Starting phenix.real_space_refine on Tue Mar 3 23:02:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ch7_30370/03_2026/7ch7_30370.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ch7_30370/03_2026/7ch7_30370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ch7_30370/03_2026/7ch7_30370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ch7_30370/03_2026/7ch7_30370.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ch7_30370/03_2026/7ch7_30370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ch7_30370/03_2026/7ch7_30370.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 58 5.16 5 C 5914 2.51 5 N 1572 2.21 5 O 1654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9198 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1871 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "B" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1871 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "C" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2006 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 18, 'TRANS': 246} Chain: "D" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2006 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 18, 'TRANS': 246} Chain: "E" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 722 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "F" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 722 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Time building chain proxies: 2.01, per 1000 atoms: 0.22 Number of scatterers: 9198 At special positions: 0 Unit cell: (99, 111, 110, 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 58 16.00 O 1654 8.00 N 1572 7.00 C 5914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 302.4 milliseconds 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 57.8% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 17 through 29 removed outlier: 3.787A pdb=" N LEU A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 52 removed outlier: 4.387A pdb=" N LEU A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.552A pdb=" N ILE A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 98 removed outlier: 4.154A pdb=" N LEU A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 112 removed outlier: 4.169A pdb=" N ALA A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 removed outlier: 4.560A pdb=" N LEU A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 135 Processing helix chain 'A' and resid 138 through 175 removed outlier: 4.742A pdb=" N SER A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Proline residue: A 146 - end of helix removed outlier: 3.541A pdb=" N ILE A 153 " --> pdb=" O TRP A 149 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 195 through 224 removed outlier: 3.715A pdb=" N LEU A 199 " --> pdb=" O TRP A 195 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLY A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 259 removed outlier: 3.917A pdb=" N SER A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 29 removed outlier: 3.787A pdb=" N LEU B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 52 removed outlier: 4.388A pdb=" N LEU B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 79 removed outlier: 3.551A pdb=" N ILE B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 98 removed outlier: 4.152A pdb=" N LEU B 93 " --> pdb=" O MET B 89 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 112 removed outlier: 4.170A pdb=" N ALA B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 127 removed outlier: 4.561A pdb=" N LEU B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 138 through 175 removed outlier: 4.742A pdb=" N SER B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Proline residue: B 146 - end of helix removed outlier: 3.541A pdb=" N ILE B 153 " --> pdb=" O TRP B 149 " (cutoff:3.500A) Proline residue: B 156 - end of helix Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 195 through 224 removed outlier: 3.714A pdb=" N LEU B 199 " --> pdb=" O TRP B 195 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 259 removed outlier: 3.916A pdb=" N SER B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 55 Processing helix chain 'C' and resid 78 through 85 Processing helix chain 'C' and resid 101 through 114 Proline residue: C 109 - end of helix Processing helix chain 'C' and resid 117 through 133 removed outlier: 3.710A pdb=" N GLU C 130 " --> pdb=" O MET C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 146 through 160 removed outlier: 3.726A pdb=" N ARG C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 192 removed outlier: 3.725A pdb=" N SER C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN C 191 " --> pdb=" O ILE C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 228 through 234 Processing helix chain 'C' and resid 237 through 246 removed outlier: 3.683A pdb=" N PHE C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 55 Processing helix chain 'D' and resid 78 through 85 Processing helix chain 'D' and resid 101 through 114 Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 117 through 133 removed outlier: 3.709A pdb=" N GLU D 130 " --> pdb=" O MET D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 138 Processing helix chain 'D' and resid 146 through 160 removed outlier: 3.726A pdb=" N ARG D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 192 removed outlier: 3.725A pdb=" N SER D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 228 through 234 Processing helix chain 'D' and resid 237 through 246 removed outlier: 3.682A pdb=" N PHE D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 removed outlier: 3.696A pdb=" N GLU E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 51 through 66 Processing helix chain 'E' and resid 78 through 88 Processing helix chain 'F' and resid 25 through 30 removed outlier: 3.697A pdb=" N GLU F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 36 Processing helix chain 'F' and resid 51 through 66 Processing helix chain 'F' and resid 78 through 88 Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 32 removed outlier: 4.512A pdb=" N LEU C 29 " --> pdb=" O ARG C 12 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG C 12 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL C 31 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASP C 10 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 90 through 91 removed outlier: 5.894A pdb=" N PHE C 168 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C 37 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N SER C 202 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE C 39 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ALA C 219 " --> pdb=" O ILE C 223 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ILE C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 27 through 32 removed outlier: 4.511A pdb=" N LEU D 29 " --> pdb=" O ARG D 12 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG D 12 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL D 31 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASP D 10 " --> pdb=" O VAL D 31 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 90 through 91 removed outlier: 5.894A pdb=" N PHE D 168 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR D 37 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N SER D 202 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE D 39 " --> pdb=" O SER D 202 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ALA D 219 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ILE D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 5 through 9 removed outlier: 3.893A pdb=" N LEU E 16 " --> pdb=" O ASP E 43 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE E 42 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 5 through 9 removed outlier: 3.893A pdb=" N LEU F 16 " --> pdb=" O ASP F 43 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE F 42 " --> pdb=" O GLN F 75 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2996 1.34 - 1.46: 1730 1.46 - 1.57: 4536 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 9370 Sorted by residual: bond pdb=" CA GLU C 162 " pdb=" C GLU C 162 " ideal model delta sigma weight residual 1.531 1.517 0.014 7.40e-03 1.83e+04 3.68e+00 bond pdb=" CA GLU D 162 " pdb=" C GLU D 162 " ideal model delta sigma weight residual 1.531 1.518 0.013 7.40e-03 1.83e+04 3.06e+00 bond pdb=" CA GLU D 170 " pdb=" C GLU D 170 " ideal model delta sigma weight residual 1.531 1.520 0.012 7.40e-03 1.83e+04 2.43e+00 bond pdb=" CA SER B 114 " pdb=" C SER B 114 " ideal model delta sigma weight residual 1.525 1.510 0.015 1.02e-02 9.61e+03 2.27e+00 bond pdb=" CA GLU C 170 " pdb=" C GLU C 170 " ideal model delta sigma weight residual 1.531 1.520 0.011 7.40e-03 1.83e+04 2.24e+00 ... (remaining 9365 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 12476 2.75 - 5.50: 233 5.50 - 8.25: 13 8.25 - 11.00: 4 11.00 - 13.76: 4 Bond angle restraints: 12730 Sorted by residual: angle pdb=" C PRO C 251 " pdb=" N VAL C 252 " pdb=" CA VAL C 252 " ideal model delta sigma weight residual 122.59 119.80 2.79 7.20e-01 1.93e+00 1.50e+01 angle pdb=" C PRO D 251 " pdb=" N VAL D 252 " pdb=" CA VAL D 252 " ideal model delta sigma weight residual 122.59 119.80 2.79 7.20e-01 1.93e+00 1.50e+01 angle pdb=" N ILE C 211 " pdb=" CA ILE C 211 " pdb=" C ILE C 211 " ideal model delta sigma weight residual 113.71 110.19 3.52 9.50e-01 1.11e+00 1.37e+01 angle pdb=" N GLY A 113 " pdb=" CA GLY A 113 " pdb=" C GLY A 113 " ideal model delta sigma weight residual 114.66 110.08 4.58 1.24e+00 6.50e-01 1.36e+01 angle pdb=" N ILE D 211 " pdb=" CA ILE D 211 " pdb=" C ILE D 211 " ideal model delta sigma weight residual 113.71 110.22 3.49 9.50e-01 1.11e+00 1.35e+01 ... (remaining 12725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 4813 15.81 - 31.61: 534 31.61 - 47.42: 174 47.42 - 63.23: 79 63.23 - 79.04: 4 Dihedral angle restraints: 5604 sinusoidal: 2164 harmonic: 3440 Sorted by residual: dihedral pdb=" CA LEU F 95 " pdb=" C LEU F 95 " pdb=" N PRO F 96 " pdb=" CA PRO F 96 " ideal model delta harmonic sigma weight residual -180.00 -150.99 -29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA LEU E 95 " pdb=" C LEU E 95 " pdb=" N PRO E 96 " pdb=" CA PRO E 96 " ideal model delta harmonic sigma weight residual -180.00 -151.00 -29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA GLU D 162 " pdb=" C GLU D 162 " pdb=" N PRO D 163 " pdb=" CA PRO D 163 " ideal model delta harmonic sigma weight residual -180.00 -159.17 -20.83 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 5601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 717 0.030 - 0.060: 536 0.060 - 0.089: 179 0.089 - 0.119: 80 0.119 - 0.149: 16 Chirality restraints: 1528 Sorted by residual: chirality pdb=" CA PRO D 163 " pdb=" N PRO D 163 " pdb=" C PRO D 163 " pdb=" CB PRO D 163 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA PRO C 163 " pdb=" N PRO C 163 " pdb=" C PRO C 163 " pdb=" CB PRO C 163 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" CA PRO E 96 " pdb=" N PRO E 96 " pdb=" C PRO E 96 " pdb=" CB PRO E 96 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 1525 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 95 " 0.074 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO F 96 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO F 96 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO F 96 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 95 " -0.074 5.00e-02 4.00e+02 1.11e-01 1.99e+01 pdb=" N PRO E 96 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO E 96 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO E 96 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 140 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.03e+00 pdb=" C LEU B 140 " 0.025 2.00e-02 2.50e+03 pdb=" O LEU B 140 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG B 141 " -0.008 2.00e-02 2.50e+03 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 301 2.66 - 3.22: 10345 3.22 - 3.78: 15437 3.78 - 4.34: 20279 4.34 - 4.90: 32211 Nonbonded interactions: 78573 Sorted by model distance: nonbonded pdb=" O TYR B 75 " pdb=" OG1 THR B 79 " model vdw 2.096 3.040 nonbonded pdb=" O TYR A 75 " pdb=" OG1 THR A 79 " model vdw 2.096 3.040 nonbonded pdb=" OG SER A 228 " pdb=" OG SER B 228 " model vdw 2.142 3.040 nonbonded pdb=" O VAL A 51 " pdb=" OG SER A 55 " model vdw 2.170 3.040 nonbonded pdb=" O TRP B 168 " pdb=" OG SER B 171 " model vdw 2.170 3.040 ... (remaining 78568 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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 group one per residue 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: 1.090 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.770 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 : 0.007 0.046 9370 Z= 0.372 Angle : 0.939 13.756 12730 Z= 0.514 Chirality : 0.047 0.149 1528 Planarity : 0.006 0.112 1604 Dihedral : 16.386 79.037 3392 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 26.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.56 % Favored : 86.44 % Rotamer: Outliers : 18.11 % Allowed : 15.09 % Favored : 66.80 % 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: -4.81 (0.20), residues: 1202 helix: -3.04 (0.15), residues: 646 sheet: -2.97 (0.57), residues: 66 loop : -3.26 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 21 TYR 0.012 0.001 TYR B 49 PHE 0.016 0.002 PHE A 148 TRP 0.010 0.001 TRP A 149 HIS 0.003 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00746 ( 9370) covalent geometry : angle 0.93913 (12730) hydrogen bonds : bond 0.20311 ( 472) hydrogen bonds : angle 8.59872 ( 1374) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 302 time to evaluate : 0.345 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 26 MET cc_start: 0.8774 (ppp) cc_final: 0.8473 (ppp) REVERT: A 90 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9017 (tm) REVERT: A 106 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8264 (mt) REVERT: A 134 MET cc_start: 0.8875 (tpt) cc_final: 0.8608 (tpt) REVERT: A 191 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8108 (p0) REVERT: A 197 MET cc_start: 0.7746 (tpt) cc_final: 0.7313 (tpp) REVERT: B 47 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7622 (mm-40) REVERT: B 90 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8949 (tm) REVERT: B 176 SER cc_start: 0.7851 (m) cc_final: 0.7509 (t) REVERT: B 197 MET cc_start: 0.8078 (tpt) cc_final: 0.7701 (tpp) REVERT: C 64 GLU cc_start: 0.5016 (mp0) cc_final: 0.4796 (mp0) REVERT: C 90 LEU cc_start: 0.8493 (tp) cc_final: 0.8005 (tt) REVERT: C 120 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8593 (tm) REVERT: C 130 GLU cc_start: 0.7540 (tp30) cc_final: 0.7274 (tp30) REVERT: C 207 GLU cc_start: 0.8465 (tp30) cc_final: 0.8228 (tp30) REVERT: D 89 MET cc_start: 0.7410 (mmm) cc_final: 0.7117 (mmm) REVERT: D 130 GLU cc_start: 0.7718 (tp30) cc_final: 0.7292 (tp30) REVERT: D 187 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9179 (pt) REVERT: D 233 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8527 (tp-100) REVERT: D 256 TYR cc_start: 0.8482 (t80) cc_final: 0.8227 (t80) REVERT: E 44 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8833 (pt) REVERT: E 57 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9072 (tp) REVERT: E 66 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8590 (mmtm) REVERT: E 70 ASN cc_start: 0.6975 (t0) cc_final: 0.6233 (t0) REVERT: E 80 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8576 (mmmm) REVERT: E 86 LYS cc_start: 0.8765 (tppp) cc_final: 0.8541 (tppt) REVERT: F 4 SER cc_start: 0.6724 (p) cc_final: 0.6166 (m) REVERT: F 44 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8752 (pt) REVERT: F 57 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9035 (tp) REVERT: F 70 ASN cc_start: 0.7320 (t0) cc_final: 0.6707 (t0) REVERT: F 80 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8544 (mmmm) REVERT: F 86 LYS cc_start: 0.8830 (tppp) cc_final: 0.8524 (tppt) outliers start: 180 outliers final: 81 residues processed: 420 average time/residue: 0.0793 time to fit residues: 47.7040 Evaluate side-chains 327 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 232 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 191 ASN Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 20 ASN Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain F residue 87 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.0020 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN A 220 ASN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN C 57 GLN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 226 HIS D 57 GLN D 175 GLN D 226 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.084860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.071862 restraints weight = 27108.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.073841 restraints weight = 15428.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.075227 restraints weight = 10375.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.076266 restraints weight = 7821.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.076469 restraints weight = 6348.425| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9370 Z= 0.173 Angle : 0.830 9.632 12730 Z= 0.395 Chirality : 0.047 0.254 1528 Planarity : 0.006 0.099 1604 Dihedral : 12.141 61.504 1471 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 13.08 % Allowed : 22.64 % Favored : 64.29 % 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: -3.01 (0.22), residues: 1202 helix: -1.48 (0.18), residues: 654 sheet: -1.64 (0.66), residues: 50 loop : -2.67 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 135 TYR 0.020 0.002 TYR A 75 PHE 0.010 0.002 PHE A 185 TRP 0.020 0.002 TRP E 7 HIS 0.005 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9370) covalent geometry : angle 0.83043 (12730) hydrogen bonds : bond 0.04529 ( 472) hydrogen bonds : angle 5.89455 ( 1374) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 288 time to evaluate : 0.333 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 26 MET cc_start: 0.8685 (ppp) cc_final: 0.8437 (ppp) REVERT: A 56 MET cc_start: 0.7756 (ttp) cc_final: 0.7190 (ptt) REVERT: A 89 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7413 (ppp) REVERT: A 90 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8762 (tm) REVERT: A 106 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7796 (mt) REVERT: A 195 TRP cc_start: 0.7195 (p90) cc_final: 0.6463 (p90) REVERT: A 197 MET cc_start: 0.7454 (tpt) cc_final: 0.7094 (tpp) REVERT: A 198 ASP cc_start: 0.7592 (t0) cc_final: 0.7340 (m-30) REVERT: B 56 MET cc_start: 0.7696 (ttp) cc_final: 0.7001 (ptp) REVERT: B 58 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8438 (mp) REVERT: B 65 PHE cc_start: 0.7882 (m-10) cc_final: 0.7674 (m-10) REVERT: B 89 MET cc_start: 0.7711 (tmm) cc_final: 0.7499 (ppp) REVERT: B 90 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8679 (tm) REVERT: B 135 MET cc_start: 0.7960 (mtm) cc_final: 0.7331 (mtm) REVERT: B 161 ILE cc_start: 0.9297 (mt) cc_final: 0.9019 (tp) REVERT: B 198 ASP cc_start: 0.7786 (t0) cc_final: 0.7366 (t0) REVERT: C 116 LEU cc_start: 0.9188 (tp) cc_final: 0.8901 (tp) REVERT: C 120 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8419 (tm) REVERT: C 130 GLU cc_start: 0.7983 (tp30) cc_final: 0.7730 (tp30) REVERT: C 167 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8097 (pmm) REVERT: C 184 VAL cc_start: 0.9488 (p) cc_final: 0.9287 (p) REVERT: C 207 GLU cc_start: 0.8176 (tp30) cc_final: 0.7813 (tp30) REVERT: C 256 TYR cc_start: 0.8160 (t80) cc_final: 0.7749 (t80) REVERT: D 87 MET cc_start: 0.8003 (mtm) cc_final: 0.7732 (mtt) REVERT: D 90 LEU cc_start: 0.8358 (tp) cc_final: 0.8041 (tt) REVERT: D 130 GLU cc_start: 0.7874 (tp30) cc_final: 0.7608 (tp30) REVERT: D 180 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7235 (ttt) REVERT: D 187 ILE cc_start: 0.9482 (pt) cc_final: 0.9216 (pt) REVERT: D 233 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8384 (tp40) REVERT: D 235 ASN cc_start: 0.8350 (t0) cc_final: 0.8122 (t0) REVERT: D 256 TYR cc_start: 0.8386 (t80) cc_final: 0.8171 (t80) REVERT: E 44 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8672 (pp) REVERT: E 64 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8693 (mt) REVERT: E 86 LYS cc_start: 0.8586 (tppp) cc_final: 0.8304 (tppt) REVERT: F 44 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8599 (pp) REVERT: F 64 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8708 (mt) REVERT: F 80 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8449 (mmmm) REVERT: F 86 LYS cc_start: 0.8573 (tppp) cc_final: 0.8319 (tppt) REVERT: F 89 ASN cc_start: 0.8544 (t0) cc_final: 0.7922 (t0) outliers start: 130 outliers final: 79 residues processed: 373 average time/residue: 0.0744 time to fit residues: 40.7640 Evaluate side-chains 323 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 231 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 167 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 57 GLN Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 66 LYS Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 63 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 80 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 54 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN D 57 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.084277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.071255 restraints weight = 27505.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.072967 restraints weight = 15656.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.074497 restraints weight = 11038.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075220 restraints weight = 8277.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.075936 restraints weight = 6968.371| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9370 Z= 0.161 Angle : 0.784 9.468 12730 Z= 0.373 Chirality : 0.048 0.307 1528 Planarity : 0.005 0.096 1604 Dihedral : 10.733 59.705 1415 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 11.67 % Allowed : 24.85 % Favored : 63.48 % 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: -2.33 (0.23), residues: 1202 helix: -1.00 (0.19), residues: 652 sheet: -0.90 (0.62), residues: 62 loop : -2.31 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 151 TYR 0.020 0.002 TYR D 261 PHE 0.011 0.002 PHE A 65 TRP 0.020 0.001 TRP B 195 HIS 0.004 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9370) covalent geometry : angle 0.78366 (12730) hydrogen bonds : bond 0.04147 ( 472) hydrogen bonds : angle 5.59953 ( 1374) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 258 time to evaluate : 0.281 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 26 MET cc_start: 0.8674 (ppp) cc_final: 0.8467 (ppp) REVERT: A 56 MET cc_start: 0.7815 (ttp) cc_final: 0.7262 (ptt) REVERT: A 90 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8730 (tm) REVERT: A 106 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7677 (mt) REVERT: A 197 MET cc_start: 0.7532 (tpt) cc_final: 0.7189 (tpp) REVERT: A 198 ASP cc_start: 0.7732 (t0) cc_final: 0.7259 (t0) REVERT: B 56 MET cc_start: 0.7737 (ttp) cc_final: 0.7008 (ptp) REVERT: B 58 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8313 (mp) REVERT: B 90 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8638 (tm) REVERT: B 197 MET cc_start: 0.7535 (tpp) cc_final: 0.7193 (tpp) REVERT: C 130 GLU cc_start: 0.7886 (tp30) cc_final: 0.7608 (tp30) REVERT: C 207 GLU cc_start: 0.8108 (tp30) cc_final: 0.7843 (mm-30) REVERT: C 256 TYR cc_start: 0.8073 (t80) cc_final: 0.7698 (t80) REVERT: D 89 MET cc_start: 0.7951 (mtt) cc_final: 0.7738 (mtt) REVERT: D 187 ILE cc_start: 0.9478 (pt) cc_final: 0.9223 (pt) REVERT: D 233 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8392 (tp-100) REVERT: E 22 GLN cc_start: 0.8753 (pm20) cc_final: 0.8500 (pm20) REVERT: E 23 ASP cc_start: 0.7976 (m-30) cc_final: 0.7454 (m-30) REVERT: E 44 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8602 (pp) REVERT: E 86 LYS cc_start: 0.8598 (tppp) cc_final: 0.8297 (tppt) REVERT: F 5 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.6780 (tp) REVERT: F 44 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8550 (pp) REVERT: F 86 LYS cc_start: 0.8598 (tppp) cc_final: 0.8362 (tppt) REVERT: F 89 ASN cc_start: 0.8601 (t0) cc_final: 0.7930 (t0) outliers start: 116 outliers final: 76 residues processed: 335 average time/residue: 0.0727 time to fit residues: 35.7546 Evaluate side-chains 322 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 239 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 88 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.084660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.071517 restraints weight = 27401.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.073525 restraints weight = 15577.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.074889 restraints weight = 10479.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.075851 restraints weight = 7936.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.076576 restraints weight = 6535.406| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9370 Z= 0.177 Angle : 0.763 9.611 12730 Z= 0.365 Chirality : 0.048 0.426 1528 Planarity : 0.005 0.095 1604 Dihedral : 9.929 57.689 1390 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 12.17 % Allowed : 24.25 % Favored : 63.58 % 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: -2.10 (0.23), residues: 1202 helix: -0.79 (0.19), residues: 652 sheet: -0.87 (0.60), residues: 62 loop : -2.24 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 151 TYR 0.014 0.002 TYR D 261 PHE 0.021 0.002 PHE B 219 TRP 0.019 0.002 TRP A 195 HIS 0.003 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9370) covalent geometry : angle 0.76338 (12730) hydrogen bonds : bond 0.03928 ( 472) hydrogen bonds : angle 5.51776 ( 1374) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 251 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8644 (ppp) cc_final: 0.8421 (ppp) REVERT: A 56 MET cc_start: 0.7834 (ttp) cc_final: 0.7196 (ptt) REVERT: A 90 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8677 (tm) REVERT: A 106 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7657 (mt) REVERT: A 195 TRP cc_start: 0.7154 (p90) cc_final: 0.6862 (p90) REVERT: B 54 LEU cc_start: 0.8380 (tp) cc_final: 0.8102 (mt) REVERT: B 56 MET cc_start: 0.7798 (ttp) cc_final: 0.7152 (ptp) REVERT: B 90 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8591 (tm) REVERT: B 133 GLU cc_start: 0.8516 (tt0) cc_final: 0.8150 (mt-10) REVERT: B 135 MET cc_start: 0.8104 (mtm) cc_final: 0.7219 (mtm) REVERT: B 219 PHE cc_start: 0.7469 (t80) cc_final: 0.7266 (t80) REVERT: B 257 MET cc_start: 0.7955 (ttm) cc_final: 0.7656 (ttm) REVERT: C 87 MET cc_start: 0.8052 (mtm) cc_final: 0.7841 (mtt) REVERT: C 130 GLU cc_start: 0.7978 (tp30) cc_final: 0.7598 (tp30) REVERT: C 207 GLU cc_start: 0.8081 (tp30) cc_final: 0.7671 (mm-30) REVERT: C 256 TYR cc_start: 0.8144 (t80) cc_final: 0.7784 (t80) REVERT: D 187 ILE cc_start: 0.9503 (pt) cc_final: 0.9266 (pt) REVERT: D 233 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8214 (tp-100) REVERT: E 22 GLN cc_start: 0.8784 (pm20) cc_final: 0.8473 (pm20) REVERT: E 44 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8578 (pp) REVERT: E 86 LYS cc_start: 0.8580 (tppp) cc_final: 0.8349 (tppt) REVERT: F 37 LYS cc_start: 0.8477 (tppp) cc_final: 0.8218 (tppp) REVERT: F 44 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8503 (pp) REVERT: F 86 LYS cc_start: 0.8624 (tppp) cc_final: 0.8360 (tppt) outliers start: 121 outliers final: 86 residues processed: 333 average time/residue: 0.0761 time to fit residues: 36.9908 Evaluate side-chains 321 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 230 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 81 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 61 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 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 = 0.3443 r_free = 0.3443 target = 0.084799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.071522 restraints weight = 27396.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.073533 restraints weight = 15686.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.074831 restraints weight = 10649.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.075840 restraints weight = 8144.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.076253 restraints weight = 6671.331| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9370 Z= 0.163 Angle : 0.764 10.409 12730 Z= 0.365 Chirality : 0.048 0.355 1528 Planarity : 0.005 0.092 1604 Dihedral : 9.587 57.330 1384 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 11.07 % Allowed : 25.86 % Favored : 63.08 % 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: -2.00 (0.23), residues: 1202 helix: -0.63 (0.19), residues: 656 sheet: -1.53 (0.55), residues: 74 loop : -2.20 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 151 TYR 0.012 0.002 TYR E 82 PHE 0.018 0.002 PHE B 65 TRP 0.017 0.002 TRP B 195 HIS 0.003 0.001 HIS D 113 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9370) covalent geometry : angle 0.76417 (12730) hydrogen bonds : bond 0.03701 ( 472) hydrogen bonds : angle 5.47245 ( 1374) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 246 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8669 (ppp) cc_final: 0.8410 (ppp) REVERT: A 56 MET cc_start: 0.7853 (ttp) cc_final: 0.7121 (ptt) REVERT: A 106 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7607 (mt) REVERT: A 195 TRP cc_start: 0.7250 (p90) cc_final: 0.6527 (p90) REVERT: A 197 MET cc_start: 0.7551 (tpp) cc_final: 0.7280 (tpp) REVERT: A 198 ASP cc_start: 0.7682 (t0) cc_final: 0.7445 (m-30) REVERT: B 54 LEU cc_start: 0.8406 (tp) cc_final: 0.8123 (mt) REVERT: B 133 GLU cc_start: 0.8480 (tt0) cc_final: 0.8185 (mt-10) REVERT: B 197 MET cc_start: 0.7410 (tpp) cc_final: 0.6713 (tpp) REVERT: C 80 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8525 (tp) REVERT: C 89 MET cc_start: 0.8151 (ttm) cc_final: 0.7848 (ttm) REVERT: C 91 PHE cc_start: 0.7710 (m-80) cc_final: 0.7281 (m-80) REVERT: C 130 GLU cc_start: 0.7845 (tp30) cc_final: 0.7528 (tp30) REVERT: C 256 TYR cc_start: 0.8150 (t80) cc_final: 0.7805 (t80) REVERT: D 40 MET cc_start: 0.6607 (mtp) cc_final: 0.6356 (mtp) REVERT: D 64 GLU cc_start: 0.4218 (mp0) cc_final: 0.3991 (mp0) REVERT: D 187 ILE cc_start: 0.9490 (pt) cc_final: 0.9267 (pt) REVERT: D 233 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8219 (tp-100) REVERT: E 22 GLN cc_start: 0.8785 (pm20) cc_final: 0.8563 (pm20) REVERT: E 44 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8574 (pp) REVERT: E 86 LYS cc_start: 0.8596 (tppp) cc_final: 0.8351 (tppt) REVERT: F 86 LYS cc_start: 0.8621 (tppp) cc_final: 0.8345 (tppt) outliers start: 110 outliers final: 87 residues processed: 317 average time/residue: 0.0767 time to fit residues: 35.4772 Evaluate side-chains 324 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 234 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 73 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 87 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.083799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.070080 restraints weight = 27595.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.072143 restraints weight = 15176.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.073571 restraints weight = 10085.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.074499 restraints weight = 7608.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.075101 restraints weight = 6237.059| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9370 Z= 0.179 Angle : 0.767 9.655 12730 Z= 0.368 Chirality : 0.048 0.233 1528 Planarity : 0.005 0.095 1604 Dihedral : 9.168 56.787 1372 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 10.46 % Allowed : 26.46 % Favored : 63.08 % 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: -1.96 (0.23), residues: 1202 helix: -0.55 (0.19), residues: 658 sheet: -1.94 (0.49), residues: 90 loop : -2.17 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 151 TYR 0.012 0.002 TYR E 82 PHE 0.021 0.002 PHE B 219 TRP 0.026 0.002 TRP B 195 HIS 0.003 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9370) covalent geometry : angle 0.76688 (12730) hydrogen bonds : bond 0.03736 ( 472) hydrogen bonds : angle 5.49092 ( 1374) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 236 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8816 (ppp) cc_final: 0.8612 (ppp) REVERT: A 56 MET cc_start: 0.7880 (ttp) cc_final: 0.7049 (ptt) REVERT: A 89 MET cc_start: 0.7530 (ppp) cc_final: 0.7206 (ppp) REVERT: A 106 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7633 (mt) REVERT: A 195 TRP cc_start: 0.7512 (p90) cc_final: 0.6794 (p90) REVERT: A 197 MET cc_start: 0.7484 (tpp) cc_final: 0.6858 (tpp) REVERT: A 198 ASP cc_start: 0.7856 (t0) cc_final: 0.7519 (m-30) REVERT: B 54 LEU cc_start: 0.8456 (tp) cc_final: 0.8078 (mt) REVERT: B 106 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7723 (mt) REVERT: B 133 GLU cc_start: 0.8615 (tt0) cc_final: 0.8306 (mt-10) REVERT: B 197 MET cc_start: 0.7303 (tpp) cc_final: 0.6956 (tpp) REVERT: C 130 GLU cc_start: 0.8026 (tp30) cc_final: 0.7648 (tp30) REVERT: C 256 TYR cc_start: 0.8211 (t80) cc_final: 0.7858 (t80) REVERT: D 64 GLU cc_start: 0.4626 (mp0) cc_final: 0.4248 (mp0) REVERT: D 130 GLU cc_start: 0.7428 (tp30) cc_final: 0.7170 (tp30) REVERT: D 233 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8314 (tp-100) REVERT: E 9 GLN cc_start: 0.6896 (tt0) cc_final: 0.6123 (tp40) REVERT: E 44 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8691 (pp) REVERT: E 86 LYS cc_start: 0.8799 (tppp) cc_final: 0.8489 (tppt) REVERT: F 86 LYS cc_start: 0.8827 (tppp) cc_final: 0.8474 (tppt) outliers start: 104 outliers final: 84 residues processed: 307 average time/residue: 0.0780 time to fit residues: 34.9532 Evaluate side-chains 309 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 222 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.084643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.071607 restraints weight = 27211.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.073607 restraints weight = 15577.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.074901 restraints weight = 10515.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.075887 restraints weight = 8021.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.076269 restraints weight = 6571.295| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9370 Z= 0.175 Angle : 0.787 9.386 12730 Z= 0.376 Chirality : 0.048 0.289 1528 Planarity : 0.005 0.093 1604 Dihedral : 9.067 57.881 1371 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 10.76 % Allowed : 27.67 % Favored : 61.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.23), residues: 1202 helix: -0.46 (0.19), residues: 656 sheet: -1.75 (0.50), residues: 90 loop : -2.14 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 46 TYR 0.011 0.002 TYR E 82 PHE 0.029 0.002 PHE A 219 TRP 0.031 0.002 TRP B 195 HIS 0.003 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9370) covalent geometry : angle 0.78671 (12730) hydrogen bonds : bond 0.03719 ( 472) hydrogen bonds : angle 5.48072 ( 1374) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 239 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8685 (ppp) cc_final: 0.8023 (tmm) REVERT: A 56 MET cc_start: 0.7829 (ttp) cc_final: 0.7111 (ptt) REVERT: A 106 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7726 (mt) REVERT: A 195 TRP cc_start: 0.7299 (p90) cc_final: 0.6603 (p90) REVERT: A 197 MET cc_start: 0.7504 (tpp) cc_final: 0.6865 (tpp) REVERT: A 198 ASP cc_start: 0.7632 (t0) cc_final: 0.7292 (m-30) REVERT: B 106 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7826 (mt) REVERT: B 133 GLU cc_start: 0.8432 (tt0) cc_final: 0.8170 (mt-10) REVERT: B 196 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.5360 (ttm170) REVERT: B 197 MET cc_start: 0.7465 (tpp) cc_final: 0.6904 (tpp) REVERT: C 91 PHE cc_start: 0.7636 (m-80) cc_final: 0.7231 (m-80) REVERT: C 130 GLU cc_start: 0.7853 (tp30) cc_final: 0.7543 (tp30) REVERT: C 256 TYR cc_start: 0.8150 (t80) cc_final: 0.7864 (t80) REVERT: D 91 PHE cc_start: 0.7696 (m-80) cc_final: 0.7353 (m-80) REVERT: D 130 GLU cc_start: 0.7497 (tp30) cc_final: 0.7280 (tp30) REVERT: D 233 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8214 (tp-100) REVERT: D 256 TYR cc_start: 0.8100 (t80) cc_final: 0.7839 (t80) REVERT: E 9 GLN cc_start: 0.6851 (tt0) cc_final: 0.6277 (tp40) REVERT: E 80 LYS cc_start: 0.8733 (mmmm) cc_final: 0.8531 (mmmm) REVERT: E 86 LYS cc_start: 0.8679 (tppp) cc_final: 0.8430 (tppt) REVERT: E 89 ASN cc_start: 0.8503 (t0) cc_final: 0.8239 (t0) REVERT: F 86 LYS cc_start: 0.8674 (tppp) cc_final: 0.8366 (tppt) outliers start: 107 outliers final: 93 residues processed: 314 average time/residue: 0.0832 time to fit residues: 37.7852 Evaluate side-chains 325 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 229 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 17 optimal weight: 6.9990 chunk 108 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 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 = 0.3487 r_free = 0.3487 target = 0.086813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.073084 restraints weight = 27042.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.075276 restraints weight = 14932.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.076667 restraints weight = 9886.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.077531 restraints weight = 7439.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.078334 restraints weight = 6188.457| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9370 Z= 0.148 Angle : 0.790 9.268 12730 Z= 0.377 Chirality : 0.047 0.256 1528 Planarity : 0.005 0.088 1604 Dihedral : 8.785 58.791 1368 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 8.85 % Allowed : 29.07 % Favored : 62.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.23), residues: 1202 helix: -0.37 (0.19), residues: 666 sheet: -1.34 (0.60), residues: 70 loop : -2.14 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 46 TYR 0.010 0.002 TYR D 261 PHE 0.035 0.002 PHE D 243 TRP 0.016 0.001 TRP E 7 HIS 0.004 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9370) covalent geometry : angle 0.78992 (12730) hydrogen bonds : bond 0.03537 ( 472) hydrogen bonds : angle 5.43929 ( 1374) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 238 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8817 (ppp) cc_final: 0.8226 (tmm) REVERT: A 56 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7073 (ptt) REVERT: A 89 MET cc_start: 0.7357 (ppp) cc_final: 0.7021 (ppp) REVERT: A 195 TRP cc_start: 0.7513 (p90) cc_final: 0.6957 (p90) REVERT: A 197 MET cc_start: 0.7455 (tpp) cc_final: 0.6778 (tpp) REVERT: A 198 ASP cc_start: 0.7847 (t0) cc_final: 0.7447 (m-30) REVERT: B 89 MET cc_start: 0.7400 (ppp) cc_final: 0.7036 (ppp) REVERT: B 133 GLU cc_start: 0.8644 (tt0) cc_final: 0.8388 (mt-10) REVERT: B 197 MET cc_start: 0.7174 (tpp) cc_final: 0.6817 (tpp) REVERT: C 90 LEU cc_start: 0.8400 (tp) cc_final: 0.8199 (tt) REVERT: C 91 PHE cc_start: 0.7377 (m-80) cc_final: 0.7023 (m-80) REVERT: C 130 GLU cc_start: 0.7996 (tp30) cc_final: 0.7731 (tp30) REVERT: C 256 TYR cc_start: 0.8164 (t80) cc_final: 0.7924 (t80) REVERT: D 85 LYS cc_start: 0.8325 (mttm) cc_final: 0.7868 (mtpt) REVERT: D 91 PHE cc_start: 0.7314 (m-80) cc_final: 0.7045 (m-80) REVERT: D 233 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8332 (tp-100) REVERT: D 256 TYR cc_start: 0.8121 (t80) cc_final: 0.7808 (t80) REVERT: E 9 GLN cc_start: 0.7075 (tt0) cc_final: 0.6573 (tp40) REVERT: E 86 LYS cc_start: 0.8869 (tppp) cc_final: 0.8534 (tppt) REVERT: E 89 ASN cc_start: 0.8745 (t0) cc_final: 0.8419 (t0) REVERT: F 86 LYS cc_start: 0.8855 (tppp) cc_final: 0.8488 (tppt) outliers start: 88 outliers final: 74 residues processed: 302 average time/residue: 0.0778 time to fit residues: 34.3160 Evaluate side-chains 304 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 229 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 97 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 24 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 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 = 0.3502 r_free = 0.3502 target = 0.087746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.074603 restraints weight = 27045.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.076652 restraints weight = 15398.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.077977 restraints weight = 10364.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.079016 restraints weight = 7930.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.079559 restraints weight = 6442.385| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9370 Z= 0.149 Angle : 0.806 9.179 12730 Z= 0.384 Chirality : 0.047 0.240 1528 Planarity : 0.005 0.087 1604 Dihedral : 8.464 59.200 1360 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 8.25 % Allowed : 29.58 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.23), residues: 1202 helix: -0.31 (0.19), residues: 670 sheet: -0.85 (0.60), residues: 80 loop : -2.09 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 46 TYR 0.019 0.002 TYR C 261 PHE 0.028 0.002 PHE B 219 TRP 0.015 0.001 TRP E 7 HIS 0.006 0.001 HIS C 113 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9370) covalent geometry : angle 0.80575 (12730) hydrogen bonds : bond 0.03543 ( 472) hydrogen bonds : angle 5.41384 ( 1374) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 233 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8589 (ppp) cc_final: 0.7990 (tmm) REVERT: A 56 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7035 (ptt) REVERT: A 89 MET cc_start: 0.7458 (ppp) cc_final: 0.7143 (ppp) REVERT: A 195 TRP cc_start: 0.7129 (p90) cc_final: 0.6572 (p90) REVERT: A 197 MET cc_start: 0.7514 (tpp) cc_final: 0.6885 (tpp) REVERT: A 198 ASP cc_start: 0.7548 (t0) cc_final: 0.7218 (m-30) REVERT: B 76 LEU cc_start: 0.8749 (mp) cc_final: 0.8371 (mt) REVERT: B 89 MET cc_start: 0.7357 (ppp) cc_final: 0.7135 (ppp) REVERT: B 133 GLU cc_start: 0.8387 (tt0) cc_final: 0.8174 (mt-10) REVERT: B 197 MET cc_start: 0.7466 (tpp) cc_final: 0.7228 (tpp) REVERT: C 91 PHE cc_start: 0.7498 (m-80) cc_final: 0.7054 (m-80) REVERT: C 256 TYR cc_start: 0.8083 (t80) cc_final: 0.7851 (t80) REVERT: D 91 PHE cc_start: 0.7321 (m-80) cc_final: 0.7106 (m-80) REVERT: D 233 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8226 (tp-100) REVERT: D 256 TYR cc_start: 0.7956 (t80) cc_final: 0.7657 (t80) REVERT: E 9 GLN cc_start: 0.6854 (tt0) cc_final: 0.6553 (tp40) REVERT: E 86 LYS cc_start: 0.8681 (tppp) cc_final: 0.8405 (tppt) REVERT: F 86 LYS cc_start: 0.8694 (tppp) cc_final: 0.8392 (tppt) outliers start: 82 outliers final: 72 residues processed: 290 average time/residue: 0.0777 time to fit residues: 32.8779 Evaluate side-chains 296 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 223 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 51 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.088312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.075224 restraints weight = 27296.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.077234 restraints weight = 15468.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.078690 restraints weight = 10442.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.079318 restraints weight = 7822.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.080244 restraints weight = 6682.265| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9370 Z= 0.153 Angle : 0.831 9.057 12730 Z= 0.396 Chirality : 0.049 0.246 1528 Planarity : 0.005 0.084 1604 Dihedral : 8.342 59.863 1355 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 7.24 % Allowed : 31.49 % Favored : 61.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.24), residues: 1202 helix: -0.23 (0.20), residues: 662 sheet: -0.50 (0.66), residues: 70 loop : -2.06 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 46 TYR 0.018 0.002 TYR C 261 PHE 0.040 0.002 PHE D 243 TRP 0.014 0.001 TRP F 7 HIS 0.006 0.001 HIS C 113 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9370) covalent geometry : angle 0.83104 (12730) hydrogen bonds : bond 0.03570 ( 472) hydrogen bonds : angle 5.41031 ( 1374) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 238 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8583 (ppp) cc_final: 0.7988 (tmm) REVERT: A 56 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7017 (ptt) REVERT: A 89 MET cc_start: 0.7438 (ppp) cc_final: 0.7134 (ppp) REVERT: A 195 TRP cc_start: 0.7103 (p90) cc_final: 0.6564 (p90) REVERT: A 197 MET cc_start: 0.7537 (tpp) cc_final: 0.7003 (tpp) REVERT: A 198 ASP cc_start: 0.7556 (t0) cc_final: 0.7226 (m-30) REVERT: B 76 LEU cc_start: 0.8722 (mp) cc_final: 0.8341 (mt) REVERT: B 89 MET cc_start: 0.7406 (ppp) cc_final: 0.7154 (ppp) REVERT: B 133 GLU cc_start: 0.8486 (tt0) cc_final: 0.8192 (mt-10) REVERT: B 197 MET cc_start: 0.7582 (tpp) cc_final: 0.7361 (tpp) REVERT: C 75 MET cc_start: 0.6063 (pmm) cc_final: 0.5784 (pmm) REVERT: C 80 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8693 (mt) REVERT: C 87 MET cc_start: 0.8800 (mmt) cc_final: 0.8546 (mmm) REVERT: C 91 PHE cc_start: 0.7283 (m-80) cc_final: 0.6924 (m-80) REVERT: C 256 TYR cc_start: 0.8061 (t80) cc_final: 0.7839 (t80) REVERT: D 91 PHE cc_start: 0.7267 (m-80) cc_final: 0.6987 (m-80) REVERT: D 233 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8215 (tp-100) REVERT: D 256 TYR cc_start: 0.7951 (t80) cc_final: 0.7658 (t80) REVERT: E 86 LYS cc_start: 0.8684 (tppp) cc_final: 0.8390 (tppt) REVERT: F 86 LYS cc_start: 0.8723 (tppp) cc_final: 0.8404 (tppt) outliers start: 72 outliers final: 64 residues processed: 288 average time/residue: 0.0780 time to fit residues: 32.4425 Evaluate side-chains 293 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 227 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 103 optimal weight: 8.9990 chunk 72 optimal weight: 0.0040 chunk 5 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS D 226 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.089213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.075852 restraints weight = 27141.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.077969 restraints weight = 15700.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.079329 restraints weight = 10681.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.080391 restraints weight = 8198.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.080990 restraints weight = 6776.877| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9370 Z= 0.153 Angle : 0.853 11.682 12730 Z= 0.405 Chirality : 0.049 0.302 1528 Planarity : 0.005 0.082 1604 Dihedral : 8.256 59.144 1351 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 7.34 % Allowed : 31.79 % Favored : 60.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.24), residues: 1202 helix: -0.11 (0.20), residues: 656 sheet: -0.60 (0.62), residues: 82 loop : -2.12 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 46 TYR 0.017 0.002 TYR C 261 PHE 0.038 0.002 PHE D 243 TRP 0.012 0.001 TRP F 7 HIS 0.009 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9370) covalent geometry : angle 0.85295 (12730) hydrogen bonds : bond 0.03574 ( 472) hydrogen bonds : angle 5.32178 ( 1374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1427.78 seconds wall clock time: 25 minutes 28.05 seconds (1528.05 seconds total)