Starting phenix.real_space_refine on Thu Mar 13 22:08:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sr8_25399/03_2025/7sr8_25399.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sr8_25399/03_2025/7sr8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sr8_25399/03_2025/7sr8_25399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sr8_25399/03_2025/7sr8_25399.map" model { file = "/net/cci-nas-00/data/ceres_data/7sr8_25399/03_2025/7sr8_25399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sr8_25399/03_2025/7sr8_25399.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.48, per 1000 atoms: 0.60 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: 2.38 Conformation dependent library (CDL) restraints added in 971.4 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: 1.00 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: 2.74 Time building geometry restraints manager: 2.80 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: 0.470 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.600 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 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 9273 Z= 0.233 Angle : 0.619 9.761 12552 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 : 9.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (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 TRP 0.007 0.001 TRP R 120 HIS 0.010 0.001 HIS R 224 PHE 0.019 0.001 PHE R 375 TYR 0.026 0.001 TYR R 354 ARG 0.006 0.000 ARG A 200 *********************** 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 : 1.029 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 85 MET cc_start: 0.6486 (ttp) cc_final: 0.6281 (ttm) REVERT: R 100 ASP cc_start: 0.8329 (m-30) cc_final: 0.8083 (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: 0.1971 time to fit residues: 61.7131 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 : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.168305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.136228 restraints weight = 12414.972| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.46 r_work: 0.3464 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9273 Z= 0.281 Angle : 0.586 7.292 12552 Z= 0.312 Chirality : 0.044 0.147 1412 Planarity : 0.005 0.077 1585 Dihedral : 8.099 170.326 1317 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.03 % Allowed : 8.43 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1123 helix: 2.23 (0.26), residues: 392 sheet: 0.52 (0.30), residues: 309 loop : -0.16 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.008 0.001 HIS R 224 PHE 0.019 0.002 PHE A 73 TYR 0.030 0.002 TYR R 354 ARG 0.006 0.001 ARG E 18 *********************** 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 223 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 1.006 Fit side-chains REVERT: A 74 HIS cc_start: 0.7505 (OUTLIER) cc_final: 0.6439 (t-90) REVERT: A 187 LYS cc_start: 0.8396 (tmtt) cc_final: 0.7938 (tptp) REVERT: E 192 MET cc_start: 0.7851 (ptt) cc_final: 0.7488 (ptt) REVERT: R 229 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8068 (tp) REVERT: R 354 TYR cc_start: 0.8381 (m-10) cc_final: 0.7673 (m-10) REVERT: R 374 GLU cc_start: 0.8039 (tp30) cc_final: 0.7738 (tp30) outliers start: 20 outliers final: 13 residues processed: 209 average time/residue: 0.2011 time to fit residues: 58.8153 Evaluate side-chains 202 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 213 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 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 24 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 34 optimal weight: 0.0870 chunk 39 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.171821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.140663 restraints weight = 12572.271| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.36 r_work: 0.3518 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9273 Z= 0.150 Angle : 0.509 6.072 12552 Z= 0.269 Chirality : 0.042 0.148 1412 Planarity : 0.004 0.069 1585 Dihedral : 7.658 167.016 1317 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.63 % Allowed : 12.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.26), residues: 1123 helix: 2.38 (0.26), residues: 393 sheet: 0.55 (0.30), residues: 307 loop : -0.12 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.007 0.001 HIS R 224 PHE 0.013 0.001 PHE R 375 TYR 0.015 0.001 TYR E 190 ARG 0.004 0.000 ARG A 200 *********************** 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 218 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 1.008 Fit side-chains REVERT: A 74 HIS cc_start: 0.7539 (OUTLIER) cc_final: 0.6568 (t-90) REVERT: A 187 LYS cc_start: 0.8240 (tmtt) cc_final: 0.7816 (tptp) REVERT: E 192 MET cc_start: 0.7760 (ptt) cc_final: 0.7508 (ptt) REVERT: R 72 ASN cc_start: 0.8492 (m-40) cc_final: 0.8210 (m-40) REVERT: R 85 MET cc_start: 0.6536 (ttp) cc_final: 0.6236 (ttm) REVERT: R 154 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.7125 (t80) REVERT: R 229 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8092 (tp) REVERT: R 354 TYR cc_start: 0.8326 (m-10) cc_final: 0.7677 (m-10) outliers start: 16 outliers final: 9 residues processed: 206 average time/residue: 0.2138 time to fit residues: 61.8831 Evaluate side-chains 193 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 270 ILE Chi-restraints excluded: chain R residue 84 HIS 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 244 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 90 optimal weight: 0.0070 chunk 106 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6800 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.171009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.139969 restraints weight = 12354.521| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.24 r_work: 0.3568 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9273 Z= 0.155 Angle : 0.504 6.402 12552 Z= 0.265 Chirality : 0.041 0.142 1412 Planarity : 0.004 0.065 1585 Dihedral : 7.287 159.544 1317 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.54 % Allowed : 13.82 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1123 helix: 2.39 (0.26), residues: 393 sheet: 0.66 (0.30), residues: 302 loop : -0.18 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.006 0.001 HIS R 224 PHE 0.012 0.001 PHE R 375 TYR 0.024 0.001 TYR R 354 ARG 0.006 0.000 ARG A 200 *********************** 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 217 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 0.908 Fit side-chains REVERT: A 74 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.6804 (t-90) REVERT: A 187 LYS cc_start: 0.8180 (tmtt) cc_final: 0.7789 (tptp) REVERT: E 93 MET cc_start: 0.8501 (tpp) cc_final: 0.8290 (tpp) REVERT: E 140 MET cc_start: 0.6547 (mtm) cc_final: 0.6340 (mtm) REVERT: R 229 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8100 (tp) outliers start: 25 outliers final: 19 residues processed: 200 average time/residue: 0.2052 time to fit residues: 58.0682 Evaluate side-chains 202 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 105 TYR 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 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 84 HIS 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 323 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 15 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.163031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.131745 restraints weight = 12541.754| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.18 r_work: 0.3427 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9273 Z= 0.370 Angle : 0.615 7.460 12552 Z= 0.327 Chirality : 0.046 0.188 1412 Planarity : 0.005 0.065 1585 Dihedral : 7.459 151.664 1317 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.96 % Allowed : 15.24 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1123 helix: 1.96 (0.26), residues: 393 sheet: 0.22 (0.29), residues: 316 loop : -0.38 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 211 HIS 0.007 0.001 HIS R 224 PHE 0.017 0.002 PHE A 100 TYR 0.016 0.002 TYR E 95 ARG 0.006 0.000 ARG G 27 *********************** 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 224 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 1.016 Fit side-chains REVERT: A 187 LYS cc_start: 0.8313 (tmtt) cc_final: 0.7806 (tptp) REVERT: R 85 MET cc_start: 0.6783 (ttp) cc_final: 0.6482 (ttm) REVERT: R 305 MET cc_start: 0.8901 (tpt) cc_final: 0.8617 (tpp) outliers start: 39 outliers final: 28 residues processed: 200 average time/residue: 0.2339 time to fit residues: 66.4960 Evaluate side-chains 199 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 1.770 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 105 TYR 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 19 LEU Chi-restraints excluded: chain E residue 37 VAL 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 84 HIS Chi-restraints excluded: chain R residue 89 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 105 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.166589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.136146 restraints weight = 12525.595| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.20 r_work: 0.3474 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9273 Z= 0.222 Angle : 0.548 7.002 12552 Z= 0.290 Chirality : 0.043 0.175 1412 Planarity : 0.004 0.063 1585 Dihedral : 7.082 145.961 1317 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.85 % Allowed : 16.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.25), residues: 1123 helix: 2.01 (0.26), residues: 392 sheet: 0.16 (0.29), residues: 315 loop : -0.40 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS R 224 PHE 0.013 0.001 PHE A 73 TYR 0.013 0.001 TYR E 102 ARG 0.004 0.000 ARG G 13 *********************** 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 213 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 1.022 Fit side-chains REVERT: A 74 HIS cc_start: 0.7756 (OUTLIER) cc_final: 0.6623 (t-90) REVERT: A 187 LYS cc_start: 0.8148 (tmtt) cc_final: 0.7671 (tptp) REVERT: R 72 ASN cc_start: 0.8870 (m-40) cc_final: 0.8586 (m-40) REVERT: R 85 MET cc_start: 0.6450 (ttp) cc_final: 0.6135 (ttm) REVERT: R 305 MET cc_start: 0.8986 (tpt) cc_final: 0.8571 (tpp) outliers start: 28 outliers final: 22 residues processed: 199 average time/residue: 0.2047 time to fit residues: 57.4371 Evaluate side-chains 202 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 105 TYR 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 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 84 HIS Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 119 THR 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 6 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.163760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.133423 restraints weight = 12610.656| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.22 r_work: 0.3423 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9273 Z= 0.276 Angle : 0.579 7.591 12552 Z= 0.307 Chirality : 0.044 0.190 1412 Planarity : 0.005 0.062 1585 Dihedral : 6.902 138.314 1317 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.15 % Allowed : 16.46 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1123 helix: 1.92 (0.26), residues: 393 sheet: 0.16 (0.29), residues: 308 loop : -0.47 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.007 0.001 HIS R 224 PHE 0.013 0.001 PHE A 73 TYR 0.014 0.001 TYR R 343 ARG 0.004 0.000 ARG A 200 *********************** 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 213 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.998 Fit side-chains REVERT: A 74 HIS cc_start: 0.7795 (OUTLIER) cc_final: 0.6683 (t-90) REVERT: A 133 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7791 (mm) REVERT: A 187 LYS cc_start: 0.8235 (tmtt) cc_final: 0.7705 (tptp) REVERT: B 301 LYS cc_start: 0.8011 (mmtm) cc_final: 0.7759 (mmtm) REVERT: B 339 TRP cc_start: 0.8316 (OUTLIER) cc_final: 0.7973 (m100) REVERT: E 68 PHE cc_start: 0.7594 (m-10) cc_final: 0.7172 (m-10) REVERT: R 72 ASN cc_start: 0.8909 (m-40) cc_final: 0.8657 (m-40) REVERT: R 132 TYR cc_start: 0.8115 (t80) cc_final: 0.7794 (t80) REVERT: R 233 MET cc_start: 0.7557 (tpt) cc_final: 0.6829 (ttp) REVERT: R 305 MET cc_start: 0.8960 (tpt) cc_final: 0.8573 (tpp) outliers start: 31 outliers final: 26 residues processed: 197 average time/residue: 0.1893 time to fit residues: 52.7743 Evaluate side-chains 205 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 95 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 105 TYR 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 B residue 339 TRP 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 84 HIS Chi-restraints excluded: chain R residue 89 THR Chi-restraints excluded: chain R residue 119 THR 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 Chi-restraints excluded: chain R residue 366 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 175 GLN E 179 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.167447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.135833 restraints weight = 12724.177| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.36 r_work: 0.3468 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9273 Z= 0.184 Angle : 0.540 7.299 12552 Z= 0.287 Chirality : 0.042 0.161 1412 Planarity : 0.004 0.062 1585 Dihedral : 6.481 129.430 1317 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.35 % Allowed : 16.87 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1123 helix: 2.07 (0.26), residues: 394 sheet: 0.28 (0.29), residues: 305 loop : -0.50 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS R 224 PHE 0.012 0.001 PHE A 73 TYR 0.014 0.001 TYR E 190 ARG 0.006 0.000 ARG A 200 *********************** 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 214 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 1.050 Fit side-chains REVERT: A 74 HIS cc_start: 0.7606 (OUTLIER) cc_final: 0.6533 (t-90) REVERT: A 133 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7682 (mm) REVERT: A 187 LYS cc_start: 0.8113 (tmtt) cc_final: 0.7605 (tptp) REVERT: B 16 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.7461 (m110) REVERT: B 339 TRP cc_start: 0.8034 (OUTLIER) cc_final: 0.7653 (m100) REVERT: R 85 MET cc_start: 0.6508 (ttp) cc_final: 0.6246 (ttm) REVERT: R 132 TYR cc_start: 0.8034 (t80) cc_final: 0.7681 (t80) REVERT: R 229 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8107 (tp) REVERT: R 305 MET cc_start: 0.8850 (tpt) cc_final: 0.8485 (tpp) outliers start: 33 outliers final: 23 residues processed: 196 average time/residue: 0.1898 time to fit residues: 53.0764 Evaluate side-chains 203 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 105 TYR 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 339 TRP 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 89 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 119 THR 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 318 LEU Chi-restraints excluded: chain R residue 323 LEU Chi-restraints excluded: chain R residue 366 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 175 GLN E 179 GLN ** R 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.167326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.136395 restraints weight = 12402.771| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.27 r_work: 0.3492 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9273 Z= 0.202 Angle : 0.553 7.251 12552 Z= 0.292 Chirality : 0.043 0.180 1412 Planarity : 0.004 0.061 1585 Dihedral : 6.352 124.104 1317 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.95 % Allowed : 17.38 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 1123 helix: 2.06 (0.26), residues: 394 sheet: 0.34 (0.29), residues: 304 loop : -0.52 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.006 0.001 HIS R 224 PHE 0.012 0.001 PHE A 73 TYR 0.013 0.001 TYR E 190 ARG 0.009 0.000 ARG E 18 *********************** 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 210 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 74 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.6677 (t-90) REVERT: A 133 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7729 (mm) REVERT: A 187 LYS cc_start: 0.8113 (tmtt) cc_final: 0.7596 (tptp) REVERT: B 339 TRP cc_start: 0.8266 (OUTLIER) cc_final: 0.7912 (m100) REVERT: G 13 ARG cc_start: 0.6512 (mmm160) cc_final: 0.6239 (ptm-80) REVERT: G 21 MET cc_start: 0.4502 (mtp) cc_final: 0.4149 (mtp) REVERT: R 85 MET cc_start: 0.6548 (ttp) cc_final: 0.6294 (ttm) REVERT: R 132 TYR cc_start: 0.8100 (t80) cc_final: 0.7742 (t80) REVERT: R 229 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8124 (tp) REVERT: R 305 MET cc_start: 0.8955 (tpt) cc_final: 0.8593 (tpp) outliers start: 29 outliers final: 23 residues processed: 193 average time/residue: 0.1885 time to fit residues: 51.9130 Evaluate side-chains 203 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 133 LEU Chi-restraints excluded: chain B residue 105 TYR 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 181 THR 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 339 TRP Chi-restraints excluded: chain G residue 19 LEU 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 119 THR 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 Chi-restraints excluded: chain R residue 323 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 108 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 13 optimal weight: 0.0980 chunk 43 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.163333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.132146 restraints weight = 12636.308| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.36 r_work: 0.3418 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9273 Z= 0.319 Angle : 0.615 7.379 12552 Z= 0.326 Chirality : 0.045 0.194 1412 Planarity : 0.005 0.060 1585 Dihedral : 6.497 117.700 1317 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.15 % Allowed : 17.28 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 1123 helix: 1.76 (0.26), residues: 393 sheet: 0.04 (0.29), residues: 305 loop : -0.63 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.007 0.001 HIS R 224 PHE 0.013 0.002 PHE A 100 TYR 0.014 0.002 TYR E 102 ARG 0.008 0.001 ARG E 18 ********************** 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 206 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 1.054 Fit side-chains REVERT: A 74 HIS cc_start: 0.7673 (OUTLIER) cc_final: 0.6530 (t-90) REVERT: A 133 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7734 (mm) REVERT: A 187 LYS cc_start: 0.8162 (tmtt) cc_final: 0.7583 (tptp) REVERT: B 339 TRP cc_start: 0.8142 (OUTLIER) cc_final: 0.7792 (m100) REVERT: R 120 TRP cc_start: 0.8022 (t-100) cc_final: 0.7651 (t-100) REVERT: R 132 TYR cc_start: 0.8081 (t80) cc_final: 0.7754 (t80) REVERT: R 305 MET cc_start: 0.8868 (tpt) cc_final: 0.8520 (tpp) outliers start: 31 outliers final: 26 residues processed: 191 average time/residue: 0.1915 time to fit residues: 52.1850 Evaluate side-chains 202 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 95 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 105 TYR 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 181 THR 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 339 TRP Chi-restraints excluded: chain G residue 19 LEU 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 119 THR 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 Chi-restraints excluded: chain R residue 323 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 77 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 3 optimal weight: 0.0370 chunk 84 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.8060 ------------------------------------------------------------------------------- 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 = 0.4004 r_free = 0.4004 target = 0.168087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.138148 restraints weight = 12553.924| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.19 r_work: 0.3505 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9273 Z= 0.176 Angle : 0.556 8.342 12552 Z= 0.293 Chirality : 0.043 0.190 1412 Planarity : 0.004 0.061 1585 Dihedral : 6.097 109.989 1317 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.74 % Allowed : 17.78 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1123 helix: 2.04 (0.26), residues: 388 sheet: 0.20 (0.29), residues: 304 loop : -0.54 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.007 0.001 HIS R 224 PHE 0.011 0.001 PHE A 73 TYR 0.014 0.001 TYR E 190 ARG 0.007 0.000 ARG E 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5279.42 seconds wall clock time: 93 minutes 41.15 seconds (5621.15 seconds total)