Starting phenix.real_space_refine on Fri Jul 3 16:11:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t60_41062/07_2026/8t60_41062.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t60_41062/07_2026/8t60_41062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t60_41062/07_2026/8t60_41062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t60_41062/07_2026/8t60_41062.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t60_41062/07_2026/8t60_41062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t60_41062/07_2026/8t60_41062.map" } resolution = 3.29 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 126 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 34 5.16 5 Na 1 4.78 5 C 4855 2.51 5 N 1216 2.21 5 O 1397 1.98 5 H 7418 0.53 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-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14921 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 417, 6516 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 12, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Conformer: "B" Number of residues, atoms: 417, 6516 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 12, 'TRANS': 404} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 bond proxies already assigned to first conformer: 6574 Chain: "B" Number of atoms: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1832 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "H" Number of atoms: 3396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 3396 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 11, 'TRANS': 217} Chain: "L" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 3155 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 10, 'TRANS': 199} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' NA': 1} Chain breaks: 1 Time building chain proxies: 3.66, per 1000 atoms: 0.25 Number of scatterers: 14921 At special positions: 0 Unit cell: (68.8, 83.42, 173.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 Na 1 11.00 O 1397 8.00 N 1216 7.00 C 4855 6.00 H 7418 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 562.0 milliseconds 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1796 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 14 sheets defined 39.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 4 through 36 removed outlier: 3.522A pdb=" N LYS A 8 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA A 15 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TYR A 31 " --> pdb=" O MET A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 58 removed outlier: 3.895A pdb=" N ASP A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 69 removed outlier: 4.134A pdb=" N MET A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 63 " --> pdb=" O ASP A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 95 removed outlier: 3.587A pdb=" N LEU A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 removed outlier: 3.556A pdb=" N PHE A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 134 removed outlier: 4.241A pdb=" N VAL A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Proline residue: A 126 - end of helix removed outlier: 4.745A pdb=" N VAL A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 140 through 145 removed outlier: 3.558A pdb=" N LEU A 144 " --> pdb=" O GLU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 171 removed outlier: 3.769A pdb=" N ARG A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 176 through 200 removed outlier: 3.672A pdb=" N MET A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 Processing helix chain 'A' and resid 230 through 261 removed outlier: 3.563A pdb=" N ALA A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 254 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N TYR A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 273 Processing helix chain 'A' and resid 274 through 285 removed outlier: 4.058A pdb=" N ALA A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 293 Processing helix chain 'A' and resid 294 through 317 Proline residue: A 306 - end of helix Processing helix chain 'A' and resid 323 through 355 removed outlier: 4.361A pdb=" N VAL A 346 " --> pdb=" O TRP A 342 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 349 " --> pdb=" O GLN A 345 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 395 removed outlier: 3.669A pdb=" N SER A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLN A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR A 373 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 417 Processing helix chain 'A' and resid 417 through 432 removed outlier: 3.853A pdb=" N PHE A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.697A pdb=" N ASP H 86 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'L' and resid 183 through 187 removed outlier: 3.685A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 183 through 187' Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.572A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 78 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 59 removed outlier: 6.627A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N MET B 34 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.787A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.850A pdb=" N GLY H 10 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 121 through 124 removed outlier: 4.428A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 121 through 124 removed outlier: 4.428A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 151 through 154 removed outlier: 3.995A pdb=" N THR H 205 " --> pdb=" O HIS H 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.407A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.508A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.680A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.605A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 89 through 90 removed outlier: 3.538A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.583A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 153 through 154 385 hydrogen bonds defined for protein. 1076 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: 2.90 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7414 1.03 - 1.23: 47 1.23 - 1.43: 3272 1.43 - 1.62: 4321 1.62 - 1.82: 54 Bond restraints: 15108 Sorted by residual: bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" N GLU H 1 " pdb=" H GLU H 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C THR A 121 " pdb=" O THR A 121 " ideal model delta sigma weight residual 1.236 1.247 -0.010 1.15e-02 7.56e+03 8.12e-01 bond pdb=" C VAL A 185 " pdb=" O VAL A 185 " ideal model delta sigma weight residual 1.237 1.246 -0.009 1.17e-02 7.31e+03 6.03e-01 bond pdb=" N ILE A 125 " pdb=" CA ILE A 125 " ideal model delta sigma weight residual 1.463 1.472 -0.009 1.20e-02 6.94e+03 5.33e-01 ... (remaining 15103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 25209 0.98 - 1.97: 1861 1.97 - 2.95: 91 2.95 - 3.94: 39 3.94 - 4.92: 9 Bond angle restraints: 27209 Sorted by residual: angle pdb=" N GLY A 395 " pdb=" CA GLY A 395 " pdb=" C GLY A 395 " ideal model delta sigma weight residual 111.12 115.25 -4.13 1.49e+00 4.50e-01 7.67e+00 angle pdb=" N ASP A 124 " pdb=" CA ASP A 124 " pdb=" C ASP A 124 " ideal model delta sigma weight residual 111.69 114.17 -2.48 1.23e+00 6.61e-01 4.08e+00 angle pdb=" CA GLY B 107 " pdb=" C GLY B 107 " pdb=" N LYS B 108 " ideal model delta sigma weight residual 114.61 117.12 -2.51 1.26e+00 6.30e-01 3.98e+00 angle pdb=" N ARG A 139 " pdb=" CA ARG A 139 " pdb=" CB ARG A 139 " ideal model delta sigma weight residual 113.65 110.82 2.83 1.47e+00 4.63e-01 3.71e+00 angle pdb=" N ALA A 173 " pdb=" CA ALA A 173 " pdb=" CB ALA A 173 " ideal model delta sigma weight residual 113.65 110.95 2.70 1.47e+00 4.63e-01 3.38e+00 ... (remaining 27204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 6656 16.61 - 33.23: 373 33.23 - 49.84: 123 49.84 - 66.45: 63 66.45 - 83.06: 4 Dihedral angle restraints: 7219 sinusoidal: 3778 harmonic: 3441 Sorted by residual: dihedral pdb=" CA LEU A 130 " pdb=" C LEU A 130 " pdb=" N VAL A 131 " pdb=" CA VAL A 131 " ideal model delta harmonic sigma weight residual -180.00 -162.94 -17.06 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA LEU A 393 " pdb=" C LEU A 393 " pdb=" N ILE A 394 " pdb=" CA ILE A 394 " ideal model delta harmonic sigma weight residual 180.00 -163.39 -16.61 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA VAL H 142 " pdb=" C VAL H 142 " pdb=" N LYS H 143 " pdb=" CA LYS H 143 " ideal model delta harmonic sigma weight residual -180.00 -164.01 -15.99 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 7216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 776 0.031 - 0.061: 285 0.061 - 0.092: 73 0.092 - 0.123: 59 0.123 - 0.153: 6 Chirality restraints: 1199 Sorted by residual: chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CA VAL H 37 " pdb=" N VAL H 37 " pdb=" C VAL H 37 " pdb=" CB VAL H 37 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA VAL A 204 " pdb=" N VAL A 204 " pdb=" C VAL A 204 " pdb=" CB VAL A 204 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 1196 not shown) Planarity restraints: 2238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 164 " 0.015 5.00e-02 4.00e+02 2.31e-02 8.53e-01 pdb=" N PRO A 165 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 125 " 0.015 5.00e-02 4.00e+02 2.25e-02 8.07e-01 pdb=" N PRO H 126 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO H 126 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO H 126 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 49 " -0.009 2.00e-02 2.50e+03 5.16e-03 8.00e-01 pdb=" CG TYR L 49 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR L 49 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR L 49 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR L 49 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR L 49 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR L 49 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR L 49 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR L 49 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR L 49 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 TYR L 49 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR L 49 " -0.001 2.00e-02 2.50e+03 ... (remaining 2235 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 1835 2.26 - 2.84: 33084 2.84 - 3.43: 36041 3.43 - 4.01: 49785 4.01 - 4.60: 76207 Nonbonded interactions: 196952 Sorted by model distance: nonbonded pdb=" HH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 1.673 2.450 nonbonded pdb=" O THR A 159 " pdb=" HG1 THR A 163 " model vdw 1.693 2.450 nonbonded pdb=" OD2 ASP L 151 " pdb=" HD1 HIS L 189 " model vdw 1.708 2.450 nonbonded pdb=" OH TYR A 32 " pdb=" HD1 HIS A 98 " model vdw 1.720 2.450 nonbonded pdb=" O ASP L 82 " pdb=" HH TYR L 86 " model vdw 1.722 2.450 ... (remaining 196947 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=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.110 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.170 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 : 0.003 0.034 7695 Z= 0.135 Angle : 0.510 4.922 10484 Z= 0.282 Chirality : 0.040 0.153 1199 Planarity : 0.003 0.024 1303 Dihedral : 11.070 81.545 2655 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.85 % Allowed : 8.14 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.28), residues: 967 helix: 2.23 (0.29), residues: 340 sheet: 0.60 (0.37), residues: 224 loop : -1.66 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.015 0.001 TYR L 49 PHE 0.012 0.001 PHE A 20 TRP 0.008 0.001 TRP B 106 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 7690) covalent geometry : angle 0.50979 / 0.28 (10474) SS BOND : bond 0.00367 / 0.20 ( 5) SS BOND : angle 0.71237 / 0.37 ( 10) hydrogen bonds : bond 0.11819 / 7.68 ( 370) hydrogen bonds : angle 5.52280 / 4.21 ( 1076) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8155 (tpt) cc_final: 0.7785 (tpt) REVERT: A 348 MET cc_start: 0.5442 (ttt) cc_final: 0.5209 (tpt) REVERT: A 423 MET cc_start: 0.7815 (ttt) cc_final: 0.7563 (ttm) REVERT: B 4 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8239 (mp) REVERT: B 25 SER cc_start: 0.8167 (p) cc_final: 0.7942 (m) REVERT: B 34 MET cc_start: 0.7313 (mpp) cc_final: 0.6962 (mtt) REVERT: L 170 ASP cc_start: 0.8551 (m-30) cc_final: 0.7814 (p0) outliers start: 15 outliers final: 5 residues processed: 151 average time/residue: 0.1651 time to fit residues: 34.5159 Evaluate side-chains 114 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain H residue 50 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.136098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.113239 restraints weight = 50800.037| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 3.05 r_work: 0.3599 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7695 Z= 0.130 Angle : 0.542 5.385 10484 Z= 0.289 Chirality : 0.041 0.160 1199 Planarity : 0.003 0.052 1303 Dihedral : 5.240 56.904 1069 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.23 % Allowed : 12.33 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.28), residues: 967 helix: 2.00 (0.28), residues: 340 sheet: 0.71 (0.36), residues: 224 loop : -1.73 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 70 TYR 0.022 0.001 TYR A 257 PHE 0.027 0.001 PHE A 20 TRP 0.006 0.001 TRP H 47 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 7690) covalent geometry : angle 0.54146 / 0.29 (10474) SS BOND : bond 0.00635 / 0.33 ( 5) SS BOND : angle 0.98628 / 0.52 ( 10) hydrogen bonds : bond 0.05186 / 3.35 ( 370) hydrogen bonds : angle 4.82655 / 3.60 ( 1076) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8269 (tpt) cc_final: 0.7922 (tpt) REVERT: A 348 MET cc_start: 0.5429 (ttt) cc_final: 0.5169 (tpt) REVERT: A 423 MET cc_start: 0.7932 (ttt) cc_final: 0.7660 (ttm) REVERT: B 4 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8229 (mp) REVERT: B 34 MET cc_start: 0.7333 (mpp) cc_final: 0.6995 (mtt) REVERT: H 79 TYR cc_start: 0.8143 (m-80) cc_final: 0.7887 (m-80) REVERT: L 170 ASP cc_start: 0.8648 (m-30) cc_final: 0.7830 (p0) outliers start: 10 outliers final: 7 residues processed: 123 average time/residue: 0.1479 time to fit residues: 25.8104 Evaluate side-chains 113 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 204 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.135089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.112611 restraints weight = 47310.607| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.92 r_work: 0.3591 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7695 Z= 0.144 Angle : 0.544 4.963 10484 Z= 0.291 Chirality : 0.040 0.160 1199 Planarity : 0.003 0.035 1303 Dihedral : 4.875 42.371 1065 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.48 % Allowed : 13.69 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.27), residues: 967 helix: 1.91 (0.28), residues: 340 sheet: 0.66 (0.36), residues: 224 loop : -1.80 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 70 TYR 0.025 0.001 TYR A 257 PHE 0.022 0.001 PHE A 20 TRP 0.008 0.001 TRP H 47 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 7690) covalent geometry : angle 0.54376 / 0.29 (10474) SS BOND : bond 0.00425 / 0.22 ( 5) SS BOND : angle 0.83091 / 0.48 ( 10) hydrogen bonds : bond 0.05030 / 3.24 ( 370) hydrogen bonds : angle 4.70822 / 3.49 ( 1076) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8293 (tpt) cc_final: 0.7918 (tpt) REVERT: A 227 ILE cc_start: 0.7296 (tt) cc_final: 0.6984 (pt) REVERT: A 348 MET cc_start: 0.5420 (ttt) cc_final: 0.5152 (tpt) REVERT: A 423 MET cc_start: 0.7941 (ttt) cc_final: 0.7671 (ttm) REVERT: B 4 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8245 (mp) REVERT: B 34 MET cc_start: 0.7342 (mpp) cc_final: 0.6978 (mtt) REVERT: H 100 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8218 (mt) REVERT: L 170 ASP cc_start: 0.8684 (m-30) cc_final: 0.7865 (p0) outliers start: 12 outliers final: 5 residues processed: 114 average time/residue: 0.1460 time to fit residues: 23.9236 Evaluate side-chains 111 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.0670 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.135679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.112674 restraints weight = 52437.922| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.10 r_work: 0.3586 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7695 Z= 0.128 Angle : 0.526 4.861 10484 Z= 0.281 Chirality : 0.040 0.157 1199 Planarity : 0.003 0.030 1303 Dihedral : 4.832 42.034 1065 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.60 % Allowed : 13.56 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.28), residues: 967 helix: 1.99 (0.28), residues: 340 sheet: 0.65 (0.35), residues: 233 loop : -1.73 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 70 TYR 0.022 0.001 TYR A 257 PHE 0.018 0.001 PHE A 20 TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 7690) covalent geometry : angle 0.52560 / 0.28 (10474) SS BOND : bond 0.00386 / 0.20 ( 5) SS BOND : angle 0.66909 / 0.40 ( 10) hydrogen bonds : bond 0.04630 / 2.99 ( 370) hydrogen bonds : angle 4.51243 / 3.32 ( 1076) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8331 (tpt) cc_final: 0.7968 (tpt) REVERT: A 227 ILE cc_start: 0.7247 (tt) cc_final: 0.6964 (pt) REVERT: A 239 MET cc_start: 0.8342 (mtp) cc_final: 0.7981 (mtp) REVERT: A 423 MET cc_start: 0.7948 (ttt) cc_final: 0.7672 (ttm) REVERT: B 4 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8241 (mp) REVERT: B 34 MET cc_start: 0.7305 (mpp) cc_final: 0.6971 (mtt) REVERT: H 100 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8216 (mt) REVERT: L 170 ASP cc_start: 0.8726 (m-30) cc_final: 0.7831 (p0) outliers start: 13 outliers final: 7 residues processed: 121 average time/residue: 0.1495 time to fit residues: 25.8865 Evaluate side-chains 113 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.133275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.110490 restraints weight = 50157.869| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.00 r_work: 0.3556 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7695 Z= 0.184 Angle : 0.568 4.923 10484 Z= 0.307 Chirality : 0.041 0.163 1199 Planarity : 0.004 0.028 1303 Dihedral : 4.933 41.367 1063 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.60 % Allowed : 13.32 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.27), residues: 967 helix: 1.74 (0.28), residues: 340 sheet: 0.71 (0.35), residues: 230 loop : -1.88 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 38 TYR 0.023 0.002 TYR L 49 PHE 0.011 0.001 PHE H 146 TRP 0.009 0.002 TRP H 47 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 7690) covalent geometry : angle 0.56723 / 0.31 (10474) SS BOND : bond 0.00428 / 0.22 ( 5) SS BOND : angle 0.92729 / 0.55 ( 10) hydrogen bonds : bond 0.05222 / 3.35 ( 370) hydrogen bonds : angle 4.69318 / 3.45 ( 1076) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8362 (tpt) cc_final: 0.7956 (tpt) REVERT: A 227 ILE cc_start: 0.7322 (tt) cc_final: 0.6969 (pt) REVERT: A 239 MET cc_start: 0.8169 (mtp) cc_final: 0.7955 (mtp) REVERT: A 423 MET cc_start: 0.7961 (ttt) cc_final: 0.7682 (ttm) REVERT: B 4 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8329 (mp) REVERT: B 34 MET cc_start: 0.7411 (mpp) cc_final: 0.7097 (mtt) REVERT: H 100 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8316 (mt) REVERT: L 170 ASP cc_start: 0.8769 (m-30) cc_final: 0.7949 (p0) outliers start: 13 outliers final: 8 residues processed: 115 average time/residue: 0.1425 time to fit residues: 23.8056 Evaluate side-chains 112 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 163 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 62 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.135135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.113110 restraints weight = 44065.157| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.78 r_work: 0.3602 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.003 0.030 7695 Z= 0.123 Angle : 0.527 5.273 10484 Z= 0.282 Chirality : 0.040 0.160 1199 Planarity : 0.003 0.027 1303 Dihedral : 4.803 41.241 1063 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.36 % Allowed : 14.92 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.28), residues: 967 helix: 1.94 (0.28), residues: 340 sheet: 0.91 (0.36), residues: 216 loop : -1.80 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 139 TYR 0.023 0.001 TYR A 257 PHE 0.014 0.001 PHE A 20 TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 7690) covalent geometry : angle 0.52712 / 0.28 (10474) SS BOND : bond 0.00375 / 0.20 ( 5) SS BOND : angle 0.63960 / 0.39 ( 10) hydrogen bonds : bond 0.04620 / 2.97 ( 370) hydrogen bonds : angle 4.46460 / 3.27 ( 1076) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8316 (tpt) cc_final: 0.7947 (tpt) REVERT: A 227 ILE cc_start: 0.7351 (tt) cc_final: 0.7012 (pt) REVERT: A 423 MET cc_start: 0.7885 (ttt) cc_final: 0.7683 (ttm) REVERT: B 4 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8282 (mp) REVERT: B 34 MET cc_start: 0.7346 (mpp) cc_final: 0.6996 (mtt) REVERT: H 100 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8222 (mt) REVERT: L 170 ASP cc_start: 0.8731 (m-30) cc_final: 0.7893 (p0) outliers start: 11 outliers final: 8 residues processed: 115 average time/residue: 0.1624 time to fit residues: 27.1333 Evaluate side-chains 114 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.134244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.111385 restraints weight = 50805.872| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.01 r_work: 0.3571 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7695 Z= 0.150 Angle : 0.541 6.242 10484 Z= 0.291 Chirality : 0.040 0.159 1199 Planarity : 0.003 0.028 1303 Dihedral : 4.827 40.870 1063 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.48 % Allowed : 15.17 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.28), residues: 967 helix: 1.89 (0.28), residues: 341 sheet: 1.00 (0.37), residues: 213 loop : -1.85 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 70 TYR 0.021 0.001 TYR A 257 PHE 0.012 0.001 PHE A 20 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 7690) covalent geometry : angle 0.54043 / 0.29 (10474) SS BOND : bond 0.00388 / 0.20 ( 5) SS BOND : angle 0.80200 / 0.48 ( 10) hydrogen bonds : bond 0.04828 / 3.10 ( 370) hydrogen bonds : angle 4.52556 / 3.32 ( 1076) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8325 (tpt) cc_final: 0.7948 (tpt) REVERT: A 227 ILE cc_start: 0.7392 (tt) cc_final: 0.7074 (pt) REVERT: A 423 MET cc_start: 0.7935 (ttt) cc_final: 0.7654 (ttm) REVERT: B 4 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8339 (mp) REVERT: B 34 MET cc_start: 0.7438 (mpp) cc_final: 0.7108 (mtt) REVERT: H 100 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8302 (mt) REVERT: L 170 ASP cc_start: 0.8756 (m-30) cc_final: 0.7945 (p0) outliers start: 12 outliers final: 9 residues processed: 114 average time/residue: 0.1505 time to fit residues: 25.1335 Evaluate side-chains 113 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.0670 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 67 optimal weight: 0.0040 chunk 0 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.134353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.111570 restraints weight = 50086.714| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.98 r_work: 0.3576 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7695 Z= 0.149 Angle : 0.538 5.539 10484 Z= 0.290 Chirality : 0.040 0.158 1199 Planarity : 0.003 0.029 1303 Dihedral : 4.854 40.563 1063 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.48 % Allowed : 15.54 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.28), residues: 967 helix: 1.86 (0.28), residues: 341 sheet: 0.94 (0.37), residues: 214 loop : -1.84 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 139 TYR 0.030 0.001 TYR A 257 PHE 0.010 0.001 PHE A 20 TRP 0.009 0.001 TRP H 47 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 7690) covalent geometry : angle 0.53734 / 0.29 (10474) SS BOND : bond 0.00396 / 0.20 ( 5) SS BOND : angle 0.75477 / 0.45 ( 10) hydrogen bonds : bond 0.04818 / 3.09 ( 370) hydrogen bonds : angle 4.49893 / 3.30 ( 1076) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8318 (tpt) cc_final: 0.7948 (tpt) REVERT: A 227 ILE cc_start: 0.7368 (tt) cc_final: 0.7059 (pt) REVERT: A 423 MET cc_start: 0.7930 (ttt) cc_final: 0.7650 (ttm) REVERT: B 4 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8345 (mp) REVERT: B 34 MET cc_start: 0.7445 (mpp) cc_final: 0.7129 (mtt) REVERT: B 59 TYR cc_start: 0.8475 (m-80) cc_final: 0.8194 (m-80) REVERT: H 100 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8303 (mt) REVERT: L 170 ASP cc_start: 0.8765 (m-30) cc_final: 0.7887 (p0) outliers start: 12 outliers final: 10 residues processed: 111 average time/residue: 0.1532 time to fit residues: 24.3531 Evaluate side-chains 110 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.135167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.112596 restraints weight = 48586.024| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.94 r_work: 0.3592 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7695 Z= 0.122 Angle : 0.521 5.198 10484 Z= 0.279 Chirality : 0.040 0.160 1199 Planarity : 0.003 0.029 1303 Dihedral : 4.751 40.758 1063 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.60 % Allowed : 15.41 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.28), residues: 967 helix: 1.95 (0.28), residues: 341 sheet: 0.99 (0.37), residues: 214 loop : -1.76 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 70 TYR 0.022 0.001 TYR A 257 PHE 0.012 0.001 PHE B 121 TRP 0.009 0.001 TRP H 47 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 7690) covalent geometry : angle 0.52075 / 0.28 (10474) SS BOND : bond 0.00365 / 0.19 ( 5) SS BOND : angle 0.66993 / 0.42 ( 10) hydrogen bonds : bond 0.04511 / 2.89 ( 370) hydrogen bonds : angle 4.39247 / 3.22 ( 1076) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8291 (tpt) cc_final: 0.7941 (tpt) REVERT: A 227 ILE cc_start: 0.7403 (tt) cc_final: 0.7107 (pt) REVERT: B 4 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8266 (mp) REVERT: B 34 MET cc_start: 0.7430 (mpp) cc_final: 0.7087 (mtt) REVERT: H 100 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8234 (mt) REVERT: L 170 ASP cc_start: 0.8745 (m-30) cc_final: 0.7893 (p0) outliers start: 13 outliers final: 10 residues processed: 113 average time/residue: 0.1467 time to fit residues: 23.9554 Evaluate side-chains 110 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.135368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.113400 restraints weight = 44041.084| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.77 r_work: 0.3609 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7695 Z= 0.123 Angle : 0.520 5.883 10484 Z= 0.278 Chirality : 0.040 0.158 1199 Planarity : 0.003 0.029 1303 Dihedral : 4.718 40.747 1063 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.60 % Allowed : 15.41 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.28), residues: 967 helix: 1.93 (0.28), residues: 342 sheet: 0.93 (0.37), residues: 216 loop : -1.75 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 139 TYR 0.023 0.001 TYR A 257 PHE 0.010 0.001 PHE A 20 TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 7690) covalent geometry : angle 0.51957 / 0.28 (10474) SS BOND : bond 0.00367 / 0.19 ( 5) SS BOND : angle 0.65978 / 0.40 ( 10) hydrogen bonds : bond 0.04408 / 2.83 ( 370) hydrogen bonds : angle 4.35315 / 3.18 ( 1076) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1934 Ramachandran restraints generated. 967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 121 is missing expected H atoms. Skipping. Residue LEU 293 is missing expected H atoms. Skipping. Residue TYR 355 is missing expected H atoms. Skipping. Residue TYR 369 is missing expected H atoms. Skipping. Residue TYR 396 is missing expected H atoms. Skipping. Residue MET 410 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8348 (tpt) cc_final: 0.8041 (tpt) REVERT: A 227 ILE cc_start: 0.7398 (tt) cc_final: 0.7107 (pt) REVERT: B 4 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8346 (mp) REVERT: B 34 MET cc_start: 0.7639 (mpp) cc_final: 0.7314 (mtt) REVERT: B 75 LYS cc_start: 0.9067 (mmpt) cc_final: 0.8787 (mmtt) REVERT: H 100 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8314 (mt) REVERT: L 170 ASP cc_start: 0.8836 (m-30) cc_final: 0.7926 (p0) outliers start: 13 outliers final: 11 residues processed: 114 average time/residue: 0.1509 time to fit residues: 24.5595 Evaluate side-chains 114 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.135562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.113692 restraints weight = 53878.381| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.38 r_work: 0.3579 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7695 Z= 0.113 Angle : 0.509 5.780 10484 Z= 0.272 Chirality : 0.040 0.155 1199 Planarity : 0.003 0.029 1303 Dihedral : 4.635 40.893 1063 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.48 % Allowed : 15.66 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.28), residues: 967 helix: 2.09 (0.28), residues: 336 sheet: 0.96 (0.36), residues: 218 loop : -1.66 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 139 TYR 0.020 0.001 TYR A 257 PHE 0.014 0.001 PHE B 121 TRP 0.008 0.001 TRP H 47 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 7690) covalent geometry : angle 0.50928 / 0.27 (10474) SS BOND : bond 0.00340 / 0.18 ( 5) SS BOND : angle 0.59637 / 0.37 ( 10) hydrogen bonds : bond 0.04174 / 2.68 ( 370) hydrogen bonds : angle 4.26950 / 3.12 ( 1076) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3505.86 seconds wall clock time: 60 minutes 12.06 seconds (3612.06 seconds total)