275 Planarity : 0.004 0.055 1406 Dihedral : 5.143 22.130 1122 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.16 % Allowed : 7.56 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.15 (0.27), residues: 1010 helix: 1.81 (0.26), residues: 406 sheet: 0.28 (0.34), residues: 224 loop : 0.03 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 38 TYR 0.013 0.001 TYR B 105 PHE 0.021 0.001 PHE G 61 TRP 0.024 0.002 TRP B 82 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8187) covalent geometry : angle 0.62199 (11092) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.98022 ( 2) hydrogen bonds : bond 0.04380 ( 438) hydrogen bonds : angle 4.62189 ( 1233) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 ARG cc_start: 0.9215 (ttm110) cc_final: 0.8840 (mtm110) REVERT: G 18 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8768 (tp40) REVERT: G 21 MET cc_start: 0.9325 (mmm) cc_final: 0.9066 (mmm) REVERT: G 32 LYS cc_start: 0.9373 (mmmm) cc_final: 0.9029 (mmmm) REVERT: G 47 GLU cc_start: 0.8692 (mp0) cc_final: 0.8151 (mp0) REVERT: G 48 ASP cc_start: 0.8784 (t0) cc_final: 0.8459 (t0) REVERT: A 271 ASN cc_start: 0.9220 (m-40) cc_final: 0.8950 (m110) REVERT: A 330 GLU cc_start: 0.9362 (mm-30) cc_final: 0.8897 (mp0) REVERT: N 18 LEU cc_start: 0.8057 (mt) cc_final: 0.7797 (mp) REVERT: N 34 MET cc_start: 0.8530 (mtp) cc_final: 0.8208 (mtp) REVERT: N 73 ASP cc_start: 0.7926 (t0) cc_final: 0.7628 (t0) REVERT: N 93 VAL cc_start: 0.9148 (t) cc_final: 0.8766 (p) REVERT: N 107 CYS cc_start: 0.8787 (m) cc_final: 0.8551 (m) REVERT: B 38 ASP cc_start: 0.9101 (t0) cc_final: 0.8726 (p0) REVERT: B 172 GLU cc_start: 0.9194 (pt0) cc_final: 0.8975 (pp20) REVERT: B 209 LYS cc_start: 0.8553 (mttt) cc_final: 0.8140 (mttp) REVERT: B 254 ASP cc_start: 0.8806 (t70) cc_final: 0.8421 (t0) REVERT: B 280 LYS cc_start: 0.9279 (ttmm) cc_final: 0.8688 (ttmt) REVERT: R 83 SER cc_start: 0.9056 (m) cc_final: 0.8809 (t) outliers start: 10 outliers final: 4 residues processed: 161 average time/residue: 0.1186 time to fit residues: 24.1732 Evaluate side-chains 139 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 289 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 32 optimal weight: 0.1980 chunk 29 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 1 GLN B 293 ASN R 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.080889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.058734 restraints weight = 21386.256| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.39 r_work: 0.2796 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8188 Z= 0.208 Angle : 0.619 6.846 11094 Z= 0.324 Chirality : 0.043 0.140 1275 Planarity : 0.004 0.028 1406 Dihedral : 4.873 20.910 1122 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.86 % Allowed : 8.84 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.27), residues: 1010 helix: 1.92 (0.26), residues: 415 sheet: 0.12 (0.35), residues: 207 loop : 0.05 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 223 TYR 0.011 0.001 TYR N 95 PHE 0.019 0.002 PHE G 61 TRP 0.020 0.002 TRP B 82 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 8187) covalent geometry : angle 0.61887 (11092) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.75708 ( 2) hydrogen bonds : bond 0.04281 ( 438) hydrogen bonds : angle 4.41062 ( 1233) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8846 (mm-30) REVERT: G 20 LYS cc_start: 0.9414 (ptmm) cc_final: 0.9043 (pttp) REVERT: G 21 MET cc_start: 0.9350 (mmm) cc_final: 0.9083 (mmm) REVERT: G 32 LYS cc_start: 0.9393 (mmmm) cc_final: 0.9155 (mmmm) REVERT: G 48 ASP cc_start: 0.8852 (t0) cc_final: 0.8613 (t0) REVERT: A 60 MET cc_start: 0.9198 (mmm) cc_final: 0.8985 (mmm) REVERT: A 266 LEU cc_start: 0.9459 (mt) cc_final: 0.9164 (mt) REVERT: A 271 ASN cc_start: 0.9258 (m-40) cc_final: 0.8964 (m110) REVERT: A 330 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8904 (mp0) REVERT: N 18 LEU cc_start: 0.8167 (mt) cc_final: 0.7902 (mp) REVERT: N 33 LYS cc_start: 0.8829 (tttt) cc_final: 0.8245 (tttm) REVERT: N 34 MET cc_start: 0.8537 (mtp) cc_final: 0.8117 (mtp) REVERT: N 73 ASP cc_start: 0.8177 (t0) cc_final: 0.7853 (t0) REVERT: N 83 MET cc_start: 0.8995 (mtm) cc_final: 0.8736 (ptp) REVERT: N 107 CYS cc_start: 0.8872 (m) cc_final: 0.8576 (m) REVERT: N 120 GLN cc_start: 0.9070 (mm110) cc_final: 0.8415 (mm-40) REVERT: B 8 ARG cc_start: 0.8903 (mtt180) cc_final: 0.8558 (mtt-85) REVERT: B 23 LYS cc_start: 0.9162 (mtmt) cc_final: 0.8889 (mttp) REVERT: B 38 ASP cc_start: 0.9200 (t0) cc_final: 0.8969 (p0) REVERT: B 209 LYS cc_start: 0.8734 (mttt) cc_final: 0.8475 (mtpp) REVERT: B 217 MET cc_start: 0.8550 (ppp) cc_final: 0.8171 (ppp) REVERT: B 254 ASP cc_start: 0.8970 (t70) cc_final: 0.8549 (t0) REVERT: B 280 LYS cc_start: 0.9303 (ttmm) cc_final: 0.8933 (ttmm) outliers start: 16 outliers final: 10 residues processed: 150 average time/residue: 0.1221 time to fit residues: 23.2381 Evaluate side-chains 136 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 289 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 71 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 82 GLN R 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.081192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.059443 restraints weight = 21029.301| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.51 r_work: 0.2819 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8188 Z= 0.141 Angle : 0.562 6.168 11094 Z= 0.294 Chirality : 0.042 0.141 1275 Planarity : 0.003 0.030 1406 Dihedral : 4.544 18.350 1122 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.63 % Allowed : 11.86 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.45 (0.27), residues: 1010 helix: 2.21 (0.26), residues: 408 sheet: 0.35 (0.36), residues: 198 loop : 0.07 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 38 TYR 0.011 0.001 TYR N 95 PHE 0.016 0.001 PHE G 61 TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8187) covalent geometry : angle 0.56166 (11092) SS BOND : bond 0.00085 ( 1) SS BOND : angle 0.89074 ( 2) hydrogen bonds : bond 0.03875 ( 438) hydrogen bonds : angle 4.22389 ( 1233) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8934 (mm-30) REVERT: G 20 LYS cc_start: 0.9418 (ptmm) cc_final: 0.9043 (pttp) REVERT: G 21 MET cc_start: 0.9368 (mmm) cc_final: 0.9074 (mmm) REVERT: G 32 LYS cc_start: 0.9352 (mmmm) cc_final: 0.9145 (mmmm) REVERT: G 48 ASP cc_start: 0.8804 (t0) cc_final: 0.8511 (t0) REVERT: A 60 MET cc_start: 0.9161 (mmm) cc_final: 0.8882 (mmm) REVERT: A 271 ASN cc_start: 0.9224 (m-40) cc_final: 0.8914 (m110) REVERT: A 330 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8894 (mp0) REVERT: N 18 LEU cc_start: 0.8119 (mt) cc_final: 0.7836 (mp) REVERT: N 73 ASP cc_start: 0.8213 (t0) cc_final: 0.7816 (t0) REVERT: N 76 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9090 (ptmm) REVERT: N 93 VAL cc_start: 0.9084 (t) cc_final: 0.8692 (p) REVERT: B 8 ARG cc_start: 0.8928 (mtt180) cc_final: 0.8705 (mtt-85) REVERT: B 38 ASP cc_start: 0.9229 (t0) cc_final: 0.8905 (p0) REVERT: B 217 MET cc_start: 0.8594 (ppp) cc_final: 0.8203 (ppp) REVERT: B 254 ASP cc_start: 0.8925 (t70) cc_final: 0.8462 (t0) REVERT: B 280 LYS cc_start: 0.9161 (ttmm) cc_final: 0.8718 (ttmm) REVERT: R 84 ASP cc_start: 0.9141 (m-30) cc_final: 0.8072 (t70) REVERT: R 307 ARG cc_start: 0.7401 (mmp80) cc_final: 0.7148 (mmp80) outliers start: 14 outliers final: 7 residues processed: 147 average time/residue: 0.1199 time to fit residues: 22.5461 Evaluate side-chains 137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.079158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.057305 restraints weight = 21288.506| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.50 r_work: 0.2782 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8188 Z= 0.212 Angle : 0.606 7.390 11094 Z= 0.317 Chirality : 0.042 0.155 1275 Planarity : 0.004 0.030 1406 Dihedral : 4.584 18.527 1122 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.56 % Allowed : 12.91 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.27), residues: 1010 helix: 2.21 (0.26), residues: 408 sheet: 0.31 (0.36), residues: 199 loop : -0.06 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 38 TYR 0.014 0.001 TYR B 264 PHE 0.017 0.002 PHE G 61 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 8187) covalent geometry : angle 0.60606 (11092) SS BOND : bond 0.00005 ( 1) SS BOND : angle 0.74840 ( 2) hydrogen bonds : bond 0.04083 ( 438) hydrogen bonds : angle 4.24299 ( 1233) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 GLU cc_start: 0.9356 (mm-30) cc_final: 0.9024 (mm-30) REVERT: G 20 LYS cc_start: 0.9441 (ptmm) cc_final: 0.9052 (pttp) REVERT: G 21 MET cc_start: 0.9364 (mmm) cc_final: 0.9072 (mmm) REVERT: G 48 ASP cc_start: 0.8834 (t0) cc_final: 0.8563 (t0) REVERT: A 271 ASN cc_start: 0.9258 (m-40) cc_final: 0.8916 (m110) REVERT: A 330 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8886 (mp0) REVERT: N 18 LEU cc_start: 0.8228 (mt) cc_final: 0.7879 (mp) REVERT: N 73 ASP cc_start: 0.8256 (t0) cc_final: 0.7847 (t0) REVERT: B 8 ARG cc_start: 0.8948 (mtt180) cc_final: 0.8720 (tpp80) REVERT: B 10 GLU cc_start: 0.9569 (tt0) cc_final: 0.9283 (mt-10) REVERT: B 217 MET cc_start: 0.8641 (ppp) cc_final: 0.8324 (ppp) REVERT: B 254 ASP cc_start: 0.9108 (t70) cc_final: 0.8703 (t70) REVERT: B 280 LYS cc_start: 0.9214 (ttmm) cc_final: 0.8819 (ttmm) outliers start: 22 outliers final: 15 residues processed: 145 average time/residue: 0.1174 time to fit residues: 21.7832 Evaluate side-chains 139 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 289 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.080009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.058385 restraints weight = 20948.287| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.49 r_work: 0.2802 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8188 Z= 0.159 Angle : 0.574 8.437 11094 Z= 0.298 Chirality : 0.041 0.154 1275 Planarity : 0.003 0.031 1406 Dihedral : 4.419 17.299 1122 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.21 % Allowed : 13.02 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.44 (0.27), residues: 1010 helix: 2.33 (0.25), residues: 408 sheet: 0.21 (0.35), residues: 200 loop : -0.02 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 38 TYR 0.012 0.001 TYR N 95 PHE 0.015 0.001 PHE G 61 TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8187) covalent geometry : angle 0.57413 (11092) SS BOND : bond 0.00034 ( 1) SS BOND : angle 0.65888 ( 2) hydrogen bonds : bond 0.03829 ( 438) hydrogen bonds : angle 4.10861 ( 1233) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 GLU cc_start: 0.9385 (mm-30) cc_final: 0.9028 (mm-30) REVERT: G 20 LYS cc_start: 0.9439 (ptmm) cc_final: 0.9036 (pttp) REVERT: G 21 MET cc_start: 0.9354 (mmm) cc_final: 0.9083 (mmm) REVERT: G 22 GLU cc_start: 0.8747 (tt0) cc_final: 0.8398 (tt0) REVERT: G 48 ASP cc_start: 0.8821 (t0) cc_final: 0.8548 (t0) REVERT: A 271 ASN cc_start: 0.9242 (m-40) cc_final: 0.8907 (m110) REVERT: A 330 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8870 (mp0) REVERT: N 5 GLN cc_start: 0.8775 (tp40) cc_final: 0.8520 (tp40) REVERT: N 18 LEU cc_start: 0.8244 (mt) cc_final: 0.7927 (mp) REVERT: N 38 ARG cc_start: 0.8999 (ptt180) cc_final: 0.8645 (ptm160) REVERT: N 73 ASP cc_start: 0.8265 (t0) cc_final: 0.7716 (t0) REVERT: N 80 TYR cc_start: 0.8577 (m-80) cc_final: 0.8373 (m-80) REVERT: N 120 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8490 (mm110) REVERT: B 10 GLU cc_start: 0.9578 (tt0) cc_final: 0.9223 (mt-10) REVERT: B 23 LYS cc_start: 0.9437 (tppt) cc_final: 0.9155 (mttp) REVERT: B 38 ASP cc_start: 0.9217 (t0) cc_final: 0.9016 (p0) REVERT: B 217 MET cc_start: 0.8635 (ppp) cc_final: 0.8289 (ppp) REVERT: B 254 ASP cc_start: 0.9186 (t70) cc_final: 0.8797 (t70) REVERT: B 280 LYS cc_start: 0.9148 (ttmm) cc_final: 0.8742 (ttmm) outliers start: 19 outliers final: 14 residues processed: 146 average time/residue: 0.1089 time to fit residues: 20.8072 Evaluate side-chains 138 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 83 SER Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 289 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 0.0870 chunk 87 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.080854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.059296 restraints weight = 21072.258| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.53 r_work: 0.2826 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8188 Z= 0.130 Angle : 0.568 7.937 11094 Z= 0.293 Chirality : 0.041 0.156 1275 Planarity : 0.003 0.030 1406 Dihedral : 4.276 18.885 1122 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.98 % Allowed : 14.19 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.52 (0.27), residues: 1010 helix: 2.41 (0.25), residues: 405 sheet: 0.28 (0.35), residues: 198 loop : 0.02 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 129 TYR 0.010 0.001 TYR B 264 PHE 0.012 0.001 PHE G 61 TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8187) covalent geometry : angle 0.56764 (11092) SS BOND : bond 0.00035 ( 1) SS BOND : angle 0.57580 ( 2) hydrogen bonds : bond 0.03615 ( 438) hydrogen bonds : angle 4.05411 ( 1233) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 GLU cc_start: 0.9434 (mm-30) cc_final: 0.9156 (mm-30) REVERT: G 21 MET cc_start: 0.9369 (mmm) cc_final: 0.9094 (mmm) REVERT: G 22 GLU cc_start: 0.8764 (tt0) cc_final: 0.8402 (tt0) REVERT: G 48 ASP cc_start: 0.8687 (t0) cc_final: 0.8385 (t0) REVERT: A 271 ASN cc_start: 0.9224 (m-40) cc_final: 0.8858 (m110) REVERT: A 330 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8848 (mp0) REVERT: N 5 GLN cc_start: 0.8770 (tp40) cc_final: 0.8552 (tp40) REVERT: N 18 LEU cc_start: 0.8153 (mt) cc_final: 0.7787 (mp) REVERT: N 38 ARG cc_start: 0.8974 (ptt180) cc_final: 0.8720 (ptm160) REVERT: N 73 ASP cc_start: 0.8221 (t0) cc_final: 0.7780 (t0) REVERT: N 76 LYS cc_start: 0.9367 (ptmm) cc_final: 0.9056 (ptmm) REVERT: N 99 CYS cc_start: 0.9243 (m) cc_final: 0.8816 (m) REVERT: B 31 SER cc_start: 0.9301 (m) cc_final: 0.8896 (p) REVERT: B 38 ASP cc_start: 0.9236 (t0) cc_final: 0.8974 (p0) REVERT: B 217 MET cc_start: 0.8665 (ppp) cc_final: 0.8277 (ppp) REVERT: B 254 ASP cc_start: 0.9121 (t70) cc_final: 0.8682 (t70) REVERT: B 262 MET cc_start: 0.8680 (tpp) cc_final: 0.8067 (tpp) REVERT: B 280 LYS cc_start: 0.9117 (ttmm) cc_final: 0.8734 (ttmm) REVERT: R 300 PHE cc_start: 0.7817 (m-10) cc_final: 0.7612 (m-10) outliers start: 17 outliers final: 12 residues processed: 147 average time/residue: 0.1128 time to fit residues: 21.5846 Evaluate side-chains 139 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 289 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.082003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.060500 restraints weight = 20923.782| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.51 r_work: 0.2857 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8188 Z= 0.115 Angle : 0.577 8.949 11094 Z= 0.291 Chirality : 0.041 0.160 1275 Planarity : 0.003 0.031 1406 Dihedral : 4.121 18.194 1122 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.86 % Allowed : 14.42 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.78 (0.27), residues: 1010 helix: 2.67 (0.25), residues: 395 sheet: 0.36 (0.35), residues: 198 loop : 0.20 (0.33), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 129 TYR 0.013 0.001 TYR B 264 PHE 0.012 0.001 PHE G 61 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8187) covalent geometry : angle 0.57660 (11092) SS BOND : bond 0.00009 ( 1) SS BOND : angle 0.51391 ( 2) hydrogen bonds : bond 0.03465 ( 438) hydrogen bonds : angle 3.94420 ( 1233) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 GLU cc_start: 0.9399 (mm-30) cc_final: 0.9142 (mm-30) REVERT: G 21 MET cc_start: 0.9376 (mmm) cc_final: 0.9117 (mmm) REVERT: G 22 GLU cc_start: 0.8748 (tt0) cc_final: 0.8355 (tt0) REVERT: G 48 ASP cc_start: 0.8690 (t0) cc_final: 0.8437 (t0) REVERT: A 271 ASN cc_start: 0.9211 (m-40) cc_final: 0.8857 (m110) REVERT: A 284 THR cc_start: 0.9596 (OUTLIER) cc_final: 0.9237 (t) REVERT: A 330 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8818 (mp0) REVERT: N 5 GLN cc_start: 0.8791 (tp40) cc_final: 0.8561 (tp40) REVERT: N 18 LEU cc_start: 0.8180 (mt) cc_final: 0.7880 (mp) REVERT: N 73 ASP cc_start: 0.8227 (t0) cc_final: 0.7590 (t0) REVERT: N 76 LYS cc_start: 0.9456 (ptmm) cc_final: 0.9173 (ptmm) REVERT: N 80 TYR cc_start: 0.8549 (m-80) cc_final: 0.8282 (m-80) REVERT: N 93 VAL cc_start: 0.9112 (t) cc_final: 0.8767 (p) REVERT: N 99 CYS cc_start: 0.9240 (m) cc_final: 0.8788 (m) REVERT: B 10 GLU cc_start: 0.9564 (tt0) cc_final: 0.9248 (mt-10) REVERT: B 15 LYS cc_start: 0.9639 (ttmt) cc_final: 0.9287 (tptp) REVERT: B 38 ASP cc_start: 0.9221 (t0) cc_final: 0.8975 (p0) REVERT: B 254 ASP cc_start: 0.9049 (t70) cc_final: 0.8650 (t0) REVERT: B 280 LYS cc_start: 0.9059 (ttmm) cc_final: 0.8709 (ttmm) outliers start: 16 outliers final: 12 residues processed: 149 average time/residue: 0.1159 time to fit residues: 22.3450 Evaluate side-chains 140 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 289 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.079159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.057371 restraints weight = 21294.312| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.51 r_work: 0.2786 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8188 Z= 0.206 Angle : 0.639 8.605 11094 Z= 0.327 Chirality : 0.042 0.172 1275 Planarity : 0.004 0.071 1406 Dihedral : 4.356 19.533 1122 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.63 % Allowed : 14.77 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.27), residues: 1010 helix: 2.46 (0.25), residues: 404 sheet: 0.26 (0.34), residues: 200 loop : 0.01 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 129 TYR 0.014 0.001 TYR B 264 PHE 0.013 0.001 PHE R 258 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 8187) covalent geometry : angle 0.63874 (11092) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.64713 ( 2) hydrogen bonds : bond 0.03893 ( 438) hydrogen bonds : angle 4.07649 ( 1233) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 GLU cc_start: 0.9382 (mm-30) cc_final: 0.9102 (mm-30) REVERT: G 21 MET cc_start: 0.9368 (mmm) cc_final: 0.9113 (mmm) REVERT: G 48 ASP cc_start: 0.8827 (t0) cc_final: 0.8579 (t0) REVERT: A 271 ASN cc_start: 0.9267 (m-40) cc_final: 0.8909 (m110) REVERT: A 330 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8862 (mp0) REVERT: N 3 GLN cc_start: 0.8576 (pt0) cc_final: 0.8352 (pt0) REVERT: N 5 GLN cc_start: 0.8801 (tp40) cc_final: 0.8578 (tp40) REVERT: N 18 LEU cc_start: 0.8343 (mt) cc_final: 0.7974 (mp) REVERT: N 73 ASP cc_start: 0.8239 (t0) cc_final: 0.7617 (t0) REVERT: N 76 LYS cc_start: 0.9454 (ptmm) cc_final: 0.9253 (ptmm) REVERT: N 80 TYR cc_start: 0.8670 (m-80) cc_final: 0.8386 (m-80) REVERT: N 83 MET cc_start: 0.8209 (mpp) cc_final: 0.7951 (mpp) REVERT: N 99 CYS cc_start: 0.9248 (m) cc_final: 0.8762 (m) REVERT: B 10 GLU cc_start: 0.9587 (tt0) cc_final: 0.9280 (mt-10) REVERT: B 15 LYS cc_start: 0.9652 (ttmt) cc_final: 0.9298 (tptp) REVERT: B 254 ASP cc_start: 0.9185 (t70) cc_final: 0.8701 (t70) REVERT: B 280 LYS cc_start: 0.9154 (ttmm) cc_final: 0.8771 (ttmm) outliers start: 14 outliers final: 13 residues processed: 139 average time/residue: 0.1074 time to fit residues: 19.6255 Evaluate side-chains 137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 289 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.081340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.059590 restraints weight = 21300.602| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.56 r_work: 0.2827 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8188 Z= 0.130 Angle : 0.603 8.833 11094 Z= 0.305 Chirality : 0.041 0.197 1275 Planarity : 0.004 0.035 1406 Dihedral : 4.161 18.926 1122 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.63 % Allowed : 15.35 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.71 (0.27), residues: 1010 helix: 2.64 (0.25), residues: 399 sheet: 0.34 (0.34), residues: 201 loop : 0.09 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 129 TYR 0.011 0.001 TYR B 264 PHE 0.011 0.001 PHE A 212 TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8187) covalent geometry : angle 0.60333 (11092) SS BOND : bond 0.00023 ( 1) SS BOND : angle 0.44693 ( 2) hydrogen bonds : bond 0.03563 ( 438) hydrogen bonds : angle 3.98115 ( 1233) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 GLU cc_start: 0.9397 (mm-30) cc_final: 0.9145 (mm-30) REVERT: G 21 MET cc_start: 0.9357 (mmm) cc_final: 0.9111 (mmm) REVERT: G 22 GLU cc_start: 0.8743 (tt0) cc_final: 0.8416 (tt0) REVERT: G 48 ASP cc_start: 0.8751 (t0) cc_final: 0.8481 (t0) REVERT: A 271 ASN cc_start: 0.9241 (m-40) cc_final: 0.8879 (m110) REVERT: A 330 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8821 (mp0) REVERT: N 1 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8338 (tm-30) REVERT: N 3 GLN cc_start: 0.8569 (pt0) cc_final: 0.8305 (pt0) REVERT: N 5 GLN cc_start: 0.8789 (tp40) cc_final: 0.8563 (tp40) REVERT: N 39 GLN cc_start: 0.9300 (tt0) cc_final: 0.8515 (tp40) REVERT: N 73 ASP cc_start: 0.8211 (t0) cc_final: 0.7701 (t0) REVERT: N 76 LYS cc_start: 0.9405 (ptmm) cc_final: 0.9078 (ptmm) REVERT: N 83 MET cc_start: 0.8144 (mpp) cc_final: 0.7881 (mpp) REVERT: N 93 VAL cc_start: 0.9105 (t) cc_final: 0.8762 (p) REVERT: N 99 CYS cc_start: 0.9261 (m) cc_final: 0.8788 (m) REVERT: B 10 GLU cc_start: 0.9577 (tt0) cc_final: 0.9289 (mt-10) REVERT: B 23 LYS cc_start: 0.9134 (mtmt) cc_final: 0.8839 (mttp) REVERT: B 254 ASP cc_start: 0.9139 (t70) cc_final: 0.8857 (t0) REVERT: B 280 LYS cc_start: 0.9100 (ttmm) cc_final: 0.8702 (ttmm) outliers start: 14 outliers final: 13 residues processed: 132 average time/residue: 0.1208 time to fit residues: 20.7513 Evaluate side-chains 135 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 75 CYS Chi-restraints excluded: chain R residue 177 THR Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 289 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.081654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.059328 restraints weight = 21714.229| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.46 r_work: 0.2800 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8188 Z= 0.175 Angle : 0.623 8.878 11094 Z= 0.317 Chirality : 0.042 0.170 1275 Planarity : 0.004 0.035 1406 Dihedral : 4.251 19.522 1122 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.86 % Allowed : 15.70 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.56 (0.27), residues: 1010 helix: 2.52 (0.25), residues: 405 sheet: 0.40 (0.35), residues: 195 loop : -0.11 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 129 TYR 0.012 0.001 TYR B 264 PHE 0.013 0.001 PHE G 61 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 8187) covalent geometry : angle 0.62318 (11092) SS BOND : bond 0.00016 ( 1) SS BOND : angle 0.55639 ( 2) hydrogen bonds : bond 0.03725 ( 438) hydrogen bonds : angle 4.02107 ( 1233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2108.06 seconds wall clock time: 36 minutes 49.76 seconds (2209.76 seconds total)