Starting phenix.real_space_refine on Tue Mar 3 23:31:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sr8_25399/03_2026/7sr8_25399.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sr8_25399/03_2026/7sr8_25399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sr8_25399/03_2026/7sr8_25399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sr8_25399/03_2026/7sr8_25399.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sr8_25399/03_2026/7sr8_25399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sr8_25399/03_2026/7sr8_25399.map" } resolution = 3.3 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= 0.007 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: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5790 2.51 5 N 1547 2.21 5 O 1682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 9083 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1850 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 453 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "E" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1800 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2298 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain breaks: 2 Chain: "R" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 75 Unusual residues: {'A6F': 1, 'OLA': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'OLA:plan-2': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 2.23, per 1000 atoms: 0.25 Number of scatterers: 9083 At special positions: 0 Unit cell: (118.8, 113.4, 124.2, 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 64 16.00 O 1682 8.00 N 1547 7.00 C 5790 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 210 " 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: 0.79 Conformation dependent library (CDL) restraints added in 300.0 milliseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 38.3% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 109 through 123 Processing helix chain 'A' and resid 124 through 127 removed outlier: 3.734A pdb=" N ARG A 127 " --> pdb=" O ARG A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 124 through 127' Processing helix chain 'A' and resid 137 through 148 removed outlier: 3.602A pdb=" N GLY A 148 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.898A pdb=" N ALA A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 196 removed outlier: 4.488A pdb=" N SER A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 235 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.516A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 removed outlier: 4.172A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 82 Processing helix chain 'R' and resid 87 through 117 removed outlier: 3.712A pdb=" N PHE R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE R 93 " --> pdb=" O THR R 89 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU R 108 " --> pdb=" O THR R 104 " (cutoff:3.500A) Proline residue: R 109 - end of helix Processing helix chain 'R' and resid 123 through 158 Proline residue: R 131 - end of helix Processing helix chain 'R' and resid 165 through 184 Processing helix chain 'R' and resid 184 through 190 Processing helix chain 'R' and resid 218 through 232 Processing helix chain 'R' and resid 232 through 252 Processing helix chain 'R' and resid 294 through 329 removed outlier: 3.729A pdb=" N VAL R 309 " --> pdb=" O MET R 305 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) Proline residue: R 319 - end of helix Processing helix chain 'R' and resid 338 through 366 removed outlier: 4.060A pdb=" N VAL R 342 " --> pdb=" O ASP R 338 " (cutoff:3.500A) Proline residue: R 361 - end of helix removed outlier: 4.084A pdb=" N ASN R 365 " --> pdb=" O PRO R 361 " (cutoff:3.500A) Processing helix chain 'R' and resid 368 through 380 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 68 removed outlier: 3.506A pdb=" N LEU A 34 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A 76 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 38 " --> pdb=" O PHE A 76 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ARG A 35 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ILE A 99 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 37 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL A 101 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU A 39 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N ASP A 103 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 98 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N PHE A 134 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE A 100 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASN A 136 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL A 102 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N VAL A 131 " --> pdb=" O TYR A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.430A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.732A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP B 82 " --> pdb=" O LEU B 70 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.484A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 152 removed outlier: 3.623A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.440A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.740A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.418A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.772A pdb=" N GLY E 10 " --> pdb=" O THR E 116 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.686A pdb=" N ARG E 160 " --> pdb=" O THR E 141 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 149 removed outlier: 3.502A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 149 removed outlier: 3.502A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 192 through 196 462 hydrogen bonds defined for protein. 1302 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: 1.42 Time building geometry restraints manager: 1.06 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: 1973 1.33 - 1.45: 2129 1.45 - 1.57: 5078 1.57 - 1.69: 1 1.69 - 1.81: 92 Bond restraints: 9273 Sorted by residual: bond pdb=" C10 OLA R 504 " pdb=" C9 OLA R 504 " ideal model delta sigma weight residual 1.332 1.466 -0.134 2.00e-02 2.50e+03 4.46e+01 bond pdb=" C10 OLA R 505 " pdb=" C9 OLA R 505 " ideal model delta sigma weight residual 1.332 1.464 -0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" O27 A6F R 501 " pdb=" S26 A6F R 501 " ideal model delta sigma weight residual 1.455 1.528 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" O28 A6F R 501 " pdb=" S26 A6F R 501 " ideal model delta sigma weight residual 1.458 1.530 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" N25 A6F R 501 " pdb=" S26 A6F R 501 " ideal model delta sigma weight residual 1.647 1.600 0.047 2.00e-02 2.50e+03 5.44e+00 ... (remaining 9268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 12364 1.95 - 3.90: 133 3.90 - 5.86: 33 5.86 - 7.81: 15 7.81 - 9.76: 7 Bond angle restraints: 12552 Sorted by residual: angle pdb=" CA ILE R 130 " pdb=" C ILE R 130 " pdb=" N PRO R 131 " ideal model delta sigma weight residual 120.83 123.22 -2.39 6.10e-01 2.69e+00 1.53e+01 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 angle pdb=" CA PRO R 186 " pdb=" N PRO R 186 " pdb=" CD PRO R 186 " ideal model delta sigma weight residual 112.00 106.70 5.30 1.40e+00 5.10e-01 1.43e+01 angle pdb=" O ILE R 130 " pdb=" C ILE R 130 " pdb=" N PRO R 131 " ideal model delta sigma weight residual 120.42 118.27 2.15 6.40e-01 2.44e+00 1.12e+01 angle pdb=" O27 A6F R 501 " pdb=" S26 A6F R 501 " pdb=" O28 A6F R 501 " ideal model delta sigma weight residual 118.66 108.90 9.76 3.00e+00 1.11e-01 1.06e+01 ... (remaining 12547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.54: 5425 32.54 - 65.09: 109 65.09 - 97.63: 4 97.63 - 130.18: 0 130.18 - 162.72: 1 Dihedral angle restraints: 5539 sinusoidal: 2219 harmonic: 3320 Sorted by residual: dihedral pdb=" CB CYS R 127 " pdb=" SG CYS R 127 " pdb=" SG CYS R 210 " pdb=" CB CYS R 210 " ideal model delta sinusoidal sigma weight residual -86.00 -171.00 85.00 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 50.71 42.29 1 1.00e+01 1.00e-02 2.50e+01 dihedral pdb=" C3 A6F R 501 " pdb=" N25 A6F R 501 " pdb=" S26 A6F R 501 " pdb=" O28 A6F R 501 " ideal model delta sinusoidal sigma weight residual 328.43 165.71 162.72 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 5536 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1080 0.045 - 0.090: 242 0.090 - 0.135: 86 0.135 - 0.180: 1 0.180 - 0.225: 3 Chirality restraints: 1412 Sorted by residual: chirality pdb=" C16 A6F R 501 " pdb=" C15 A6F R 501 " pdb=" C17 A6F R 501 " pdb=" C19 A6F R 501 " both_signs ideal model delta sigma weight residual False -2.50 -2.72 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C2 A6F R 501 " pdb=" C11 A6F R 501 " pdb=" C3 A6F R 501 " pdb=" N1 A6F R 501 " both_signs ideal model delta sigma weight residual False -2.28 -2.49 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3 A6F R 501 " pdb=" C2 A6F R 501 " pdb=" C4 A6F R 501 " pdb=" N25 A6F R 501 " both_signs ideal model delta sigma weight residual False 2.34 2.52 -0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 1409 not shown) Planarity restraints: 1585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA R 505 " 0.206 2.00e-02 2.50e+03 1.59e-01 2.54e+02 pdb=" C11 OLA R 505 " -0.091 2.00e-02 2.50e+03 pdb=" C8 OLA R 505 " 0.092 2.00e-02 2.50e+03 pdb=" C9 OLA R 505 " -0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA R 504 " -0.154 2.00e-02 2.50e+03 1.20e-01 1.45e+02 pdb=" C11 OLA R 504 " 0.073 2.00e-02 2.50e+03 pdb=" C8 OLA R 504 " -0.072 2.00e-02 2.50e+03 pdb=" C9 OLA R 504 " 0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 185 " -0.075 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO R 186 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO R 186 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO R 186 " -0.060 5.00e-02 4.00e+02 ... (remaining 1582 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 178 2.69 - 3.24: 8669 3.24 - 3.79: 14062 3.79 - 4.35: 18382 4.35 - 4.90: 31541 Nonbonded interactions: 72832 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.134 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.141 3.040 nonbonded pdb=" O ARG E 67 " pdb=" OG1 THR E 84 " model vdw 2.145 3.040 nonbonded pdb=" O PHE E 32 " pdb=" NH2 ARG E 72 " model vdw 2.197 3.120 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.236 3.040 ... (remaining 72827 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: 0.740 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.030 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 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 0.134 9276 Z= 0.173 Angle : 0.619 9.761 12558 Z= 0.300 Chirality : 0.042 0.225 1412 Planarity : 0.007 0.159 1585 Dihedral : 12.325 162.724 3384 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.51 (0.26), residues: 1123 helix: 2.45 (0.26), residues: 392 sheet: 0.75 (0.31), residues: 295 loop : -0.11 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 200 TYR 0.026 0.001 TYR R 354 PHE 0.019 0.001 PHE R 375 TRP 0.007 0.001 TRP R 120 HIS 0.010 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 9273) covalent geometry : angle 0.61882 (12552) SS BOND : bond 0.00158 ( 3) SS BOND : angle 1.33962 ( 6) hydrogen bonds : bond 0.17805 ( 458) hydrogen bonds : angle 6.35226 ( 1302) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.290 Fit side-chains REVERT: A 133 LEU cc_start: 0.8234 (mm) cc_final: 0.7975 (mm) REVERT: A 187 LYS cc_start: 0.8389 (tmtt) cc_final: 0.7854 (tptp) REVERT: B 105 TYR cc_start: 0.8303 (t80) cc_final: 0.8073 (t80) REVERT: R 100 ASP cc_start: 0.8329 (m-30) cc_final: 0.8082 (m-30) REVERT: R 296 ILE cc_start: 0.7481 (mt) cc_final: 0.7258 (tp) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.0855 time to fit residues: 27.0800 Evaluate side-chains 178 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.172152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.140329 restraints weight = 12550.166| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.45 r_work: 0.3520 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9276 Z= 0.129 Angle : 0.542 7.911 12558 Z= 0.287 Chirality : 0.043 0.149 1412 Planarity : 0.004 0.076 1585 Dihedral : 8.006 171.141 1317 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.93 % Allowed : 8.13 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.49 (0.26), residues: 1123 helix: 2.40 (0.26), residues: 393 sheet: 0.70 (0.30), residues: 308 loop : -0.10 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 18 TYR 0.029 0.001 TYR R 354 PHE 0.016 0.001 PHE A 73 TRP 0.018 0.001 TRP B 169 HIS 0.008 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9273) covalent geometry : angle 0.54141 (12552) SS BOND : bond 0.00352 ( 3) SS BOND : angle 0.73854 ( 6) hydrogen bonds : bond 0.04076 ( 458) hydrogen bonds : angle 4.91070 ( 1302) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 0.329 Fit side-chains REVERT: A 74 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.6513 (t-90) REVERT: A 187 LYS cc_start: 0.8239 (tmtt) cc_final: 0.7811 (tptp) REVERT: E 192 MET cc_start: 0.7782 (ptt) cc_final: 0.7510 (ptt) REVERT: R 72 ASN cc_start: 0.8560 (m-40) cc_final: 0.8224 (m-40) REVERT: R 154 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.6994 (t80) REVERT: R 229 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7978 (tp) REVERT: R 354 TYR cc_start: 0.8255 (m-10) cc_final: 0.7677 (m-10) outliers start: 19 outliers final: 12 residues processed: 216 average time/residue: 0.0954 time to fit residues: 28.7388 Evaluate side-chains 199 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 244 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 9.9990 chunk 47 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 0.0070 chunk 48 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.170662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.139659 restraints weight = 12465.361| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.37 r_work: 0.3521 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9276 Z= 0.125 Angle : 0.524 6.694 12558 Z= 0.277 Chirality : 0.042 0.143 1412 Planarity : 0.004 0.069 1585 Dihedral : 7.708 167.324 1317 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.03 % Allowed : 11.79 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.41 (0.26), residues: 1123 helix: 2.37 (0.26), residues: 393 sheet: 0.60 (0.30), residues: 307 loop : -0.13 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 200 TYR 0.016 0.001 TYR R 354 PHE 0.013 0.001 PHE A 73 TRP 0.014 0.001 TRP B 169 HIS 0.007 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9273) covalent geometry : angle 0.52301 (12552) SS BOND : bond 0.00614 ( 3) SS BOND : angle 1.22704 ( 6) hydrogen bonds : bond 0.03795 ( 458) hydrogen bonds : angle 4.73248 ( 1302) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 74 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.6578 (t-90) REVERT: A 133 LEU cc_start: 0.8182 (mm) cc_final: 0.7788 (mm) REVERT: A 187 LYS cc_start: 0.8248 (tmtt) cc_final: 0.7808 (tptp) REVERT: E 192 MET cc_start: 0.7774 (ptt) cc_final: 0.7471 (ptt) REVERT: R 154 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.7000 (t80) REVERT: R 229 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8029 (tp) REVERT: R 354 TYR cc_start: 0.8361 (m-10) cc_final: 0.7551 (m-10) outliers start: 20 outliers final: 15 residues processed: 198 average time/residue: 0.0866 time to fit residues: 24.4711 Evaluate side-chains 201 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 315 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 60 optimal weight: 0.3980 chunk 72 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.169650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.139112 restraints weight = 12746.961| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.27 r_work: 0.3501 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9276 Z= 0.135 Angle : 0.520 6.640 12558 Z= 0.276 Chirality : 0.042 0.137 1412 Planarity : 0.004 0.065 1585 Dihedral : 7.370 158.827 1317 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.95 % Allowed : 12.70 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.31 (0.25), residues: 1123 helix: 2.30 (0.26), residues: 393 sheet: 0.62 (0.30), residues: 299 loop : -0.24 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 200 TYR 0.013 0.001 TYR R 354 PHE 0.012 0.001 PHE A 73 TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9273) covalent geometry : angle 0.51911 (12552) SS BOND : bond 0.00489 ( 3) SS BOND : angle 1.36436 ( 6) hydrogen bonds : bond 0.03683 ( 458) hydrogen bonds : angle 4.63418 ( 1302) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.400 Fit side-chains REVERT: A 74 HIS cc_start: 0.7819 (OUTLIER) cc_final: 0.6798 (t-90) REVERT: A 133 LEU cc_start: 0.8355 (mm) cc_final: 0.7926 (mm) REVERT: A 187 LYS cc_start: 0.8214 (tmtt) cc_final: 0.7810 (tptp) REVERT: R 154 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.7098 (t80) REVERT: R 191 MET cc_start: 0.6673 (tpp) cc_final: 0.6303 (tpp) REVERT: R 229 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8105 (tp) REVERT: R 233 MET cc_start: 0.7553 (tpt) cc_final: 0.7332 (tpt) outliers start: 29 outliers final: 19 residues processed: 206 average time/residue: 0.0854 time to fit residues: 25.2747 Evaluate side-chains 205 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 323 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 98 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 179 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.168730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.137632 restraints weight = 12517.480| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.33 r_work: 0.3483 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9276 Z= 0.129 Angle : 0.518 7.429 12558 Z= 0.274 Chirality : 0.042 0.158 1412 Planarity : 0.004 0.063 1585 Dihedral : 7.091 150.711 1317 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.85 % Allowed : 14.43 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.32 (0.25), residues: 1123 helix: 2.32 (0.26), residues: 393 sheet: 0.62 (0.30), residues: 299 loop : -0.26 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 27 TYR 0.017 0.001 TYR R 354 PHE 0.012 0.001 PHE A 73 TRP 0.012 0.001 TRP B 169 HIS 0.007 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9273) covalent geometry : angle 0.51759 (12552) SS BOND : bond 0.00315 ( 3) SS BOND : angle 0.78141 ( 6) hydrogen bonds : bond 0.03617 ( 458) hydrogen bonds : angle 4.58395 ( 1302) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.348 Fit side-chains REVERT: A 74 HIS cc_start: 0.7625 (OUTLIER) cc_final: 0.6616 (t-90) REVERT: A 187 LYS cc_start: 0.8119 (tmtt) cc_final: 0.7668 (tptp) REVERT: R 229 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8134 (tp) outliers start: 28 outliers final: 20 residues processed: 207 average time/residue: 0.0857 time to fit residues: 25.5754 Evaluate side-chains 207 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 179 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.170696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140230 restraints weight = 12612.423| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.29 r_work: 0.3514 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9276 Z= 0.107 Angle : 0.504 6.763 12558 Z= 0.265 Chirality : 0.042 0.162 1412 Planarity : 0.004 0.062 1585 Dihedral : 6.781 142.019 1317 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.13 % Allowed : 15.75 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.26), residues: 1123 helix: 2.50 (0.26), residues: 388 sheet: 0.71 (0.31), residues: 287 loop : -0.23 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 200 TYR 0.016 0.001 TYR R 354 PHE 0.011 0.001 PHE A 73 TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9273) covalent geometry : angle 0.50422 (12552) SS BOND : bond 0.00337 ( 3) SS BOND : angle 0.49623 ( 6) hydrogen bonds : bond 0.03415 ( 458) hydrogen bonds : angle 4.45648 ( 1302) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.346 Fit side-chains REVERT: A 74 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.6794 (t-90) REVERT: A 107 TYR cc_start: 0.8216 (m-80) cc_final: 0.8005 (m-80) REVERT: A 187 LYS cc_start: 0.8127 (tmtt) cc_final: 0.7699 (tptp) REVERT: B 334 SER cc_start: 0.8890 (OUTLIER) cc_final: 0.8679 (m) REVERT: R 72 ASN cc_start: 0.8664 (m-40) cc_final: 0.8391 (m-40) REVERT: R 154 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.7119 (t80) REVERT: R 184 MET cc_start: 0.7777 (mmp) cc_final: 0.7485 (tpp) REVERT: R 229 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8141 (tp) REVERT: R 233 MET cc_start: 0.7558 (tpt) cc_final: 0.7336 (tpt) outliers start: 21 outliers final: 16 residues processed: 201 average time/residue: 0.0844 time to fit residues: 24.4727 Evaluate side-chains 203 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 244 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 7.9990 chunk 13 optimal weight: 0.0040 chunk 38 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 179 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.169792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.137818 restraints weight = 12587.319| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.40 r_work: 0.3499 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9276 Z= 0.121 Angle : 0.522 6.799 12558 Z= 0.275 Chirality : 0.042 0.165 1412 Planarity : 0.004 0.061 1585 Dihedral : 6.495 132.885 1317 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.54 % Allowed : 17.28 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.36 (0.25), residues: 1123 helix: 2.46 (0.26), residues: 387 sheet: 0.67 (0.31), residues: 287 loop : -0.31 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 200 TYR 0.012 0.001 TYR E 190 PHE 0.011 0.001 PHE R 375 TRP 0.011 0.001 TRP B 169 HIS 0.006 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9273) covalent geometry : angle 0.52042 (12552) SS BOND : bond 0.00232 ( 3) SS BOND : angle 1.86393 ( 6) hydrogen bonds : bond 0.03485 ( 458) hydrogen bonds : angle 4.47246 ( 1302) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.348 Fit side-chains REVERT: A 74 HIS cc_start: 0.7610 (OUTLIER) cc_final: 0.6635 (t-90) REVERT: A 187 LYS cc_start: 0.8105 (tmtt) cc_final: 0.7655 (tptp) REVERT: A 189 PHE cc_start: 0.7807 (m-80) cc_final: 0.7592 (m-10) REVERT: B 334 SER cc_start: 0.8825 (OUTLIER) cc_final: 0.8620 (m) REVERT: G 21 MET cc_start: 0.4214 (mtp) cc_final: 0.3857 (mtp) REVERT: E 140 MET cc_start: 0.6977 (mtm) cc_final: 0.6488 (mtm) REVERT: R 154 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.7047 (t80) REVERT: R 229 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8126 (tp) outliers start: 25 outliers final: 20 residues processed: 198 average time/residue: 0.0820 time to fit residues: 23.2499 Evaluate side-chains 201 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 252 CYS Chi-restraints excluded: chain R residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 105 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.165749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135080 restraints weight = 12442.610| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.27 r_work: 0.3451 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9276 Z= 0.169 Angle : 0.570 6.834 12558 Z= 0.303 Chirality : 0.043 0.172 1412 Planarity : 0.004 0.061 1585 Dihedral : 6.405 123.745 1317 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.95 % Allowed : 16.77 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.25), residues: 1123 helix: 2.19 (0.26), residues: 393 sheet: 0.67 (0.30), residues: 294 loop : -0.47 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.024 0.001 TYR R 354 PHE 0.014 0.001 PHE A 73 TRP 0.012 0.001 TRP B 211 HIS 0.007 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9273) covalent geometry : angle 0.56861 (12552) SS BOND : bond 0.00418 ( 3) SS BOND : angle 1.68770 ( 6) hydrogen bonds : bond 0.03798 ( 458) hydrogen bonds : angle 4.63532 ( 1302) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.340 Fit side-chains REVERT: A 78 VAL cc_start: 0.6064 (OUTLIER) cc_final: 0.5851 (p) REVERT: A 187 LYS cc_start: 0.8029 (tmtt) cc_final: 0.7525 (tptp) REVERT: R 184 MET cc_start: 0.7814 (mmp) cc_final: 0.7493 (tpp) outliers start: 29 outliers final: 24 residues processed: 192 average time/residue: 0.0839 time to fit residues: 23.2178 Evaluate side-chains 199 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 252 CYS Chi-restraints excluded: chain R residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.166308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.134362 restraints weight = 12490.510| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.47 r_work: 0.3472 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9276 Z= 0.155 Angle : 0.579 9.695 12558 Z= 0.302 Chirality : 0.043 0.189 1412 Planarity : 0.004 0.061 1585 Dihedral : 6.268 117.814 1317 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.95 % Allowed : 16.77 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.03 (0.25), residues: 1123 helix: 2.16 (0.26), residues: 392 sheet: 0.53 (0.30), residues: 298 loop : -0.56 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 200 TYR 0.013 0.001 TYR E 102 PHE 0.016 0.001 PHE A 189 TRP 0.011 0.001 TRP B 169 HIS 0.007 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9273) covalent geometry : angle 0.57805 (12552) SS BOND : bond 0.00405 ( 3) SS BOND : angle 1.22816 ( 6) hydrogen bonds : bond 0.03778 ( 458) hydrogen bonds : angle 4.62581 ( 1302) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.318 Fit side-chains REVERT: A 78 VAL cc_start: 0.6370 (OUTLIER) cc_final: 0.6097 (p) REVERT: A 187 LYS cc_start: 0.8085 (tmtt) cc_final: 0.7577 (tptp) REVERT: R 120 TRP cc_start: 0.8141 (t-100) cc_final: 0.7748 (t-100) REVERT: R 233 MET cc_start: 0.7566 (tpt) cc_final: 0.6821 (ttp) outliers start: 29 outliers final: 24 residues processed: 185 average time/residue: 0.0817 time to fit residues: 21.8529 Evaluate side-chains 196 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 366 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.167087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.134501 restraints weight = 12528.760| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.51 r_work: 0.3485 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9276 Z= 0.130 Angle : 0.565 7.476 12558 Z= 0.295 Chirality : 0.043 0.207 1412 Planarity : 0.004 0.061 1585 Dihedral : 6.064 111.178 1317 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.64 % Allowed : 17.28 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.13 (0.25), residues: 1123 helix: 2.26 (0.26), residues: 388 sheet: 0.58 (0.30), residues: 298 loop : -0.48 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 200 TYR 0.015 0.001 TYR R 343 PHE 0.024 0.001 PHE E 68 TRP 0.011 0.001 TRP B 169 HIS 0.007 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9273) covalent geometry : angle 0.56457 (12552) SS BOND : bond 0.00354 ( 3) SS BOND : angle 1.14886 ( 6) hydrogen bonds : bond 0.03595 ( 458) hydrogen bonds : angle 4.55794 ( 1302) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 74 HIS cc_start: 0.7651 (OUTLIER) cc_final: 0.6643 (t-90) REVERT: A 187 LYS cc_start: 0.8041 (tmtt) cc_final: 0.7531 (tptp) REVERT: G 21 MET cc_start: 0.4188 (mtp) cc_final: 0.3797 (mtp) REVERT: R 120 TRP cc_start: 0.8087 (t-100) cc_final: 0.7782 (t-100) REVERT: R 229 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8140 (tp) outliers start: 26 outliers final: 21 residues processed: 188 average time/residue: 0.0882 time to fit residues: 23.7045 Evaluate side-chains 198 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 218 ARG Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 154 TYR Chi-restraints excluded: chain R residue 193 CYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 366 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 8.9990 chunk 109 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 18 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.170110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.138254 restraints weight = 12413.167| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.41 r_work: 0.3508 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9276 Z= 0.115 Angle : 0.562 11.232 12558 Z= 0.290 Chirality : 0.042 0.184 1412 Planarity : 0.004 0.061 1585 Dihedral : 5.895 106.374 1317 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.13 % Allowed : 17.99 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.21 (0.26), residues: 1123 helix: 2.34 (0.26), residues: 388 sheet: 0.63 (0.30), residues: 300 loop : -0.46 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 200 TYR 0.013 0.001 TYR E 190 PHE 0.019 0.001 PHE E 68 TRP 0.011 0.001 TRP B 169 HIS 0.006 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9273) covalent geometry : angle 0.56159 (12552) SS BOND : bond 0.00362 ( 3) SS BOND : angle 1.14106 ( 6) hydrogen bonds : bond 0.03471 ( 458) hydrogen bonds : angle 4.48073 ( 1302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2375.77 seconds wall clock time: 41 minutes 24.75 seconds (2484.75 seconds total)