Starting phenix.real_space_refine on Thu Feb 13 15:53:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ch7_30370/02_2025/7ch7_30370.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ch7_30370/02_2025/7ch7_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ch7_30370/02_2025/7ch7_30370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ch7_30370/02_2025/7ch7_30370.map" model { file = "/net/cci-nas-00/data/ceres_data/7ch7_30370/02_2025/7ch7_30370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ch7_30370/02_2025/7ch7_30370.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.47, per 1000 atoms: 0.59 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: 2.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.98 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: 2.44 Time building geometry restraints manager: 2.90 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: 0.04 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.970 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.170 ------------------------------------------------------------------------------- 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= 0.491 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 : 26.29 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP A 149 HIS 0.003 0.001 HIS C 203 PHE 0.016 0.002 PHE A 148 TYR 0.012 0.001 TYR B 49 ARG 0.005 0.001 ARG C 21 *********************** 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 : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8774 (ppp) cc_final: 0.8469 (ppp) REVERT: A 90 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9014 (tm) REVERT: A 106 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8261 (mt) REVERT: A 134 MET cc_start: 0.8875 (tpt) cc_final: 0.8606 (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: 0.7314 (tpp) REVERT: B 47 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7623 (mm-40) REVERT: B 90 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8948 (tm) REVERT: B 176 SER cc_start: 0.7851 (m) cc_final: 0.7525 (t) REVERT: B 197 MET cc_start: 0.8078 (tpt) cc_final: 0.7696 (tpp) REVERT: C 64 GLU cc_start: 0.5016 (mp0) cc_final: 0.4795 (mp0) REVERT: C 90 LEU cc_start: 0.8493 (tp) cc_final: 0.8007 (tt) REVERT: C 120 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8599 (tm) REVERT: C 130 GLU cc_start: 0.7540 (tp30) cc_final: 0.7273 (tp30) REVERT: C 207 GLU cc_start: 0.8465 (tp30) cc_final: 0.8230 (tp30) REVERT: D 130 GLU cc_start: 0.7718 (tp30) cc_final: 0.7293 (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: 0.8528 (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: 0.8839 (pt) REVERT: E 57 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9075 (tp) REVERT: E 66 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8591 (mmtm) REVERT: E 70 ASN cc_start: 0.6974 (t0) cc_final: 0.6232 (t0) REVERT: E 86 LYS cc_start: 0.8765 (tppp) cc_final: 0.8538 (tppt) REVERT: F 4 SER cc_start: 0.6724 (p) cc_final: 0.6164 (m) REVERT: F 44 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8753 (pt) REVERT: F 57 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9036 (tp) REVERT: F 70 ASN cc_start: 0.7320 (t0) cc_final: 0.6706 (t0) REVERT: F 80 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8537 (mmmm) REVERT: F 86 LYS cc_start: 0.8830 (tppp) cc_final: 0.8524 (tppt) outliers start: 180 outliers final: 83 residues processed: 420 average time/residue: 0.2019 time to fit residues: 117.9765 Evaluate side-chains 328 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 232 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 178 LYS 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 178 LYS 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 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 99 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 F 60 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.084182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.071142 restraints weight = 27243.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.073143 restraints weight = 15597.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.074413 restraints weight = 10505.305| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9370 Z= 0.271 Angle : 0.830 10.061 12730 Z= 0.396 Chirality : 0.047 0.236 1528 Planarity : 0.006 0.100 1604 Dihedral : 12.340 63.952 1475 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 13.18 % Allowed : 23.14 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.21), residues: 1202 helix: -1.58 (0.18), residues: 656 sheet: -1.64 (0.65), residues: 50 loop : -2.77 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 7 HIS 0.004 0.001 HIS C 113 PHE 0.010 0.002 PHE A 185 TYR 0.012 0.002 TYR E 82 ARG 0.005 0.001 ARG D 135 *********************** 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 415 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 284 time to evaluate : 1.044 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: 0.8714 (ppp) cc_final: 0.8457 (ppp) REVERT: A 56 MET cc_start: 0.7685 (ttp) cc_final: 0.7248 (ptt) REVERT: A 89 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7414 (ppp) REVERT: A 90 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8783 (tm) REVERT: A 106 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7849 (mt) REVERT: A 195 TRP cc_start: 0.7358 (p90) cc_final: 0.6602 (p90) REVERT: A 197 MET cc_start: 0.7470 (tpt) cc_final: 0.7062 (tpp) REVERT: A 198 ASP cc_start: 0.7706 (t0) cc_final: 0.7435 (m-30) REVERT: B 56 MET cc_start: 0.7686 (ttp) cc_final: 0.7075 (ptp) REVERT: B 89 MET cc_start: 0.7860 (tmm) cc_final: 0.7576 (ppp) REVERT: B 90 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8701 (tm) REVERT: B 135 MET cc_start: 0.8013 (mtm) cc_final: 0.7400 (mtm) REVERT: B 161 ILE cc_start: 0.9304 (mt) cc_final: 0.9011 (tp) REVERT: B 176 SER cc_start: 0.7748 (m) cc_final: 0.7346 (t) REVERT: B 198 ASP cc_start: 0.7946 (t0) cc_final: 0.7487 (t0) REVERT: C 116 LEU cc_start: 0.9187 (tp) cc_final: 0.8910 (tp) REVERT: C 120 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8468 (tm) REVERT: C 130 GLU cc_start: 0.7970 (tp30) cc_final: 0.7695 (tp30) REVERT: C 167 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8104 (pmm) REVERT: C 207 GLU cc_start: 0.8227 (tp30) cc_final: 0.7881 (tp30) REVERT: D 87 MET cc_start: 0.8018 (mtm) cc_final: 0.7806 (mtt) REVERT: D 130 GLU cc_start: 0.7882 (tp30) cc_final: 0.7607 (tp30) REVERT: D 180 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7265 (ttt) REVERT: D 187 ILE cc_start: 0.9468 (pt) cc_final: 0.9215 (pt) REVERT: D 233 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8452 (tp40) REVERT: E 44 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8675 (pp) REVERT: E 64 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8751 (mt) REVERT: E 66 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8539 (mmtm) REVERT: E 80 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8524 (mmmm) REVERT: E 86 LYS cc_start: 0.8589 (tppp) cc_final: 0.8300 (tppt) REVERT: F 44 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8631 (pp) REVERT: F 64 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8750 (mt) REVERT: F 80 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8486 (mmmm) REVERT: F 86 LYS cc_start: 0.8578 (tppp) cc_final: 0.8316 (tppt) REVERT: F 89 ASN cc_start: 0.8561 (t0) cc_final: 0.8000 (t0) outliers start: 131 outliers final: 78 residues processed: 370 average time/residue: 0.1826 time to fit residues: 96.2194 Evaluate side-chains 318 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 227 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 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 178 LYS 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 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 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 178 LYS Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP 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 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 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 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 201 VAL 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 43 optimal weight: 0.7980 chunk 49 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 80 optimal weight: 0.1980 chunk 5 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.085124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.071951 restraints weight = 27774.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.073943 restraints weight = 15773.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.075339 restraints weight = 10659.766| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9370 Z= 0.238 Angle : 0.782 9.509 12730 Z= 0.371 Chirality : 0.048 0.363 1528 Planarity : 0.005 0.096 1604 Dihedral : 10.863 59.919 1423 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 11.37 % Allowed : 25.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.23), residues: 1202 helix: -0.97 (0.19), residues: 648 sheet: -0.88 (0.62), residues: 62 loop : -2.35 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 195 HIS 0.004 0.001 HIS D 122 PHE 0.013 0.002 PHE B 65 TYR 0.021 0.002 TYR D 261 ARG 0.004 0.000 ARG C 77 *********************** 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 375 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 262 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7803 (ttp) cc_final: 0.7275 (ptt) REVERT: A 89 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7377 (ppp) REVERT: A 90 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8807 (tm) REVERT: A 106 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7689 (mt) REVERT: A 197 MET cc_start: 0.7529 (tpt) cc_final: 0.7147 (tpp) REVERT: A 198 ASP cc_start: 0.7837 (t0) cc_final: 0.7368 (t0) REVERT: A 205 LYS cc_start: 0.8282 (mttm) cc_final: 0.7977 (mmtt) REVERT: B 56 MET cc_start: 0.7781 (ttp) cc_final: 0.7038 (ptp) REVERT: B 89 MET cc_start: 0.7849 (tmm) cc_final: 0.7558 (ppp) REVERT: B 90 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8695 (tm) REVERT: B 133 GLU cc_start: 0.8539 (tt0) cc_final: 0.8290 (mt-10) REVERT: B 176 SER cc_start: 0.7736 (m) cc_final: 0.7298 (t) REVERT: B 195 TRP cc_start: 0.7626 (p90) cc_final: 0.7384 (p90) REVERT: B 197 MET cc_start: 0.7533 (tpp) cc_final: 0.7179 (tpp) REVERT: C 57 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7877 (pt0) REVERT: C 130 GLU cc_start: 0.7984 (tp30) cc_final: 0.7721 (tp30) REVERT: C 207 GLU cc_start: 0.8242 (tp30) cc_final: 0.7959 (mm-30) REVERT: C 256 TYR cc_start: 0.8201 (t80) cc_final: 0.7707 (t80) REVERT: D 89 MET cc_start: 0.7925 (mtt) cc_final: 0.7640 (mtt) REVERT: D 187 ILE cc_start: 0.9491 (pt) cc_final: 0.9238 (pt) REVERT: D 233 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8458 (tp-100) REVERT: E 44 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8676 (pp) REVERT: E 80 LYS cc_start: 0.8856 (mmmt) cc_final: 0.8611 (mmmm) REVERT: E 86 LYS cc_start: 0.8627 (tppp) cc_final: 0.8327 (tppt) REVERT: F 5 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.6823 (tp) REVERT: F 44 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8605 (pp) REVERT: F 86 LYS cc_start: 0.8654 (tppp) cc_final: 0.8398 (tppt) REVERT: F 89 ASN cc_start: 0.8620 (t0) cc_final: 0.7962 (t0) outliers start: 113 outliers final: 76 residues processed: 341 average time/residue: 0.1925 time to fit residues: 92.7555 Evaluate side-chains 328 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 244 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 89 MET 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 178 LYS 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 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 178 LYS 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 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 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 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 244 LEU 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 54 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 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 F residue 5 LEU 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 44 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 100 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.083706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.070567 restraints weight = 27462.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.072586 restraints weight = 15806.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.073783 restraints weight = 10692.451| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9370 Z= 0.323 Angle : 0.773 9.621 12730 Z= 0.376 Chirality : 0.049 0.421 1528 Planarity : 0.006 0.097 1604 Dihedral : 10.192 58.864 1392 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 12.37 % Allowed : 25.25 % Favored : 62.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.23), residues: 1202 helix: -0.80 (0.19), residues: 660 sheet: -1.87 (0.55), residues: 74 loop : -2.29 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 195 HIS 0.004 0.001 HIS D 113 PHE 0.021 0.002 PHE B 219 TYR 0.014 0.002 TYR D 261 ARG 0.005 0.001 ARG F 46 *********************** 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 362 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 239 time to evaluate : 1.064 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 56 MET cc_start: 0.7804 (ttp) cc_final: 0.7227 (ptt) REVERT: A 89 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7385 (ppp) REVERT: A 90 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8760 (tm) REVERT: A 106 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7758 (mt) REVERT: A 195 TRP cc_start: 0.7490 (p90) cc_final: 0.7235 (p90) REVERT: B 89 MET cc_start: 0.7865 (tmm) cc_final: 0.7575 (ppp) REVERT: B 90 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8690 (tm) REVERT: B 176 SER cc_start: 0.7761 (m) cc_final: 0.7292 (t) REVERT: B 195 TRP cc_start: 0.7481 (p90) cc_final: 0.6647 (p90) REVERT: B 197 MET cc_start: 0.7500 (tpp) cc_final: 0.7283 (tpp) REVERT: C 57 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7735 (pt0) REVERT: C 130 GLU cc_start: 0.7895 (tp30) cc_final: 0.7549 (tp30) REVERT: C 207 GLU cc_start: 0.8089 (tp30) cc_final: 0.7878 (mm-30) REVERT: C 256 TYR cc_start: 0.8231 (t80) cc_final: 0.7770 (t80) REVERT: D 89 MET cc_start: 0.7929 (mtt) cc_final: 0.7487 (mtt) REVERT: D 187 ILE cc_start: 0.9476 (pt) cc_final: 0.9236 (pt) REVERT: D 233 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8219 (tp-100) REVERT: E 44 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8638 (pp) REVERT: E 80 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8596 (mmmm) REVERT: E 86 LYS cc_start: 0.8553 (tppp) cc_final: 0.8341 (tppt) REVERT: F 37 LYS cc_start: 0.8586 (tppp) cc_final: 0.8344 (tppp) REVERT: F 44 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8624 (pp) REVERT: F 86 LYS cc_start: 0.8646 (tppp) cc_final: 0.8385 (tppt) outliers start: 123 outliers final: 87 residues processed: 330 average time/residue: 0.1849 time to fit residues: 86.7202 Evaluate side-chains 310 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 216 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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 89 MET 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 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 178 LYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 207 VAL 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 134 MET 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 178 LYS 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 207 VAL 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 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 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 81 VAL 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 44 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 33 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 53 optimal weight: 30.0000 chunk 90 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 F 60 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.085632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.072373 restraints weight = 27176.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.074395 restraints weight = 15552.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.075764 restraints weight = 10478.325| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9370 Z= 0.223 Angle : 0.766 10.287 12730 Z= 0.361 Chirality : 0.048 0.382 1528 Planarity : 0.005 0.091 1604 Dihedral : 9.802 59.688 1390 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 10.87 % Allowed : 26.66 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.23), residues: 1202 helix: -0.66 (0.19), residues: 670 sheet: -1.65 (0.55), residues: 74 loop : -2.30 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 195 HIS 0.004 0.001 HIS D 122 PHE 0.030 0.002 PHE C 243 TYR 0.013 0.002 TYR D 261 ARG 0.005 0.000 ARG F 46 *********************** 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: 108 poor density : 248 time to evaluate : 1.008 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 56 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7133 (ptt) REVERT: A 89 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7380 (ppp) REVERT: A 90 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8713 (tm) REVERT: A 106 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7634 (mt) REVERT: A 195 TRP cc_start: 0.7340 (p90) cc_final: 0.6716 (p90) REVERT: A 197 MET cc_start: 0.7565 (tpp) cc_final: 0.7290 (tpp) REVERT: A 198 ASP cc_start: 0.7741 (t0) cc_final: 0.7532 (m-30) REVERT: B 54 LEU cc_start: 0.8402 (tp) cc_final: 0.8086 (mt) REVERT: B 89 MET cc_start: 0.7845 (tmm) cc_final: 0.7511 (ppp) REVERT: B 90 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8677 (tm) REVERT: B 106 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7738 (mt) REVERT: B 176 SER cc_start: 0.7717 (m) cc_final: 0.7272 (t) REVERT: B 197 MET cc_start: 0.7466 (tpp) cc_final: 0.7246 (tpp) REVERT: B 257 MET cc_start: 0.7807 (ttm) cc_final: 0.7579 (ttt) REVERT: C 57 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7638 (pt0) REVERT: C 87 MET cc_start: 0.7774 (mtp) cc_final: 0.7293 (mtt) REVERT: C 91 PHE cc_start: 0.7559 (m-80) cc_final: 0.7150 (m-80) REVERT: C 130 GLU cc_start: 0.7845 (tp30) cc_final: 0.7549 (tp30) REVERT: C 207 GLU cc_start: 0.8108 (tp30) cc_final: 0.7794 (mm-30) REVERT: C 256 TYR cc_start: 0.8180 (t80) cc_final: 0.7753 (t80) REVERT: D 180 MET cc_start: 0.8279 (tpp) cc_final: 0.7958 (tpp) REVERT: D 187 ILE cc_start: 0.9468 (pt) cc_final: 0.9239 (pt) REVERT: D 233 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8195 (tp-100) REVERT: D 256 TYR cc_start: 0.8096 (t80) cc_final: 0.7796 (t80) REVERT: E 44 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8596 (pp) REVERT: E 80 LYS cc_start: 0.8856 (mmmt) cc_final: 0.8604 (mmmm) REVERT: E 86 LYS cc_start: 0.8547 (tppp) cc_final: 0.8313 (tppt) REVERT: F 44 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8581 (pp) REVERT: F 86 LYS cc_start: 0.8599 (tppp) cc_final: 0.8329 (tppt) outliers start: 108 outliers final: 79 residues processed: 316 average time/residue: 0.1951 time to fit residues: 87.3622 Evaluate side-chains 316 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 228 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 PHE 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 89 MET 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 122 LEU 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 178 LYS 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 220 ASN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 20 PHE 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 178 LYS 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 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 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 260 ASP Chi-restraints excluded: chain D residue 9 VAL 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 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 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 20 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 44 LEU Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 34 optimal weight: 0.1980 chunk 97 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.084929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.071097 restraints weight = 27074.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.073242 restraints weight = 14850.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.074645 restraints weight = 9816.275| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4103 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= 0.257 Angle : 0.759 10.575 12730 Z= 0.361 Chirality : 0.047 0.346 1528 Planarity : 0.005 0.091 1604 Dihedral : 9.451 59.742 1383 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 10.66 % Allowed : 26.86 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.23), residues: 1202 helix: -0.54 (0.19), residues: 668 sheet: -2.11 (0.50), residues: 90 loop : -2.15 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 195 HIS 0.003 0.001 HIS D 113 PHE 0.021 0.002 PHE B 219 TYR 0.011 0.002 TYR E 82 ARG 0.002 0.000 ARG E 46 *********************** 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 342 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 236 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7877 (ttp) cc_final: 0.7075 (ptt) REVERT: A 89 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7317 (ppp) REVERT: A 90 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8769 (tm) REVERT: A 106 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7698 (mt) REVERT: A 195 TRP cc_start: 0.7627 (p90) cc_final: 0.6916 (p90) REVERT: A 197 MET cc_start: 0.7445 (tpp) cc_final: 0.6854 (tpp) REVERT: A 198 ASP cc_start: 0.7929 (t0) cc_final: 0.7500 (m-30) REVERT: B 89 MET cc_start: 0.7888 (tmm) cc_final: 0.7492 (ppp) REVERT: B 90 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8705 (tm) REVERT: B 106 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7808 (mt) REVERT: B 197 MET cc_start: 0.7289 (tpp) cc_final: 0.6930 (tpp) REVERT: C 57 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7727 (pt0) REVERT: C 87 MET cc_start: 0.7892 (mtp) cc_final: 0.7327 (mtt) REVERT: C 91 PHE cc_start: 0.7462 (m-80) cc_final: 0.7083 (m-80) REVERT: C 130 GLU cc_start: 0.8013 (tp30) cc_final: 0.7591 (tp30) REVERT: C 256 TYR cc_start: 0.8305 (t80) cc_final: 0.7883 (t80) REVERT: D 40 MET cc_start: 0.6811 (mtp) cc_final: 0.6607 (mtp) REVERT: D 89 MET cc_start: 0.7816 (mtt) cc_final: 0.7594 (ttm) REVERT: D 187 ILE cc_start: 0.9564 (pt) cc_final: 0.9352 (pt) REVERT: D 233 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8338 (tp-100) REVERT: D 256 TYR cc_start: 0.8186 (t80) cc_final: 0.7834 (t80) REVERT: E 9 GLN cc_start: 0.7041 (tt0) cc_final: 0.6244 (tp40) REVERT: E 44 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8738 (pp) REVERT: E 64 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8936 (mp) REVERT: E 80 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8614 (mmmm) REVERT: E 86 LYS cc_start: 0.8791 (tppp) cc_final: 0.8497 (tppt) REVERT: E 89 ASN cc_start: 0.8670 (t0) cc_final: 0.8368 (t0) REVERT: F 44 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8701 (pp) REVERT: F 86 LYS cc_start: 0.8830 (tppp) cc_final: 0.8487 (tppt) outliers start: 106 outliers final: 79 residues processed: 306 average time/residue: 0.1966 time to fit residues: 84.8988 Evaluate side-chains 315 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 227 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 89 MET 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 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 178 LYS 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 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 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 178 LYS 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 37 THR 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 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 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL 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 20 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 E residue 64 LEU Chi-restraints excluded: chain E residue 73 THR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 108 optimal weight: 0.3980 chunk 62 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.084389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.070878 restraints weight = 27843.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.072842 restraints weight = 16098.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.074160 restraints weight = 11102.705| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9370 Z= 0.300 Angle : 0.778 9.811 12730 Z= 0.376 Chirality : 0.048 0.235 1528 Planarity : 0.005 0.092 1604 Dihedral : 9.400 59.418 1380 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 11.17 % Allowed : 27.67 % Favored : 61.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.24), residues: 1202 helix: -0.38 (0.20), residues: 658 sheet: -1.93 (0.52), residues: 90 loop : -2.12 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 195 HIS 0.003 0.001 HIS D 203 PHE 0.037 0.003 PHE D 243 TYR 0.012 0.002 TYR A 49 ARG 0.006 0.000 ARG E 46 *********************** 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 352 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 241 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7210 (ptt) REVERT: A 89 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7289 (ppp) REVERT: A 106 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7787 (mt) REVERT: A 195 TRP cc_start: 0.7503 (p90) cc_final: 0.6743 (p90) REVERT: A 197 MET cc_start: 0.7542 (tpp) cc_final: 0.6873 (tpp) REVERT: A 198 ASP cc_start: 0.7676 (t0) cc_final: 0.7328 (m-30) REVERT: B 106 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7885 (mt) REVERT: B 196 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.5407 (ttm170) REVERT: C 57 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7618 (pt0) REVERT: C 87 MET cc_start: 0.7803 (mtp) cc_final: 0.7335 (mtt) REVERT: C 130 GLU cc_start: 0.7810 (tp30) cc_final: 0.7514 (tp30) REVERT: C 207 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7808 (mm-30) REVERT: C 256 TYR cc_start: 0.8204 (t80) cc_final: 0.7794 (t80) REVERT: D 187 ILE cc_start: 0.9463 (pt) cc_final: 0.9258 (pt) REVERT: D 233 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8228 (tp-100) REVERT: D 256 TYR cc_start: 0.8119 (t80) cc_final: 0.7789 (t80) REVERT: E 9 GLN cc_start: 0.6986 (tt0) cc_final: 0.6340 (tp40) REVERT: E 80 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8568 (mmmm) REVERT: E 86 LYS cc_start: 0.8671 (tppp) cc_final: 0.8426 (tppt) REVERT: E 89 ASN cc_start: 0.8512 (t0) cc_final: 0.8244 (t0) REVERT: F 44 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8590 (pp) REVERT: F 86 LYS cc_start: 0.8680 (tppp) cc_final: 0.8391 (tppt) outliers start: 111 outliers final: 82 residues processed: 311 average time/residue: 0.1903 time to fit residues: 83.5501 Evaluate side-chains 313 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 224 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 89 MET 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 178 LYS 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 34 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 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 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 178 LYS 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 49 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 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 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 173 VAL 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 20 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 73 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 26 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.086772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.073364 restraints weight = 27398.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.075380 restraints weight = 15616.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.076764 restraints weight = 10684.756| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4487 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= 0.234 Angle : 0.791 9.680 12730 Z= 0.379 Chirality : 0.048 0.405 1528 Planarity : 0.005 0.089 1604 Dihedral : 8.973 59.878 1372 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 9.36 % Allowed : 29.58 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.23), residues: 1202 helix: -0.27 (0.20), residues: 656 sheet: -1.86 (0.59), residues: 70 loop : -2.12 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 195 HIS 0.005 0.001 HIS D 113 PHE 0.026 0.002 PHE B 219 TYR 0.010 0.002 TYR E 88 ARG 0.007 0.000 ARG E 46 *********************** 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 335 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 242 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7155 (ptt) REVERT: A 89 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7261 (ppp) REVERT: A 90 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8673 (tm) REVERT: A 106 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7874 (mt) REVERT: A 195 TRP cc_start: 0.7401 (p90) cc_final: 0.6858 (p90) REVERT: A 197 MET cc_start: 0.7529 (tpp) cc_final: 0.6828 (tpp) REVERT: A 198 ASP cc_start: 0.7647 (t0) cc_final: 0.7307 (m-30) REVERT: B 106 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7918 (mt) REVERT: B 196 ARG cc_start: 0.6627 (OUTLIER) cc_final: 0.5252 (ttm170) REVERT: B 197 MET cc_start: 0.7386 (tpp) cc_final: 0.6763 (tpp) REVERT: C 57 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7474 (pt0) REVERT: C 87 MET cc_start: 0.7725 (mtp) cc_final: 0.7365 (mtt) REVERT: C 91 PHE cc_start: 0.7519 (m-80) cc_final: 0.6954 (m-80) REVERT: C 112 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8201 (tm-30) REVERT: C 256 TYR cc_start: 0.8174 (t80) cc_final: 0.7835 (t80) REVERT: D 180 MET cc_start: 0.8347 (tpp) cc_final: 0.7829 (tpp) REVERT: D 187 ILE cc_start: 0.9443 (pt) cc_final: 0.9221 (pt) REVERT: D 233 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8250 (tp-100) REVERT: D 256 TYR cc_start: 0.8050 (t80) cc_final: 0.7694 (t80) REVERT: E 9 GLN cc_start: 0.6971 (tt0) cc_final: 0.6513 (tp40) REVERT: E 23 ASP cc_start: 0.8170 (m-30) cc_final: 0.7771 (m-30) REVERT: E 80 LYS cc_start: 0.8847 (mmmt) cc_final: 0.8541 (mmmm) REVERT: E 86 LYS cc_start: 0.8653 (tppp) cc_final: 0.8397 (tppt) REVERT: E 89 ASN cc_start: 0.8484 (t0) cc_final: 0.8229 (t0) REVERT: F 44 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8523 (pp) REVERT: F 86 LYS cc_start: 0.8649 (tppp) cc_final: 0.8317 (tppt) outliers start: 93 outliers final: 74 residues processed: 301 average time/residue: 0.1964 time to fit residues: 82.9692 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 : 1.030 ------------------------------------------------------------------------------- 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 89 MET 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 122 LEU 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 178 LYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 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 178 LYS 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 238 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 26 ASN 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 100 MET Chi-restraints excluded: chain C residue 113 HIS 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 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 172 PHE Chi-restraints excluded: chain D residue 173 VAL 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 20 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 44 LEU 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 82 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 97 optimal weight: 0.3980 chunk 104 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.087820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.073973 restraints weight = 26877.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.076186 restraints weight = 14789.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.077336 restraints weight = 9807.634| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4795 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= 0.229 Angle : 0.813 12.540 12730 Z= 0.388 Chirality : 0.047 0.346 1528 Planarity : 0.005 0.084 1604 Dihedral : 8.820 59.914 1369 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 8.45 % Allowed : 30.18 % Favored : 61.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.24), residues: 1202 helix: -0.15 (0.20), residues: 668 sheet: -1.39 (0.58), residues: 80 loop : -2.05 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 7 HIS 0.007 0.001 HIS D 113 PHE 0.040 0.002 PHE C 243 TYR 0.021 0.002 TYR C 261 ARG 0.007 0.000 ARG E 46 *********************** 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 324 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 240 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7671 (ttp) cc_final: 0.7004 (ptt) REVERT: A 89 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7231 (ppp) REVERT: A 90 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8773 (tm) REVERT: A 195 TRP cc_start: 0.7725 (p90) cc_final: 0.7146 (p90) REVERT: A 197 MET cc_start: 0.7422 (tpp) cc_final: 0.6733 (tpp) REVERT: A 198 ASP cc_start: 0.7896 (t0) cc_final: 0.7466 (m-30) REVERT: A 205 LYS cc_start: 0.8289 (mmtt) cc_final: 0.8071 (mmtt) REVERT: C 57 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7543 (pt0) REVERT: C 87 MET cc_start: 0.7828 (mtp) cc_final: 0.7486 (mtm) REVERT: C 91 PHE cc_start: 0.7450 (m-80) cc_final: 0.6758 (m-80) REVERT: C 256 TYR cc_start: 0.8265 (t80) cc_final: 0.7898 (t80) REVERT: D 149 MET cc_start: 0.8097 (mtm) cc_final: 0.7870 (mtm) REVERT: D 180 MET cc_start: 0.8415 (tpp) cc_final: 0.7897 (tpp) REVERT: D 187 ILE cc_start: 0.9544 (pt) cc_final: 0.9335 (pt) REVERT: D 233 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8329 (tp-100) REVERT: D 256 TYR cc_start: 0.8102 (t80) cc_final: 0.7711 (t80) REVERT: E 80 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8667 (mmmm) REVERT: E 86 LYS cc_start: 0.8841 (tppp) cc_final: 0.8515 (tppt) REVERT: E 89 ASN cc_start: 0.8716 (t0) cc_final: 0.8239 (t0) REVERT: F 9 GLN cc_start: 0.7131 (tt0) cc_final: 0.6697 (tp40) REVERT: F 44 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8682 (pp) REVERT: F 86 LYS cc_start: 0.8870 (tppp) cc_final: 0.8527 (tppt) outliers start: 84 outliers final: 72 residues processed: 297 average time/residue: 0.2044 time to fit residues: 85.6832 Evaluate side-chains 306 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 230 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL 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 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 143 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 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 178 LYS Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 37 THR 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 100 MET Chi-restraints excluded: chain C residue 113 HIS 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 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 172 PHE Chi-restraints excluded: chain D residue 173 VAL 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 20 LEU Chi-restraints excluded: chain E residue 25 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 44 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 102 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** C 226 HIS D 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.087551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.073525 restraints weight = 27219.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.075771 restraints weight = 14833.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.077259 restraints weight = 9730.138| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9370 Z= 0.249 Angle : 0.847 12.478 12730 Z= 0.402 Chirality : 0.050 0.316 1528 Planarity : 0.005 0.081 1604 Dihedral : 8.552 59.976 1362 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 7.75 % Allowed : 31.09 % Favored : 61.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.24), residues: 1202 helix: -0.11 (0.20), residues: 670 sheet: -1.11 (0.58), residues: 82 loop : -2.09 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 7 HIS 0.005 0.001 HIS C 113 PHE 0.033 0.002 PHE D 243 TYR 0.018 0.002 TYR C 261 ARG 0.011 0.000 ARG D 151 ********************** 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 309 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 232 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7721 (ttp) cc_final: 0.7099 (ptt) REVERT: A 89 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7339 (ppp) REVERT: A 90 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8728 (tm) REVERT: A 195 TRP cc_start: 0.7599 (p90) cc_final: 0.7048 (p90) REVERT: A 197 MET cc_start: 0.7462 (tpp) cc_final: 0.6785 (tpp) REVERT: A 198 ASP cc_start: 0.7757 (t0) cc_final: 0.7319 (m-30) REVERT: B 76 LEU cc_start: 0.8834 (mp) cc_final: 0.8470 (mt) REVERT: B 198 ASP cc_start: 0.7353 (p0) cc_final: 0.6568 (p0) REVERT: C 57 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7475 (pt0) REVERT: C 87 MET cc_start: 0.7823 (mtp) cc_final: 0.7437 (mtt) REVERT: C 256 TYR cc_start: 0.8238 (t80) cc_final: 0.7874 (t80) REVERT: D 89 MET cc_start: 0.7984 (ttm) cc_final: 0.7546 (ttm) REVERT: D 180 MET cc_start: 0.8365 (tpp) cc_final: 0.8159 (tpp) REVERT: D 187 ILE cc_start: 0.9526 (pt) cc_final: 0.9318 (pt) REVERT: D 233 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8301 (tp-100) REVERT: D 256 TYR cc_start: 0.8111 (t80) cc_final: 0.7733 (t80) REVERT: E 30 GLU cc_start: 0.8250 (pm20) cc_final: 0.8044 (pm20) REVERT: E 80 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8640 (mmmm) REVERT: E 86 LYS cc_start: 0.8841 (tppp) cc_final: 0.8479 (tppt) REVERT: F 86 LYS cc_start: 0.8893 (tppp) cc_final: 0.8529 (tppt) outliers start: 77 outliers final: 71 residues processed: 282 average time/residue: 0.2083 time to fit residues: 82.8235 Evaluate side-chains 298 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 224 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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 89 MET Chi-restraints excluded: chain A residue 90 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 143 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 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 178 LYS Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 TRP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 37 THR 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 113 HIS 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 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 172 PHE Chi-restraints excluded: chain D residue 173 VAL 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 20 LEU Chi-restraints excluded: chain E residue 25 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 83 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 31 optimal weight: 0.0020 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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** B 201 ASN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 HIS C 226 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.088493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.074521 restraints weight = 26943.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.076752 restraints weight = 14863.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.078329 restraints weight = 9797.783| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.5090 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= 0.241 Angle : 0.867 11.669 12730 Z= 0.411 Chirality : 0.050 0.274 1528 Planarity : 0.005 0.081 1604 Dihedral : 8.538 59.507 1360 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 7.04 % Allowed : 32.19 % Favored : 60.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.24), residues: 1202 helix: -0.07 (0.20), residues: 668 sheet: -0.81 (0.60), residues: 82 loop : -2.19 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 7 HIS 0.015 0.001 HIS C 226 PHE 0.031 0.002 PHE C 243 TYR 0.017 0.002 TYR C 261 ARG 0.006 0.000 ARG D 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2811.34 seconds wall clock time: 51 minutes 22.49 seconds (3082.49 seconds total)