Starting phenix.real_space_refine on Thu Mar 13 18:40:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ch7_30370/03_2025/7ch7_30370.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ch7_30370/03_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_30370/03_2025/7ch7_30370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ch7_30370/03_2025/7ch7_30370.map" model { file = "/net/cci-nas-00/data/ceres_data/7ch7_30370/03_2025/7ch7_30370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ch7_30370/03_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-5624/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: 5.48, per 1000 atoms: 0.60 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: 2.42 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: 0.96 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: 2.59 Time building geometry restraints manager: 2.84 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: 1.100 Set stop_for_unknowns flag: 0.010 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.470 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.130 ------------------------------------------------------------------------------- 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 : 1.065 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: 0.2083 time to fit residues: 122.5684 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 : 1.077 ------------------------------------------------------------------------------- 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 = 0.071143 restraints weight = 27243.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.073142 restraints weight = 15597.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.074416 restraints weight = 10504.784| |-----------------------------------------------------------------------------| 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 : 0.995 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: 0.8715 (ppp) cc_final: 0.8458 (ppp) REVERT: A 56 MET cc_start: 0.7685 (ttp) cc_final: 0.7248 (ptt) REVERT: A 89 MET cc_start: 0.7709 (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: 0.7471 (tpt) cc_final: 0.7063 (tpp) REVERT: A 198 ASP cc_start: 0.7706 (t0) cc_final: 0.7436 (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: 0.8012 (mtm) cc_final: 0.7401 (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: 0.7945 (t0) cc_final: 0.7485 (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: 0.8469 (tm) REVERT: C 130 GLU cc_start: 0.7968 (tp30) cc_final: 0.7695 (tp30) REVERT: C 167 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8105 (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: 0.7808 (mtt) REVERT: D 130 GLU cc_start: 0.7880 (tp30) cc_final: 0.7606 (tp30) REVERT: D 180 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7263 (ttt) REVERT: D 187 ILE cc_start: 0.9468 (pt) cc_final: 0.9216 (pt) REVERT: D 233 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8453 (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: 0.8750 (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: 0.8523 (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: 0.9047 (OUTLIER) cc_final: 0.8751 (mt) REVERT: F 80 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8485 (mmmm) REVERT: F 86 LYS cc_start: 0.8579 (tppp) cc_final: 0.8316 (tppt) REVERT: F 89 ASN cc_start: 0.8564 (t0) cc_final: 0.8003 (t0) outliers start: 131 outliers final: 78 residues processed: 370 average time/residue: 0.1768 time to fit residues: 93.7786 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 : 1.070 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.5980 chunk 5 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.085049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.071992 restraints weight = 27703.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.073998 restraints weight = 15651.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.075319 restraints weight = 10540.986| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3335 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= 0.234 Angle : 0.784 9.485 12730 Z= 0.372 Chirality : 0.048 0.379 1528 Planarity : 0.005 0.096 1604 Dihedral : 10.892 59.553 1423 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 11.07 % Allowed : 25.86 % Favored : 63.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.35 (0.23), residues: 1202 helix: -0.99 (0.19), residues: 648 sheet: -0.90 (0.62), residues: 62 loop : -2.36 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 195 HIS 0.004 0.001 HIS D 122 PHE 0.014 0.002 PHE B 65 TYR 0.021 0.002 TYR D 261 ARG 0.003 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 371 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 261 time to evaluate : 1.000 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: 0.7761 (ttp) cc_final: 0.7221 (ptt) REVERT: A 89 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7392 (ppp) REVERT: A 90 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8803 (tm) REVERT: A 106 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7687 (mt) REVERT: A 197 MET cc_start: 0.7527 (tpt) cc_final: 0.7141 (tpp) REVERT: A 198 ASP cc_start: 0.7845 (t0) cc_final: 0.7379 (t0) REVERT: A 205 LYS cc_start: 0.8293 (mttm) cc_final: 0.7987 (mmtt) REVERT: B 56 MET cc_start: 0.7786 (ttp) cc_final: 0.7039 (ptp) REVERT: B 89 MET cc_start: 0.7850 (tmm) cc_final: 0.7557 (ppp) REVERT: B 90 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8694 (tm) REVERT: B 133 GLU cc_start: 0.8546 (tt0) cc_final: 0.8295 (mt-10) REVERT: B 176 SER cc_start: 0.7742 (m) cc_final: 0.7303 (t) REVERT: B 197 MET cc_start: 0.7547 (tpp) cc_final: 0.7187 (tpp) REVERT: C 57 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7899 (pt0) REVERT: C 130 GLU cc_start: 0.7956 (tp30) cc_final: 0.7681 (tp30) REVERT: C 207 GLU cc_start: 0.8253 (tp30) cc_final: 0.7984 (mm-30) REVERT: C 256 TYR cc_start: 0.8196 (t80) cc_final: 0.7688 (t80) REVERT: D 187 ILE cc_start: 0.9497 (pt) cc_final: 0.9251 (pt) REVERT: D 233 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8470 (tp-100) REVERT: E 44 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8692 (pp) REVERT: E 80 LYS cc_start: 0.8853 (mmmt) cc_final: 0.8611 (mmmm) REVERT: E 86 LYS cc_start: 0.8625 (tppp) cc_final: 0.8324 (tppt) REVERT: F 5 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.6835 (tp) REVERT: F 44 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8617 (pp) REVERT: F 86 LYS cc_start: 0.8647 (tppp) cc_final: 0.8391 (tppt) REVERT: F 89 ASN cc_start: 0.8615 (t0) cc_final: 0.7928 (t0) outliers start: 110 outliers final: 78 residues processed: 338 average time/residue: 0.2203 time to fit residues: 106.8857 Evaluate side-chains 326 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 240 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 32 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 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 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 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 260 ASP Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 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: 4.9990 chunk 7 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 111 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.0030 chunk 73 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.085696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.072412 restraints weight = 26903.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.074375 restraints weight = 15434.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.075803 restraints weight = 10562.013| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9370 Z= 0.232 Angle : 0.748 9.783 12730 Z= 0.357 Chirality : 0.047 0.379 1528 Planarity : 0.005 0.092 1604 Dihedral : 9.959 59.415 1394 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 11.57 % Allowed : 24.95 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.07 (0.23), residues: 1202 helix: -0.73 (0.19), residues: 660 sheet: -0.99 (0.62), residues: 62 loop : -2.28 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 195 HIS 0.004 0.001 HIS D 113 PHE 0.020 0.002 PHE B 219 TYR 0.014 0.002 TYR D 261 ARG 0.006 0.000 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 371 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 256 time to evaluate : 1.068 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: 0.7870 (ttp) cc_final: 0.7200 (ptt) REVERT: A 90 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8723 (tm) REVERT: A 106 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7709 (mt) REVERT: A 133 GLU cc_start: 0.8528 (tt0) cc_final: 0.8295 (mt-10) REVERT: A 195 TRP cc_start: 0.7337 (p90) cc_final: 0.7113 (p90) REVERT: A 205 LYS cc_start: 0.8229 (mttm) cc_final: 0.7593 (mmtt) REVERT: A 253 LEU cc_start: 0.8309 (tt) cc_final: 0.8053 (tt) REVERT: B 56 MET cc_start: 0.7795 (ttp) cc_final: 0.7138 (ptp) REVERT: B 89 MET cc_start: 0.7836 (tmm) cc_final: 0.7507 (ppp) REVERT: B 90 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8684 (tm) REVERT: B 176 SER cc_start: 0.7609 (m) cc_final: 0.7188 (t) REVERT: B 197 MET cc_start: 0.7503 (tpp) cc_final: 0.7274 (tpp) REVERT: C 57 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7694 (pt0) REVERT: C 87 MET cc_start: 0.7913 (mtm) cc_final: 0.7644 (mtt) REVERT: C 130 GLU cc_start: 0.7901 (tp30) cc_final: 0.7579 (tp30) REVERT: C 235 ASN cc_start: 0.8021 (t0) cc_final: 0.7810 (t0) REVERT: C 256 TYR cc_start: 0.8172 (t80) cc_final: 0.7718 (t80) REVERT: D 187 ILE cc_start: 0.9475 (pt) cc_final: 0.9226 (pt) REVERT: D 233 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8366 (tp-100) REVERT: E 44 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8668 (pp) REVERT: E 80 LYS cc_start: 0.8850 (mmmt) cc_final: 0.8588 (mmmm) REVERT: E 86 LYS cc_start: 0.8551 (tppp) cc_final: 0.8307 (tppt) REVERT: F 44 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8568 (pp) REVERT: F 86 LYS cc_start: 0.8584 (tppp) cc_final: 0.8333 (tppt) outliers start: 115 outliers final: 73 residues processed: 332 average time/residue: 0.1945 time to fit residues: 91.0797 Evaluate side-chains 317 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 238 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 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 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 70 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 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 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 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 166 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 33 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.085507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.072207 restraints weight = 27095.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.074212 restraints weight = 15638.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.075532 restraints weight = 10654.960| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9370 Z= 0.252 Angle : 0.763 10.679 12730 Z= 0.363 Chirality : 0.048 0.394 1528 Planarity : 0.005 0.092 1604 Dihedral : 9.581 59.470 1386 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 11.07 % Allowed : 26.46 % 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: -0.58 (0.19), residues: 660 sheet: -1.71 (0.54), residues: 74 loop : -2.18 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 195 HIS 0.006 0.001 HIS C 113 PHE 0.030 0.002 PHE C 243 TYR 0.011 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 362 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 252 time to evaluate : 1.134 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: 0.7875 (ttp) cc_final: 0.7159 (ptt) REVERT: A 106 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7692 (mt) REVERT: A 195 TRP cc_start: 0.7355 (p90) cc_final: 0.6701 (p90) REVERT: A 197 MET cc_start: 0.7552 (tpp) cc_final: 0.6998 (tpp) REVERT: A 198 ASP cc_start: 0.7730 (t0) cc_final: 0.7525 (m-30) REVERT: B 54 LEU cc_start: 0.8401 (tp) cc_final: 0.8079 (mt) REVERT: B 89 MET cc_start: 0.7824 (tmm) cc_final: 0.7520 (ppp) REVERT: B 90 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8668 (tm) REVERT: B 106 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7730 (mt) REVERT: B 176 SER cc_start: 0.7736 (m) cc_final: 0.7294 (t) REVERT: B 197 MET cc_start: 0.7373 (tpp) cc_final: 0.7068 (tpp) REVERT: C 57 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7654 (pt0) REVERT: C 89 MET cc_start: 0.8033 (ttm) cc_final: 0.7737 (ttm) REVERT: C 91 PHE cc_start: 0.7707 (m-80) cc_final: 0.7071 (m-80) REVERT: C 130 GLU cc_start: 0.7852 (tp30) cc_final: 0.7559 (tp30) REVERT: C 207 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7624 (mm-30) REVERT: C 256 TYR cc_start: 0.8190 (t80) cc_final: 0.7736 (t80) REVERT: D 40 MET cc_start: 0.6566 (mtp) cc_final: 0.6364 (mtp) REVERT: D 187 ILE cc_start: 0.9490 (pt) cc_final: 0.9273 (pt) REVERT: D 233 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8180 (tp-100) REVERT: D 256 TYR cc_start: 0.8076 (t80) cc_final: 0.7800 (t80) REVERT: E 9 GLN cc_start: 0.6786 (tt0) cc_final: 0.6049 (tp40) REVERT: E 44 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8581 (pp) REVERT: E 80 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8591 (mmmm) REVERT: E 86 LYS cc_start: 0.8550 (tppp) cc_final: 0.8336 (tppt) REVERT: F 44 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8580 (pp) REVERT: F 86 LYS cc_start: 0.8612 (tppp) cc_final: 0.8342 (tppt) outliers start: 110 outliers final: 78 residues processed: 323 average time/residue: 0.1995 time to fit residues: 91.1881 Evaluate side-chains 318 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 234 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 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 72 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 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 26 ASN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 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 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 166 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 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: 0.3980 chunk 97 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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** D 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.084490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.070479 restraints weight = 27148.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.072488 restraints weight = 15006.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.073984 restraints weight = 10144.896| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9370 Z= 0.289 Angle : 0.769 9.621 12730 Z= 0.368 Chirality : 0.048 0.326 1528 Planarity : 0.005 0.091 1604 Dihedral : 9.272 59.590 1379 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 11.37 % Allowed : 26.16 % 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: -1.83 (0.23), residues: 1202 helix: -0.43 (0.19), residues: 658 sheet: -2.14 (0.49), residues: 90 loop : -2.09 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 195 HIS 0.005 0.001 HIS C 113 PHE 0.024 0.002 PHE D 91 TYR 0.011 0.002 TYR E 82 ARG 0.003 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 351 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 238 time to evaluate : 0.964 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: 0.7891 (OUTLIER) cc_final: 0.7067 (ptt) REVERT: A 89 MET cc_start: 0.7565 (ppp) cc_final: 0.7225 (ppp) REVERT: A 106 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7681 (mt) REVERT: A 195 TRP cc_start: 0.7645 (p90) cc_final: 0.6907 (p90) REVERT: A 197 MET cc_start: 0.7482 (tpp) cc_final: 0.6867 (tpp) REVERT: A 198 ASP cc_start: 0.7952 (t0) cc_final: 0.7568 (m-30) REVERT: B 89 MET cc_start: 0.7898 (tmm) cc_final: 0.7502 (ppp) REVERT: B 90 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8725 (tm) REVERT: B 106 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7799 (mt) REVERT: C 57 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7749 (pt0) REVERT: C 87 MET cc_start: 0.8106 (mtp) cc_final: 0.7419 (mtt) REVERT: C 113 HIS cc_start: 0.8027 (OUTLIER) cc_final: 0.7643 (m90) REVERT: C 130 GLU cc_start: 0.7962 (tp30) cc_final: 0.7662 (tp30) REVERT: C 207 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7952 (mm-30) REVERT: C 256 TYR cc_start: 0.8330 (t80) cc_final: 0.7891 (t80) REVERT: D 64 GLU cc_start: 0.4762 (mp0) cc_final: 0.4382 (mp0) REVERT: D 130 GLU cc_start: 0.7490 (tp30) cc_final: 0.7284 (tp30) REVERT: D 187 ILE cc_start: 0.9579 (pt) cc_final: 0.9374 (pt) REVERT: D 233 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8319 (tp-100) REVERT: D 256 TYR cc_start: 0.8238 (t80) cc_final: 0.7919 (t80) REVERT: E 44 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8737 (pp) REVERT: E 80 LYS cc_start: 0.8926 (mmmt) cc_final: 0.8615 (mmmm) REVERT: E 86 LYS cc_start: 0.8822 (tppp) cc_final: 0.8521 (tppt) REVERT: F 44 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8698 (pp) REVERT: F 86 LYS cc_start: 0.8823 (tppp) cc_final: 0.8500 (tppt) outliers start: 113 outliers final: 87 residues processed: 311 average time/residue: 0.1862 time to fit residues: 82.1469 Evaluate side-chains 324 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 229 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 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 218 LEU 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 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 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 204 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 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 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 108 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3472 r_free = 0.3472 target = 0.085986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.072590 restraints weight = 27558.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.074619 restraints weight = 15857.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.075943 restraints weight = 10796.215| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9370 Z= 0.253 Angle : 0.769 9.250 12730 Z= 0.368 Chirality : 0.048 0.321 1528 Planarity : 0.005 0.090 1604 Dihedral : 9.171 59.514 1378 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 10.46 % Allowed : 28.07 % Favored : 61.47 % 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: -1.66 (0.24), residues: 1202 helix: -0.30 (0.20), residues: 660 sheet: -1.71 (0.51), residues: 90 loop : -2.10 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 195 HIS 0.004 0.001 HIS C 113 PHE 0.035 0.002 PHE D 243 TYR 0.011 0.002 TYR B 222 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 343 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 239 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7825 (ttp) cc_final: 0.7124 (ptt) REVERT: A 106 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7781 (mt) REVERT: A 195 TRP cc_start: 0.7401 (p90) cc_final: 0.6827 (p90) REVERT: A 197 MET cc_start: 0.7517 (tpp) cc_final: 0.6889 (tpp) REVERT: A 198 ASP cc_start: 0.7652 (t0) cc_final: 0.7341 (m-30) REVERT: B 89 MET cc_start: 0.7829 (tmm) cc_final: 0.7551 (ppp) REVERT: B 90 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8608 (tm) REVERT: B 106 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7859 (mt) REVERT: B 197 MET cc_start: 0.7545 (tpp) cc_final: 0.6894 (tpp) REVERT: C 57 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7575 (pt0) REVERT: C 87 MET cc_start: 0.7734 (mtp) cc_final: 0.7201 (mtt) REVERT: C 91 PHE cc_start: 0.7438 (m-80) cc_final: 0.6994 (m-80) REVERT: C 113 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7205 (m90) REVERT: C 130 GLU cc_start: 0.7814 (tp30) cc_final: 0.7528 (tp30) REVERT: C 207 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7805 (mm-30) REVERT: C 256 TYR cc_start: 0.8202 (t80) cc_final: 0.7800 (t80) REVERT: D 113 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.7274 (m90) REVERT: D 130 GLU cc_start: 0.7530 (tp30) cc_final: 0.7329 (tp30) REVERT: D 187 ILE cc_start: 0.9474 (pt) cc_final: 0.9267 (pt) REVERT: D 233 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8199 (tp-100) REVERT: D 256 TYR cc_start: 0.8087 (t80) cc_final: 0.7767 (t80) REVERT: E 12 ASP cc_start: 0.8765 (p0) cc_final: 0.8523 (p0) REVERT: E 80 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8551 (mmmm) REVERT: E 86 LYS cc_start: 0.8667 (tppp) cc_final: 0.8420 (tppt) REVERT: E 89 ASN cc_start: 0.8493 (t0) cc_final: 0.8216 (t0) REVERT: F 44 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8588 (pp) REVERT: F 86 LYS cc_start: 0.8678 (tppp) cc_final: 0.8373 (tppt) outliers start: 104 outliers final: 84 residues processed: 308 average time/residue: 0.1834 time to fit residues: 80.8644 Evaluate side-chains 320 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 229 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 PHE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 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 236 THR 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 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 102 VAL 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 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 26 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 0.1980 chunk 86 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.085731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.072033 restraints weight = 27682.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.074193 restraints weight = 15415.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.075570 restraints weight = 10283.650| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9370 Z= 0.276 Angle : 0.781 9.274 12730 Z= 0.376 Chirality : 0.049 0.324 1528 Planarity : 0.005 0.089 1604 Dihedral : 9.037 59.650 1373 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 10.26 % Allowed : 28.27 % Favored : 61.47 % 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: -1.58 (0.24), residues: 1202 helix: -0.20 (0.20), residues: 656 sheet: -1.35 (0.53), residues: 90 loop : -2.18 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 7 HIS 0.003 0.001 HIS C 113 PHE 0.023 0.002 PHE B 219 TYR 0.012 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 334 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 232 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7796 (ttp) cc_final: 0.7070 (ptt) REVERT: A 89 MET cc_start: 0.7519 (ppp) cc_final: 0.7175 (ppp) REVERT: A 106 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7689 (mt) REVERT: A 195 TRP cc_start: 0.7576 (p90) cc_final: 0.6909 (p90) REVERT: A 197 MET cc_start: 0.7490 (tpp) cc_final: 0.6908 (tpp) REVERT: A 198 ASP cc_start: 0.7857 (t0) cc_final: 0.7468 (m-30) REVERT: B 76 LEU cc_start: 0.8908 (mp) cc_final: 0.8585 (mt) REVERT: B 197 MET cc_start: 0.7287 (tpp) cc_final: 0.6961 (tpp) REVERT: C 57 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7616 (pt0) REVERT: C 87 MET cc_start: 0.7986 (mtp) cc_final: 0.7618 (ttp) REVERT: C 91 PHE cc_start: 0.7327 (m-80) cc_final: 0.6815 (m-80) REVERT: C 113 HIS cc_start: 0.7964 (OUTLIER) cc_final: 0.7452 (m90) REVERT: C 130 GLU cc_start: 0.8005 (tp30) cc_final: 0.7695 (tp30) REVERT: C 207 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8002 (mm-30) REVERT: C 256 TYR cc_start: 0.8289 (t80) cc_final: 0.7877 (t80) REVERT: D 130 GLU cc_start: 0.7814 (tp30) cc_final: 0.7543 (tp30) REVERT: D 233 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8291 (tp-100) REVERT: D 256 TYR cc_start: 0.8184 (t80) cc_final: 0.7835 (t80) REVERT: E 12 ASP cc_start: 0.8951 (p0) cc_final: 0.8696 (p0) REVERT: E 80 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8639 (mmmm) REVERT: E 86 LYS cc_start: 0.8843 (tppp) cc_final: 0.8515 (tppt) REVERT: F 44 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8672 (pp) REVERT: F 86 LYS cc_start: 0.8824 (tppp) cc_final: 0.8479 (tppt) outliers start: 102 outliers final: 89 residues processed: 301 average time/residue: 0.2480 time to fit residues: 108.2094 Evaluate side-chains 319 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 226 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 236 THR 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 99 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 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 236 THR 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 102 VAL 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 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 82 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.086946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.073581 restraints weight = 27124.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.075602 restraints weight = 15679.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.076903 restraints weight = 10689.885| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4673 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= 0.253 Angle : 0.806 9.256 12730 Z= 0.381 Chirality : 0.049 0.352 1528 Planarity : 0.005 0.086 1604 Dihedral : 8.818 59.883 1369 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 9.26 % Allowed : 30.08 % Favored : 60.66 % 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: -1.54 (0.24), residues: 1202 helix: -0.18 (0.20), residues: 666 sheet: -1.13 (0.55), residues: 90 loop : -2.24 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 7 HIS 0.003 0.001 HIS D 122 PHE 0.039 0.002 PHE C 243 TYR 0.011 0.002 TYR B 222 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 332 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 240 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7636 (ttp) cc_final: 0.7091 (ptt) REVERT: A 89 MET cc_start: 0.7489 (ppp) cc_final: 0.7157 (ppp) REVERT: A 106 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7723 (mt) REVERT: A 195 TRP cc_start: 0.7308 (p90) cc_final: 0.6757 (p90) REVERT: A 197 MET cc_start: 0.7736 (tpp) cc_final: 0.7165 (tpp) REVERT: A 198 ASP cc_start: 0.7755 (t0) cc_final: 0.7357 (m-30) REVERT: B 76 LEU cc_start: 0.8776 (mp) cc_final: 0.8431 (mt) REVERT: B 197 MET cc_start: 0.7359 (tpp) cc_final: 0.7003 (tpp) REVERT: C 57 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7442 (pt0) REVERT: C 87 MET cc_start: 0.7679 (mtp) cc_final: 0.7451 (ttp) REVERT: C 91 PHE cc_start: 0.7351 (m-80) cc_final: 0.6803 (m-80) REVERT: C 113 HIS cc_start: 0.7726 (OUTLIER) cc_final: 0.7188 (m90) REVERT: C 207 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7864 (mm-30) REVERT: C 256 TYR cc_start: 0.8213 (t80) cc_final: 0.7834 (t80) REVERT: D 91 PHE cc_start: 0.7381 (m-80) cc_final: 0.7133 (m-80) REVERT: D 180 MET cc_start: 0.7996 (ttt) cc_final: 0.7114 (ttt) REVERT: D 233 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8219 (tp-100) REVERT: D 256 TYR cc_start: 0.8038 (t80) cc_final: 0.7698 (t80) REVERT: E 12 ASP cc_start: 0.8755 (p0) cc_final: 0.8517 (p0) REVERT: E 80 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8579 (mmmm) REVERT: E 86 LYS cc_start: 0.8664 (tppp) cc_final: 0.8370 (tppt) REVERT: F 86 LYS cc_start: 0.8700 (tppp) cc_final: 0.8372 (tppt) outliers start: 92 outliers final: 79 residues processed: 298 average time/residue: 0.2725 time to fit residues: 114.1785 Evaluate side-chains 311 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 229 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 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 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 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 238 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 26 ASN 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 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 240 VAL Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 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 55 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 102 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.086527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.073101 restraints weight = 27562.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.075151 restraints weight = 15934.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.076539 restraints weight = 10787.217| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9370 Z= 0.291 Angle : 0.848 11.126 12730 Z= 0.399 Chirality : 0.050 0.296 1528 Planarity : 0.005 0.084 1604 Dihedral : 8.783 59.265 1366 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 8.85 % Allowed : 31.29 % Favored : 59.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.16 (0.20), residues: 666 sheet: -0.72 (0.60), residues: 80 loop : -2.19 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 7 HIS 0.004 0.001 HIS E 60 PHE 0.033 0.002 PHE D 243 TYR 0.012 0.002 TYR E 82 ARG 0.007 0.000 ARG E 46 ********************** 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 328 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 240 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7689 (ttp) cc_final: 0.7112 (ptt) REVERT: A 89 MET cc_start: 0.7501 (ppp) cc_final: 0.7210 (ppp) REVERT: A 106 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7777 (mt) REVERT: A 195 TRP cc_start: 0.7366 (p90) cc_final: 0.6708 (p90) REVERT: A 197 MET cc_start: 0.7542 (tpp) cc_final: 0.6942 (tpp) REVERT: A 198 ASP cc_start: 0.7778 (t0) cc_final: 0.7360 (m-30) REVERT: B 76 LEU cc_start: 0.8783 (mp) cc_final: 0.8445 (mt) REVERT: B 197 MET cc_start: 0.7361 (tpp) cc_final: 0.7098 (tpp) REVERT: C 57 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: C 113 HIS cc_start: 0.7734 (OUTLIER) cc_final: 0.7098 (m90) REVERT: C 207 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7895 (mm-30) REVERT: C 256 TYR cc_start: 0.8248 (t80) cc_final: 0.7847 (t80) REVERT: D 180 MET cc_start: 0.8282 (ttt) cc_final: 0.7259 (ttp) REVERT: D 233 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8205 (tp-100) REVERT: D 256 TYR cc_start: 0.8057 (t80) cc_final: 0.7679 (t80) REVERT: E 9 GLN cc_start: 0.7024 (tt0) cc_final: 0.6708 (tp40) REVERT: E 80 LYS cc_start: 0.8838 (mmmt) cc_final: 0.8578 (mmmm) REVERT: E 86 LYS cc_start: 0.8678 (tppp) cc_final: 0.8408 (tppt) REVERT: E 89 ASN cc_start: 0.8497 (t0) cc_final: 0.8121 (t0) REVERT: F 22 GLN cc_start: 0.8647 (pm20) cc_final: 0.8399 (pm20) REVERT: F 86 LYS cc_start: 0.8742 (tppp) cc_final: 0.8447 (tppt) outliers start: 88 outliers final: 80 residues processed: 297 average time/residue: 0.2626 time to fit residues: 110.1982 Evaluate side-chains 315 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 232 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 178 LYS Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 186 TRP Chi-restraints excluded: chain A residue 203 LEU 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 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 236 THR 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 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 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 37 THR Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 113 HIS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 55 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 83 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 0.0000 chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.088594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.074664 restraints weight = 26814.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.076750 restraints weight = 14670.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.078307 restraints weight = 9816.140| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5073 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= 0.235 Angle : 0.869 10.915 12730 Z= 0.407 Chirality : 0.049 0.240 1528 Planarity : 0.005 0.080 1604 Dihedral : 8.729 59.913 1365 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 7.34 % Allowed : 33.10 % Favored : 59.56 % 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: -1.43 (0.24), residues: 1202 helix: -0.10 (0.20), residues: 658 sheet: -0.58 (0.67), residues: 70 loop : -2.21 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 7 HIS 0.004 0.001 HIS D 122 PHE 0.043 0.002 PHE C 243 TYR 0.013 0.002 TYR F 88 ARG 0.004 0.000 ARG E 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3128.31 seconds wall clock time: 58 minutes 0.25 seconds (3480.25 seconds total)