Starting phenix.real_space_refine on Wed Feb 14 19:25:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysl_10899/02_2024/6ysl_10899.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysl_10899/02_2024/6ysl_10899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysl_10899/02_2024/6ysl_10899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysl_10899/02_2024/6ysl_10899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysl_10899/02_2024/6ysl_10899.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysl_10899/02_2024/6ysl_10899.pdb" } resolution = 3.5 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= 0.003 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 40 5.16 5 C 6595 2.51 5 N 1646 2.21 5 O 1847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 64": "NH1" <-> "NH2" Residue "A ASP 15": "OD1" <-> "OD2" Residue "B GLU 16": "OE1" <-> "OE2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "F ARG 251": "NH1" <-> "NH2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 251": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 251": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10128 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "A" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 208 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "B" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 201 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "F" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1939 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "E" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1947 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "D" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1947 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain: "C" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1947 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Time building chain proxies: 7.00, per 1000 atoms: 0.69 Number of scatterers: 10128 At special positions: 0 Unit cell: (96.996, 110.97, 94.53, 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 40 16.00 O 1847 8.00 N 1646 7.00 C 6595 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 - 3.50 Amino acid : False - 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: 4.27 Conformation dependent library (CDL) restraints added in 1.9 seconds 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2478 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 0 sheets defined 75.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'G' and resid 3 through 24 removed outlier: 4.157A pdb=" N ILE G 7 " --> pdb=" O LYS G 3 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 51 Processing helix chain 'G' and resid 58 through 64 Processing helix chain 'G' and resid 74 through 79 removed outlier: 4.163A pdb=" N ILE G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 93 removed outlier: 3.509A pdb=" N ARG G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU G 92 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 117 removed outlier: 3.682A pdb=" N LYS G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY G 112 " --> pdb=" O PHE G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 170 removed outlier: 4.078A pdb=" N ARG G 126 " --> pdb=" O ALA G 122 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE G 128 " --> pdb=" O PHE G 124 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE G 146 " --> pdb=" O ALA G 142 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE G 147 " --> pdb=" O GLY G 143 " (cutoff:3.500A) Proline residue: G 155 - end of helix Processing helix chain 'G' and resid 177 through 199 removed outlier: 3.609A pdb=" N HIS G 181 " --> pdb=" O ASP G 177 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ILE G 183 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR G 190 " --> pdb=" O ALA G 186 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY G 197 " --> pdb=" O GLY G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 232 removed outlier: 3.879A pdb=" N MET G 222 " --> pdb=" O LEU G 218 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU G 224 " --> pdb=" O GLU G 220 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY G 225 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL G 229 " --> pdb=" O GLY G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 243 Processing helix chain 'G' and resid 247 through 252 removed outlier: 3.765A pdb=" N LEU G 252 " --> pdb=" O ALA G 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 37 removed outlier: 3.697A pdb=" N TYR A 22 " --> pdb=" O TRP A 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 Processing helix chain 'F' and resid 5 through 22 removed outlier: 3.748A pdb=" N LEU F 11 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 51 removed outlier: 4.288A pdb=" N ILE F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE F 44 " --> pdb=" O ILE F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 66 removed outlier: 3.540A pdb=" N LEU F 62 " --> pdb=" O LYS F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 77 Processing helix chain 'F' and resid 78 through 92 removed outlier: 4.886A pdb=" N GLU F 84 " --> pdb=" O PRO F 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP F 85 " --> pdb=" O MET F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 100 removed outlier: 3.738A pdb=" N SER F 100 " --> pdb=" O LEU F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 114 Processing helix chain 'F' and resid 115 through 118 Processing helix chain 'F' and resid 124 through 171 removed outlier: 3.639A pdb=" N GLY F 143 " --> pdb=" O ARG F 139 " (cutoff:3.500A) Proline residue: F 155 - end of helix Processing helix chain 'F' and resid 179 through 196 removed outlier: 5.268A pdb=" N ALA F 185 " --> pdb=" O HIS F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 232 removed outlier: 3.509A pdb=" N LEU F 230 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU F 231 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 240 removed outlier: 3.554A pdb=" N GLN F 240 " --> pdb=" O VAL F 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 24 removed outlier: 4.068A pdb=" N LEU E 22 " --> pdb=" O VAL E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 51 removed outlier: 3.560A pdb=" N ILE E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE E 44 " --> pdb=" O ILE E 40 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA E 50 " --> pdb=" O ALA E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 64 Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 84 through 89 Processing helix chain 'E' and resid 97 through 102 removed outlier: 3.734A pdb=" N ILE E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 102' Processing helix chain 'E' and resid 109 through 119 removed outlier: 4.505A pdb=" N MET E 115 " --> pdb=" O ASN E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 172 removed outlier: 3.946A pdb=" N ILE E 146 " --> pdb=" O ALA E 142 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Proline residue: E 155 - end of helix removed outlier: 3.839A pdb=" N ILE E 164 " --> pdb=" O LEU E 160 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HIS E 172 " --> pdb=" O ALA E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 199 removed outlier: 3.757A pdb=" N HIS E 181 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU E 191 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY E 197 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL E 199 " --> pdb=" O PHE E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 230 Processing helix chain 'E' and resid 234 through 242 Processing helix chain 'E' and resid 243 through 246 removed outlier: 3.678A pdb=" N LEU E 246 " --> pdb=" O LEU E 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 243 through 246' Processing helix chain 'E' and resid 248 through 254 removed outlier: 3.671A pdb=" N LEU E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS E 253 " --> pdb=" O LYS E 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 23 removed outlier: 4.074A pdb=" N GLY D 8 " --> pdb=" O THR D 4 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 51 removed outlier: 3.707A pdb=" N ILE D 36 " --> pdb=" O ASN D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 66 removed outlier: 3.854A pdb=" N VAL D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 removed outlier: 3.580A pdb=" N ILE D 79 " --> pdb=" O GLU D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 91 removed outlier: 3.668A pdb=" N LEU D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 118 Processing helix chain 'D' and resid 125 through 170 removed outlier: 3.891A pdb=" N MET D 129 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N PHE D 147 " --> pdb=" O GLY D 143 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) Proline residue: D 155 - end of helix Processing helix chain 'D' and resid 181 through 199 removed outlier: 3.791A pdb=" N ALA D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 230 Processing helix chain 'D' and resid 235 through 242 removed outlier: 4.086A pdb=" N GLN D 240 " --> pdb=" O LYS D 236 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 242 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 249 through 254 removed outlier: 4.333A pdb=" N LYS D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE D 254 " --> pdb=" O ASP D 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 249 through 254' Processing helix chain 'C' and resid 4 through 21 Processing helix chain 'C' and resid 27 through 31 removed outlier: 3.815A pdb=" N LEU C 30 " --> pdb=" O PHE C 27 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA C 31 " --> pdb=" O SER C 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 27 through 31' Processing helix chain 'C' and resid 34 through 51 Processing helix chain 'C' and resid 55 through 57 No H-bonds generated for 'chain 'C' and resid 55 through 57' Processing helix chain 'C' and resid 58 through 66 Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 84 through 92 removed outlier: 3.675A pdb=" N GLU C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 101 removed outlier: 4.264A pdb=" N SER C 100 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE C 101 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 118 Processing helix chain 'C' and resid 123 through 171 removed outlier: 4.005A pdb=" N ILE C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Proline residue: C 155 - end of helix Processing helix chain 'C' and resid 177 through 186 removed outlier: 3.626A pdb=" N ALA C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 199 removed outlier: 3.695A pdb=" N LEU C 191 " --> pdb=" O PHE C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 230 Processing helix chain 'C' and resid 237 through 243 Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 252 648 hydrogen bonds defined for protein. 1917 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: 2.64 Time building geometry restraints manager: 4.53 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: 3055 1.34 - 1.46: 1453 1.46 - 1.57: 5705 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 10293 Sorted by residual: bond pdb=" C ILE F 79 " pdb=" N PRO F 80 " ideal model delta sigma weight residual 1.334 1.383 -0.049 8.40e-03 1.42e+04 3.44e+01 bond pdb=" C ALA E 154 " pdb=" N PRO E 155 " ideal model delta sigma weight residual 1.336 1.373 -0.038 1.23e-02 6.61e+03 9.49e+00 bond pdb=" C VAL E 59 " pdb=" N PRO E 60 " ideal model delta sigma weight residual 1.336 1.372 -0.036 1.20e-02 6.94e+03 9.13e+00 bond pdb=" N GLU B 16 " pdb=" CA GLU B 16 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.31e-02 5.83e+03 6.66e+00 bond pdb=" N ASP A 15 " pdb=" CA ASP A 15 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 5.94e+00 ... (remaining 10288 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.41: 186 105.41 - 112.61: 5281 112.61 - 119.81: 3995 119.81 - 127.01: 4365 127.01 - 134.21: 104 Bond angle restraints: 13931 Sorted by residual: angle pdb=" C LEU C 78 " pdb=" N ILE C 79 " pdb=" CA ILE C 79 " ideal model delta sigma weight residual 120.24 124.27 -4.03 6.30e-01 2.52e+00 4.09e+01 angle pdb=" N GLU E 84 " pdb=" CA GLU E 84 " pdb=" C GLU E 84 " ideal model delta sigma weight residual 113.43 106.49 6.94 1.26e+00 6.30e-01 3.03e+01 angle pdb=" N ASN E 32 " pdb=" CA ASN E 32 " pdb=" C ASN E 32 " ideal model delta sigma weight residual 109.81 120.95 -11.14 2.21e+00 2.05e-01 2.54e+01 angle pdb=" C GLU G 102 " pdb=" N ASP G 103 " pdb=" CA ASP G 103 " ideal model delta sigma weight residual 121.54 131.14 -9.60 1.91e+00 2.74e-01 2.53e+01 angle pdb=" C VAL G 117 " pdb=" N ASP G 118 " pdb=" CA ASP G 118 " ideal model delta sigma weight residual 121.54 130.75 -9.21 1.91e+00 2.74e-01 2.33e+01 ... (remaining 13926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 5659 15.00 - 30.00: 410 30.00 - 45.00: 145 45.00 - 60.00: 8 60.00 - 75.00: 6 Dihedral angle restraints: 6228 sinusoidal: 2414 harmonic: 3814 Sorted by residual: dihedral pdb=" CA ALA F 234 " pdb=" C ALA F 234 " pdb=" N PRO F 235 " pdb=" CA PRO F 235 " ideal model delta harmonic sigma weight residual -180.00 -151.59 -28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA HIS F 181 " pdb=" C HIS F 181 " pdb=" N ALA F 182 " pdb=" CA ALA F 182 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ASN G 32 " pdb=" C ASN G 32 " pdb=" N PRO G 33 " pdb=" CA PRO G 33 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 6225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1227 0.060 - 0.120: 370 0.120 - 0.180: 85 0.180 - 0.240: 11 0.240 - 0.301: 1 Chirality restraints: 1694 Sorted by residual: chirality pdb=" CA ASN E 32 " pdb=" N ASN E 32 " pdb=" C ASN E 32 " pdb=" CB ASN E 32 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE D 7 " pdb=" CA ILE D 7 " pdb=" CG1 ILE D 7 " pdb=" CG2 ILE D 7 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASP G 118 " pdb=" N ASP G 118 " pdb=" C ASP G 118 " pdb=" CB ASP G 118 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1691 not shown) Planarity restraints: 1736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 197 " 0.021 2.00e-02 2.50e+03 4.24e-02 1.79e+01 pdb=" C GLY F 197 " -0.073 2.00e-02 2.50e+03 pdb=" O GLY F 197 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR F 198 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 204 " -0.012 2.00e-02 2.50e+03 1.89e-02 6.27e+00 pdb=" CG PHE E 204 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE E 204 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE E 204 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE E 204 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 204 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE E 204 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 124 " -0.023 2.00e-02 2.50e+03 1.82e-02 5.82e+00 pdb=" CG PHE C 124 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE C 124 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 124 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 124 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 124 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 124 " -0.007 2.00e-02 2.50e+03 ... (remaining 1733 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1761 2.77 - 3.30: 10211 3.30 - 3.83: 16641 3.83 - 4.37: 19622 4.37 - 4.90: 32248 Nonbonded interactions: 80483 Sorted by model distance: nonbonded pdb=" O LEU E 192 " pdb=" OG1 THR E 196 " model vdw 2.232 2.440 nonbonded pdb=" OE2 GLU B 16 " pdb=" OH TYR C 198 " model vdw 2.234 2.440 nonbonded pdb=" O LEU F 192 " pdb=" OG1 THR F 196 " model vdw 2.235 2.440 nonbonded pdb=" O GLY F 180 " pdb=" OG SER F 184 " model vdw 2.282 2.440 nonbonded pdb=" O ILE G 39 " pdb=" OG1 THR G 43 " model vdw 2.286 2.440 ... (remaining 80478 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 15 through 39) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 3 through 256) selection = (chain 'D' and resid 3 through 256) selection = (chain 'E' and resid 3 through 256) selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.110 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.720 Find NCS groups from input model: 0.720 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 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 : 0.006 0.087 10293 Z= 0.398 Angle : 1.169 12.558 13931 Z= 0.607 Chirality : 0.060 0.301 1694 Planarity : 0.008 0.059 1736 Dihedral : 12.213 74.996 3750 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.01 % Favored : 90.92 % Rotamer: Outliers : 0.47 % Allowed : 6.93 % Favored : 92.60 % 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: -4.73 (0.18), residues: 1310 helix: -2.77 (0.13), residues: 942 sheet: None (None), residues: 0 loop : -3.60 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 201 HIS 0.013 0.003 HIS C 202 PHE 0.043 0.003 PHE E 204 TYR 0.027 0.005 TYR G 153 ARG 0.004 0.001 ARG G 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 433 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 20 MET cc_start: 0.7364 (mmt) cc_final: 0.7094 (mmm) REVERT: G 68 LYS cc_start: 0.7129 (ttmt) cc_final: 0.6445 (tppt) REVERT: G 136 MET cc_start: 0.7955 (tmm) cc_final: 0.7527 (ttm) REVERT: G 139 ARG cc_start: 0.7549 (ttm110) cc_final: 0.6695 (ttt-90) REVERT: G 219 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8153 (mtp85) REVERT: G 221 VAL cc_start: 0.9235 (p) cc_final: 0.8962 (p) REVERT: G 224 GLU cc_start: 0.8435 (mp0) cc_final: 0.8168 (mp0) REVERT: B 20 VAL cc_start: 0.8659 (t) cc_final: 0.8352 (m) REVERT: F 84 GLU cc_start: 0.6442 (pp20) cc_final: 0.6168 (pm20) REVERT: F 125 ILE cc_start: 0.7587 (mm) cc_final: 0.7383 (tp) REVERT: F 176 THR cc_start: 0.8083 (t) cc_final: 0.7857 (m) REVERT: F 204 PHE cc_start: 0.7942 (m-10) cc_final: 0.7606 (m-80) REVERT: F 219 ARG cc_start: 0.8276 (mtt-85) cc_final: 0.7443 (mtt-85) REVERT: F 226 VAL cc_start: 0.9491 (p) cc_final: 0.9106 (m) REVERT: F 241 LYS cc_start: 0.6419 (pttt) cc_final: 0.6150 (pttp) REVERT: F 244 MET cc_start: 0.7025 (ptt) cc_final: 0.6799 (ptt) REVERT: E 87 GLN cc_start: 0.6902 (tm-30) cc_final: 0.6691 (tm-30) REVERT: E 129 MET cc_start: 0.8204 (tpp) cc_final: 0.7637 (mtp) REVERT: E 134 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8087 (mm-30) REVERT: E 179 LEU cc_start: 0.7621 (tt) cc_final: 0.7276 (pp) REVERT: E 217 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8463 (tptt) REVERT: D 6 LEU cc_start: 0.7847 (pt) cc_final: 0.7075 (tp) REVERT: D 81 MET cc_start: 0.5785 (tpp) cc_final: 0.5569 (tmm) REVERT: D 85 TRP cc_start: 0.6760 (p90) cc_final: 0.6407 (p90) REVERT: D 181 HIS cc_start: 0.4848 (p90) cc_final: 0.3915 (m170) REVERT: D 210 ARG cc_start: 0.8742 (mmt180) cc_final: 0.8011 (tmm160) REVERT: D 244 MET cc_start: 0.6536 (mpt) cc_final: 0.5761 (mtp) REVERT: C 72 GLN cc_start: 0.6937 (pp30) cc_final: 0.6672 (tt0) REVERT: C 87 GLN cc_start: 0.6396 (mm-40) cc_final: 0.6100 (tp-100) REVERT: C 127 ASP cc_start: 0.7381 (p0) cc_final: 0.6140 (p0) REVERT: C 181 HIS cc_start: 0.6827 (t-170) cc_final: 0.6616 (t70) REVERT: C 198 TYR cc_start: 0.6937 (m-10) cc_final: 0.6611 (m-80) outliers start: 5 outliers final: 3 residues processed: 437 average time/residue: 0.2384 time to fit residues: 140.6897 Evaluate side-chains 263 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 260 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 16 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 101 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 87 GLN G 140 HIS G 172 HIS G 202 HIS ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN F 140 HIS F 206 ASN E 140 HIS E 141 GLN E 206 ASN D 140 HIS D 175 ASN D 206 ASN C 32 ASN C 87 GLN ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 HIS ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10293 Z= 0.203 Angle : 0.770 8.555 13931 Z= 0.386 Chirality : 0.043 0.182 1694 Planarity : 0.005 0.044 1736 Dihedral : 6.711 64.816 1383 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 4.31 % Allowed : 17.42 % Favored : 78.28 % 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: -2.99 (0.21), residues: 1310 helix: -1.35 (0.16), residues: 952 sheet: None (None), residues: 0 loop : -3.43 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 201 HIS 0.004 0.001 HIS G 202 PHE 0.040 0.002 PHE C 124 TYR 0.016 0.002 TYR D 153 ARG 0.004 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 295 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 LYS cc_start: 0.7085 (ttmt) cc_final: 0.6324 (mmtm) REVERT: G 125 ILE cc_start: 0.8110 (mm) cc_final: 0.7720 (mm) REVERT: G 136 MET cc_start: 0.8002 (tmm) cc_final: 0.7780 (ttm) REVERT: G 139 ARG cc_start: 0.7615 (ttm110) cc_final: 0.6723 (ttt-90) REVERT: G 221 VAL cc_start: 0.9261 (p) cc_final: 0.8906 (p) REVERT: G 224 GLU cc_start: 0.8418 (mp0) cc_final: 0.8100 (mp0) REVERT: F 115 MET cc_start: 0.6084 (ppp) cc_final: 0.5876 (ppp) REVERT: F 131 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7386 (mp0) REVERT: F 204 PHE cc_start: 0.8011 (m-10) cc_final: 0.7391 (m-80) REVERT: F 241 LYS cc_start: 0.6559 (pttt) cc_final: 0.6079 (pttp) REVERT: E 103 ASP cc_start: 0.4996 (t70) cc_final: 0.4591 (t70) REVERT: E 187 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.7049 (m-80) REVERT: E 208 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6223 (mt) REVERT: E 217 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8345 (ttmt) REVERT: D 6 LEU cc_start: 0.7883 (pt) cc_final: 0.7389 (tp) REVERT: D 181 HIS cc_start: 0.4768 (p90) cc_final: 0.4190 (m170) REVERT: D 210 ARG cc_start: 0.8778 (mmt180) cc_final: 0.8076 (tmm160) REVERT: D 244 MET cc_start: 0.6585 (mpt) cc_final: 0.5648 (mtp) REVERT: C 87 GLN cc_start: 0.6549 (mm110) cc_final: 0.6334 (tp-100) outliers start: 46 outliers final: 24 residues processed: 324 average time/residue: 0.2012 time to fit residues: 92.5642 Evaluate side-chains 278 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 252 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 71 LYS Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 196 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN E 141 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10293 Z= 0.228 Angle : 0.761 12.931 13931 Z= 0.374 Chirality : 0.043 0.193 1694 Planarity : 0.004 0.042 1736 Dihedral : 5.920 49.182 1378 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 4.96 % Allowed : 19.85 % Favored : 75.19 % 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: -2.25 (0.22), residues: 1310 helix: -0.73 (0.16), residues: 957 sheet: None (None), residues: 0 loop : -3.41 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 85 HIS 0.003 0.001 HIS C 140 PHE 0.028 0.002 PHE G 195 TYR 0.017 0.002 TYR D 153 ARG 0.008 0.001 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 267 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 LYS cc_start: 0.7166 (ttmt) cc_final: 0.6373 (mmtm) REVERT: G 136 MET cc_start: 0.8115 (tmm) cc_final: 0.7786 (ttm) REVERT: G 139 ARG cc_start: 0.7715 (ttm110) cc_final: 0.6737 (ttt-90) REVERT: G 221 VAL cc_start: 0.9253 (p) cc_final: 0.8888 (p) REVERT: G 224 GLU cc_start: 0.8503 (mp0) cc_final: 0.8123 (mp0) REVERT: F 131 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7624 (mt-10) REVERT: F 241 LYS cc_start: 0.6521 (pttt) cc_final: 0.6084 (pttp) REVERT: E 103 ASP cc_start: 0.5148 (t70) cc_final: 0.4794 (t70) REVERT: E 129 MET cc_start: 0.8179 (tpp) cc_final: 0.7566 (mtp) REVERT: E 187 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.7046 (m-80) REVERT: E 208 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6465 (mt) REVERT: D 6 LEU cc_start: 0.7866 (pt) cc_final: 0.7406 (tp) REVERT: D 115 MET cc_start: 0.7088 (mpp) cc_final: 0.6737 (mpp) REVERT: D 181 HIS cc_start: 0.4573 (p90) cc_final: 0.4267 (m170) REVERT: D 210 ARG cc_start: 0.8735 (mmt180) cc_final: 0.8013 (tmm160) REVERT: D 222 MET cc_start: 0.7397 (mtt) cc_final: 0.7131 (mtt) REVERT: D 244 MET cc_start: 0.6676 (mpt) cc_final: 0.5662 (mtp) REVERT: C 72 GLN cc_start: 0.6472 (pm20) cc_final: 0.6230 (pp30) REVERT: C 87 GLN cc_start: 0.6534 (mm110) cc_final: 0.6272 (tp-100) REVERT: C 198 TYR cc_start: 0.6786 (m-10) cc_final: 0.6480 (m-80) outliers start: 53 outliers final: 22 residues processed: 300 average time/residue: 0.1903 time to fit residues: 82.9366 Evaluate side-chains 267 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 243 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 196 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 111 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 GLN F 72 GLN F 206 ASN E 141 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 10293 Z= 0.240 Angle : 0.757 12.199 13931 Z= 0.371 Chirality : 0.044 0.238 1694 Planarity : 0.004 0.040 1736 Dihedral : 5.710 48.350 1378 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.78 % Allowed : 21.82 % Favored : 73.41 % 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: -1.86 (0.23), residues: 1310 helix: -0.42 (0.17), residues: 952 sheet: None (None), residues: 0 loop : -3.33 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 85 HIS 0.003 0.001 HIS C 140 PHE 0.023 0.002 PHE E 195 TYR 0.017 0.002 TYR B 22 ARG 0.006 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 256 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 LYS cc_start: 0.7176 (ttmt) cc_final: 0.6423 (mmtm) REVERT: G 136 MET cc_start: 0.8143 (tmm) cc_final: 0.7878 (ttm) REVERT: G 221 VAL cc_start: 0.9277 (p) cc_final: 0.8875 (p) REVERT: G 224 GLU cc_start: 0.8496 (mp0) cc_final: 0.8112 (mp0) REVERT: F 131 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7743 (mt-10) REVERT: F 241 LYS cc_start: 0.6600 (pttt) cc_final: 0.6155 (pttp) REVERT: E 61 THR cc_start: 0.7782 (p) cc_final: 0.7443 (m) REVERT: E 129 MET cc_start: 0.8150 (tpp) cc_final: 0.7879 (tpp) REVERT: E 187 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: E 198 TYR cc_start: 0.6460 (OUTLIER) cc_final: 0.6208 (m-80) REVERT: E 208 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6718 (mt) REVERT: E 217 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8602 (tptm) REVERT: D 6 LEU cc_start: 0.7899 (pt) cc_final: 0.7496 (tp) REVERT: D 81 MET cc_start: 0.5570 (tpp) cc_final: 0.5111 (tpt) REVERT: D 181 HIS cc_start: 0.4493 (p90) cc_final: 0.4254 (m170) REVERT: D 210 ARG cc_start: 0.8706 (mmt180) cc_final: 0.8055 (tmm160) REVERT: D 244 MET cc_start: 0.6579 (mpt) cc_final: 0.5521 (mtp) REVERT: C 72 GLN cc_start: 0.6597 (pm20) cc_final: 0.6131 (pp30) outliers start: 51 outliers final: 30 residues processed: 288 average time/residue: 0.1870 time to fit residues: 78.4776 Evaluate side-chains 263 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 230 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 172 HIS Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 208 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.1980 chunk 70 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 106 optimal weight: 0.0670 chunk 86 optimal weight: 0.0870 chunk 0 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 GLN E 141 GLN C 32 ASN ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN C 202 HIS ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10293 Z= 0.194 Angle : 0.721 11.301 13931 Z= 0.355 Chirality : 0.042 0.212 1694 Planarity : 0.004 0.041 1736 Dihedral : 5.540 51.499 1378 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 4.59 % Allowed : 24.53 % Favored : 70.88 % 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: -1.61 (0.23), residues: 1310 helix: -0.21 (0.17), residues: 952 sheet: None (None), residues: 0 loop : -3.31 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 85 HIS 0.003 0.000 HIS F 172 PHE 0.029 0.002 PHE E 195 TYR 0.012 0.002 TYR D 245 ARG 0.007 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 269 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 LYS cc_start: 0.7174 (ttmt) cc_final: 0.6426 (mmtm) REVERT: G 129 MET cc_start: 0.7891 (mpp) cc_final: 0.7535 (mpp) REVERT: G 130 THR cc_start: 0.8336 (m) cc_final: 0.7908 (p) REVERT: G 136 MET cc_start: 0.8116 (tmm) cc_final: 0.7790 (ttm) REVERT: G 139 ARG cc_start: 0.7800 (ttm110) cc_final: 0.6752 (ttt-90) REVERT: G 221 VAL cc_start: 0.9255 (p) cc_final: 0.8861 (p) REVERT: G 224 GLU cc_start: 0.8493 (mp0) cc_final: 0.8127 (mp0) REVERT: F 20 MET cc_start: 0.6088 (tpt) cc_final: 0.5147 (tpt) REVERT: F 131 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7620 (mt-10) REVERT: F 208 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7388 (mm) REVERT: F 241 LYS cc_start: 0.6547 (pttt) cc_final: 0.6131 (pttp) REVERT: E 129 MET cc_start: 0.8216 (tpp) cc_final: 0.7892 (tpp) REVERT: E 187 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7175 (m-80) REVERT: E 208 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6758 (mt) REVERT: D 6 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7522 (tp) REVERT: D 20 MET cc_start: 0.7466 (mmm) cc_final: 0.6811 (tpp) REVERT: D 81 MET cc_start: 0.5512 (tpp) cc_final: 0.5172 (tpp) REVERT: D 210 ARG cc_start: 0.8686 (mmt180) cc_final: 0.8046 (tmm160) REVERT: D 244 MET cc_start: 0.6432 (mpt) cc_final: 0.5326 (mtp) REVERT: C 72 GLN cc_start: 0.6677 (pm20) cc_final: 0.6243 (pp30) REVERT: C 208 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7119 (mm) outliers start: 49 outliers final: 25 residues processed: 300 average time/residue: 0.1939 time to fit residues: 83.3193 Evaluate side-chains 270 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 240 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 172 HIS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 208 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 24 optimal weight: 0.0040 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.1980 chunk 57 optimal weight: 0.0970 chunk 10 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 GLN ** F 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN E 141 GLN ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10293 Z= 0.190 Angle : 0.726 10.379 13931 Z= 0.355 Chirality : 0.043 0.231 1694 Planarity : 0.004 0.043 1736 Dihedral : 5.363 51.396 1378 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.21 % Allowed : 25.94 % Favored : 69.85 % 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: -1.36 (0.23), residues: 1310 helix: -0.04 (0.17), residues: 945 sheet: None (None), residues: 0 loop : -3.12 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 85 HIS 0.005 0.001 HIS D 181 PHE 0.030 0.001 PHE E 195 TYR 0.018 0.002 TYR A 22 ARG 0.007 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 273 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 LYS cc_start: 0.7191 (ttmt) cc_final: 0.6439 (mmtm) REVERT: G 129 MET cc_start: 0.7942 (mpp) cc_final: 0.7697 (mpp) REVERT: G 130 THR cc_start: 0.8292 (m) cc_final: 0.7904 (p) REVERT: G 136 MET cc_start: 0.8103 (tmm) cc_final: 0.7789 (ttm) REVERT: G 139 ARG cc_start: 0.7783 (ttm110) cc_final: 0.6730 (ttt-90) REVERT: G 221 VAL cc_start: 0.9235 (p) cc_final: 0.8882 (p) REVERT: G 224 GLU cc_start: 0.8491 (mp0) cc_final: 0.8149 (mp0) REVERT: F 20 MET cc_start: 0.5993 (tpt) cc_final: 0.5234 (tpt) REVERT: F 131 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7644 (mt-10) REVERT: F 134 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8023 (mm-30) REVERT: F 208 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7270 (mm) REVERT: F 241 LYS cc_start: 0.6501 (pttt) cc_final: 0.6074 (pttp) REVERT: E 129 MET cc_start: 0.8250 (tpp) cc_final: 0.7884 (tpp) REVERT: E 187 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7171 (m-80) REVERT: E 208 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.6849 (mt) REVERT: D 6 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7498 (tp) REVERT: D 11 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6483 (tt) REVERT: D 20 MET cc_start: 0.7401 (mmm) cc_final: 0.6763 (tpp) REVERT: D 81 MET cc_start: 0.5584 (tpp) cc_final: 0.5212 (tpt) REVERT: D 210 ARG cc_start: 0.8662 (mmt180) cc_final: 0.8042 (tmm160) REVERT: D 244 MET cc_start: 0.6484 (mpt) cc_final: 0.5337 (mtp) REVERT: C 72 GLN cc_start: 0.6712 (pm20) cc_final: 0.6306 (mm-40) REVERT: C 208 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7039 (mm) outliers start: 45 outliers final: 23 residues processed: 299 average time/residue: 0.1962 time to fit residues: 84.2522 Evaluate side-chains 277 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 248 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 172 HIS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN F 206 ASN E 141 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10293 Z= 0.208 Angle : 0.745 10.216 13931 Z= 0.365 Chirality : 0.044 0.240 1694 Planarity : 0.004 0.041 1736 Dihedral : 5.061 24.905 1376 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.21 % Allowed : 27.06 % Favored : 68.73 % 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: -1.29 (0.23), residues: 1310 helix: 0.03 (0.17), residues: 944 sheet: None (None), residues: 0 loop : -3.13 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 85 HIS 0.006 0.001 HIS E 202 PHE 0.027 0.002 PHE G 195 TYR 0.018 0.002 TYR D 153 ARG 0.007 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 256 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 LYS cc_start: 0.7221 (ttmt) cc_final: 0.6475 (mmtm) REVERT: G 130 THR cc_start: 0.8306 (m) cc_final: 0.8089 (p) REVERT: G 136 MET cc_start: 0.8128 (tmm) cc_final: 0.7839 (ttm) REVERT: G 221 VAL cc_start: 0.9257 (p) cc_final: 0.8859 (p) REVERT: G 224 GLU cc_start: 0.8513 (mp0) cc_final: 0.8130 (mp0) REVERT: F 20 MET cc_start: 0.5937 (tpt) cc_final: 0.5336 (tpt) REVERT: F 131 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7627 (mt-10) REVERT: F 134 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8022 (mm-30) REVERT: F 208 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7290 (mm) REVERT: F 241 LYS cc_start: 0.6635 (pttt) cc_final: 0.6223 (pttp) REVERT: E 129 MET cc_start: 0.8271 (tpp) cc_final: 0.7878 (tpp) REVERT: E 191 LEU cc_start: 0.7614 (tt) cc_final: 0.7351 (tt) REVERT: E 198 TYR cc_start: 0.6742 (OUTLIER) cc_final: 0.6469 (m-80) REVERT: E 208 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6737 (mt) REVERT: D 6 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7525 (tp) REVERT: D 11 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6503 (tt) REVERT: D 20 MET cc_start: 0.7395 (mmm) cc_final: 0.6754 (tpp) REVERT: D 81 MET cc_start: 0.5594 (tpp) cc_final: 0.5279 (tpt) REVERT: D 210 ARG cc_start: 0.8644 (mmt180) cc_final: 0.8068 (tmm160) REVERT: D 244 MET cc_start: 0.6429 (mpt) cc_final: 0.5195 (mtp) REVERT: C 72 GLN cc_start: 0.6703 (pm20) cc_final: 0.6161 (pp30) REVERT: C 208 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7256 (mm) REVERT: C 217 LYS cc_start: 0.8266 (mmmt) cc_final: 0.8037 (mmmt) outliers start: 45 outliers final: 24 residues processed: 284 average time/residue: 0.1977 time to fit residues: 80.6705 Evaluate side-chains 275 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 245 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 172 HIS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 244 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.0170 chunk 79 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 HIS ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10293 Z= 0.213 Angle : 0.756 9.705 13931 Z= 0.372 Chirality : 0.045 0.240 1694 Planarity : 0.004 0.041 1736 Dihedral : 5.033 24.810 1376 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.12 % Allowed : 27.90 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.21 (0.23), residues: 1310 helix: 0.08 (0.17), residues: 947 sheet: None (None), residues: 0 loop : -3.11 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 85 HIS 0.004 0.001 HIS E 202 PHE 0.026 0.002 PHE G 195 TYR 0.019 0.002 TYR F 153 ARG 0.007 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 253 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 68 LYS cc_start: 0.7286 (ttmt) cc_final: 0.6514 (mmtm) REVERT: G 130 THR cc_start: 0.8212 (m) cc_final: 0.7811 (p) REVERT: G 136 MET cc_start: 0.8117 (tmm) cc_final: 0.7850 (ttm) REVERT: G 221 VAL cc_start: 0.9244 (p) cc_final: 0.8836 (p) REVERT: G 224 GLU cc_start: 0.8504 (mp0) cc_final: 0.8116 (mp0) REVERT: F 20 MET cc_start: 0.5845 (tpt) cc_final: 0.5367 (tpt) REVERT: F 131 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7646 (mt-10) REVERT: F 134 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7969 (mm-30) REVERT: F 208 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7262 (mm) REVERT: F 241 LYS cc_start: 0.6658 (pttt) cc_final: 0.6233 (pttp) REVERT: E 129 MET cc_start: 0.8287 (tpp) cc_final: 0.7888 (tpp) REVERT: E 134 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8052 (mm-30) REVERT: E 191 LEU cc_start: 0.7675 (tt) cc_final: 0.7347 (tt) REVERT: E 198 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.6417 (m-10) REVERT: E 208 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.6831 (mt) REVERT: D 6 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7519 (tp) REVERT: D 11 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6507 (tt) REVERT: D 81 MET cc_start: 0.5613 (tpp) cc_final: 0.5272 (tpt) REVERT: D 210 ARG cc_start: 0.8661 (mmt180) cc_final: 0.8087 (tmm160) REVERT: D 233 GLN cc_start: 0.7027 (tt0) cc_final: 0.6805 (tt0) REVERT: D 244 MET cc_start: 0.6298 (mpt) cc_final: 0.5088 (mtp) REVERT: C 72 GLN cc_start: 0.6721 (OUTLIER) cc_final: 0.6244 (pp30) REVERT: C 208 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7292 (mm) outliers start: 44 outliers final: 28 residues processed: 281 average time/residue: 0.1970 time to fit residues: 79.4220 Evaluate side-chains 279 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 244 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 172 HIS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 244 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.5980 chunk 115 optimal weight: 0.3980 chunk 119 optimal weight: 0.0980 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 10293 Z= 0.204 Angle : 0.760 10.063 13931 Z= 0.374 Chirality : 0.044 0.221 1694 Planarity : 0.004 0.041 1736 Dihedral : 4.964 24.637 1376 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.75 % Allowed : 28.65 % Favored : 67.60 % 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: -1.16 (0.23), residues: 1310 helix: 0.10 (0.17), residues: 953 sheet: None (None), residues: 0 loop : -3.11 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 85 HIS 0.004 0.001 HIS F 172 PHE 0.027 0.002 PHE G 195 TYR 0.022 0.002 TYR D 153 ARG 0.007 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 260 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: G 68 LYS cc_start: 0.7278 (ttmt) cc_final: 0.6490 (mmtm) REVERT: G 130 THR cc_start: 0.8209 (m) cc_final: 0.7795 (p) REVERT: G 136 MET cc_start: 0.8099 (tmm) cc_final: 0.7826 (ttm) REVERT: G 221 VAL cc_start: 0.9251 (p) cc_final: 0.8850 (p) REVERT: G 224 GLU cc_start: 0.8513 (mp0) cc_final: 0.8103 (mp0) REVERT: F 20 MET cc_start: 0.5817 (tpt) cc_final: 0.5331 (tpt) REVERT: F 131 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7511 (mt-10) REVERT: F 134 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7964 (mm-30) REVERT: F 208 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6992 (mm) REVERT: F 241 LYS cc_start: 0.6666 (pttt) cc_final: 0.6256 (pttp) REVERT: E 129 MET cc_start: 0.8282 (tpp) cc_final: 0.7843 (tpp) REVERT: E 134 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8052 (mm-30) REVERT: E 191 LEU cc_start: 0.7654 (tt) cc_final: 0.7322 (tt) REVERT: E 192 LEU cc_start: 0.7984 (mm) cc_final: 0.7278 (tp) REVERT: E 198 TYR cc_start: 0.6948 (OUTLIER) cc_final: 0.6348 (m-10) REVERT: E 208 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6799 (mt) REVERT: D 6 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7469 (tp) REVERT: D 11 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6409 (tt) REVERT: D 81 MET cc_start: 0.5606 (tpp) cc_final: 0.5295 (tpt) REVERT: D 137 GLU cc_start: 0.8246 (tm-30) cc_final: 0.8030 (tm-30) REVERT: D 210 ARG cc_start: 0.8684 (mmt180) cc_final: 0.8039 (tmm160) REVERT: D 244 MET cc_start: 0.6295 (mpt) cc_final: 0.5050 (mtp) REVERT: C 6 LEU cc_start: 0.7814 (pt) cc_final: 0.7607 (pp) REVERT: C 72 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6376 (mm-40) REVERT: C 208 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7014 (mm) outliers start: 40 outliers final: 27 residues processed: 284 average time/residue: 0.1906 time to fit residues: 78.1064 Evaluate side-chains 278 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 244 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 172 HIS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 109 optimal weight: 0.0270 overall best weight: 1.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 GLN D 202 HIS ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 10293 Z= 0.268 Angle : 0.808 18.956 13931 Z= 0.397 Chirality : 0.047 0.233 1694 Planarity : 0.004 0.039 1736 Dihedral : 4.976 24.765 1376 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.75 % Allowed : 29.21 % Favored : 67.04 % 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: -1.14 (0.23), residues: 1310 helix: 0.14 (0.17), residues: 958 sheet: None (None), residues: 0 loop : -3.22 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 85 HIS 0.003 0.001 HIS F 172 PHE 0.025 0.002 PHE G 195 TYR 0.029 0.002 TYR F 153 ARG 0.007 0.000 ARG D 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2620 Ramachandran restraints generated. 1310 Oldfield, 0 Emsley, 1310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 253 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: G 68 LYS cc_start: 0.7218 (ttmt) cc_final: 0.6461 (mmtm) REVERT: G 130 THR cc_start: 0.8257 (m) cc_final: 0.7841 (p) REVERT: G 136 MET cc_start: 0.8115 (tmm) cc_final: 0.7864 (ttm) REVERT: G 187 PHE cc_start: 0.7261 (m-80) cc_final: 0.7000 (m-80) REVERT: G 221 VAL cc_start: 0.9288 (p) cc_final: 0.9037 (p) REVERT: G 224 GLU cc_start: 0.8589 (mp0) cc_final: 0.8225 (mp0) REVERT: F 20 MET cc_start: 0.5842 (tpt) cc_final: 0.5408 (tpt) REVERT: F 131 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7481 (mt-10) REVERT: F 153 TYR cc_start: 0.8147 (m-80) cc_final: 0.7937 (m-80) REVERT: F 208 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6956 (mm) REVERT: F 241 LYS cc_start: 0.6711 (pttt) cc_final: 0.6281 (pttp) REVERT: E 129 MET cc_start: 0.8233 (tpp) cc_final: 0.7775 (tpp) REVERT: E 191 LEU cc_start: 0.7709 (tt) cc_final: 0.7355 (tt) REVERT: E 192 LEU cc_start: 0.8015 (mm) cc_final: 0.7325 (tp) REVERT: E 198 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6377 (m-10) REVERT: E 208 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7152 (mt) REVERT: D 6 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7432 (tp) REVERT: D 11 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6552 (tt) REVERT: D 32 ASN cc_start: 0.7774 (p0) cc_final: 0.7465 (p0) REVERT: D 81 MET cc_start: 0.5648 (tpp) cc_final: 0.5314 (tpt) REVERT: D 210 ARG cc_start: 0.8685 (mmt180) cc_final: 0.8095 (tmm160) REVERT: D 244 MET cc_start: 0.6340 (mpt) cc_final: 0.5125 (mtp) REVERT: C 72 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.6283 (pp30) REVERT: C 195 PHE cc_start: 0.8721 (t80) cc_final: 0.8496 (t80) REVERT: C 217 LYS cc_start: 0.8317 (mmmt) cc_final: 0.8112 (mmmt) outliers start: 40 outliers final: 31 residues processed: 276 average time/residue: 0.1963 time to fit residues: 78.5671 Evaluate side-chains 286 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 249 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 38 ILE Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 243 LEU Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain F residue 54 LYS Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 172 HIS Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 198 TYR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN E 141 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.175897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.146465 restraints weight = 17634.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.148767 restraints weight = 12020.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.150320 restraints weight = 9505.285| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 10293 Z= 0.231 Angle : 0.799 16.105 13931 Z= 0.391 Chirality : 0.046 0.239 1694 Planarity : 0.004 0.039 1736 Dihedral : 4.954 24.737 1376 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 4.03 % Allowed : 29.31 % Favored : 66.67 % 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: -0.98 (0.23), residues: 1310 helix: 0.22 (0.17), residues: 946 sheet: None (None), residues: 0 loop : -2.92 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP D 201 HIS 0.004 0.001 HIS F 172 PHE 0.027 0.002 PHE G 195 TYR 0.030 0.002 TYR F 153 ARG 0.007 0.000 ARG D 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2376.27 seconds wall clock time: 43 minutes 42.02 seconds (2622.02 seconds total)