Starting phenix.real_space_refine on Wed Sep 25 16:24:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ois_20080/09_2024/6ois_20080.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ois_20080/09_2024/6ois_20080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ois_20080/09_2024/6ois_20080.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ois_20080/09_2024/6ois_20080.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ois_20080/09_2024/6ois_20080.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ois_20080/09_2024/6ois_20080.cif" } resolution = 3.6 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= 0.007 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 62 5.16 5 C 6785 2.51 5 N 1875 2.21 5 O 2010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10732 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1016 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1034 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 9, 'TRANS': 115} Chain: "C" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2591 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 321} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1754 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain breaks: 1 Chain: "E" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2583 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1754 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain breaks: 1 Time building chain proxies: 6.63, per 1000 atoms: 0.62 Number of scatterers: 10732 At special positions: 0 Unit cell: (84.53, 96.3, 143.38, 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 62 16.00 O 2010 8.00 N 1875 7.00 C 6785 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.3 seconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 12 sheets defined 53.1% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 39 through 58 removed outlier: 3.532A pdb=" N SER A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 84 removed outlier: 3.697A pdb=" N GLN A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 102 Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.825A pdb=" N ILE A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 136 Processing helix chain 'A' and resid 138 through 149 removed outlier: 3.886A pdb=" N MET A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 removed outlier: 4.152A pdb=" N SER A 154 " --> pdb=" O MET A 151 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 155 " --> pdb=" O TYR A 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 151 through 155' Processing helix chain 'B' and resid 40 through 58 removed outlier: 3.503A pdb=" N VAL B 58 " --> pdb=" O TYR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 84 Processing helix chain 'B' and resid 89 through 103 removed outlier: 3.596A pdb=" N ARG B 103 " --> pdb=" O TRP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.527A pdb=" N ILE B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 136 Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.671A pdb=" N MET B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 removed outlier: 3.771A pdb=" N SER B 154 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 155 " --> pdb=" O TYR B 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 151 through 155' Processing helix chain 'C' and resid 53 through 99 Processing helix chain 'C' and resid 118 through 125 removed outlier: 4.017A pdb=" N HIS C 125 " --> pdb=" O GLN C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 139 removed outlier: 3.563A pdb=" N VAL C 132 " --> pdb=" O SER C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 157 through 160 No H-bonds generated for 'chain 'C' and resid 157 through 160' Processing helix chain 'C' and resid 165 through 181 removed outlier: 6.687A pdb=" N THR C 178 " --> pdb=" O ASN C 174 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ARG C 179 " --> pdb=" O TYR C 175 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 194 Processing helix chain 'C' and resid 208 through 218 Processing helix chain 'C' and resid 277 through 280 removed outlier: 3.901A pdb=" N LEU C 280 " --> pdb=" O PRO C 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 277 through 280' Processing helix chain 'C' and resid 293 through 299 removed outlier: 3.611A pdb=" N ASN C 297 " --> pdb=" O THR C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 314 Processing helix chain 'C' and resid 354 through 405 Processing helix chain 'D' and resid 118 through 125 removed outlier: 4.293A pdb=" N HIS D 125 " --> pdb=" O GLN D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 148 through 152 Processing helix chain 'D' and resid 157 through 160 No H-bonds generated for 'chain 'D' and resid 157 through 160' Processing helix chain 'D' and resid 166 through 181 removed outlier: 6.441A pdb=" N THR D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ARG D 179 " --> pdb=" O TYR D 175 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER D 180 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 196 removed outlier: 3.605A pdb=" N VAL D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 218 Processing helix chain 'D' and resid 244 through 248 removed outlier: 3.906A pdb=" N ARG D 247 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG D 248 " --> pdb=" O LEU D 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 244 through 248' Processing helix chain 'D' and resid 277 through 280 removed outlier: 3.889A pdb=" N LEU D 280 " --> pdb=" O PRO D 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 277 through 280' Processing helix chain 'D' and resid 293 through 299 Processing helix chain 'D' and resid 307 through 313 Processing helix chain 'E' and resid 53 through 98 Processing helix chain 'E' and resid 118 through 125 removed outlier: 4.134A pdb=" N HIS E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 139 Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 157 through 160 No H-bonds generated for 'chain 'E' and resid 157 through 160' Processing helix chain 'E' and resid 165 through 182 removed outlier: 3.718A pdb=" N SER E 169 " --> pdb=" O ASP E 165 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR E 178 " --> pdb=" O ASN E 174 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ARG E 179 " --> pdb=" O TYR E 175 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU E 182 " --> pdb=" O THR E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 196 removed outlier: 3.598A pdb=" N VAL E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU E 196 " --> pdb=" O VAL E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 218 Processing helix chain 'E' and resid 244 through 248 removed outlier: 3.716A pdb=" N ARG E 247 " --> pdb=" O ASP E 244 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG E 248 " --> pdb=" O LEU E 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 244 through 248' Processing helix chain 'E' and resid 277 through 280 removed outlier: 3.721A pdb=" N LEU E 280 " --> pdb=" O PRO E 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 277 through 280' Processing helix chain 'E' and resid 289 through 299 removed outlier: 3.943A pdb=" N THR E 293 " --> pdb=" O GLY E 289 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE E 295 " --> pdb=" O ARG E 291 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 314 removed outlier: 3.501A pdb=" N MET E 311 " --> pdb=" O THR E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 404 Processing helix chain 'F' and resid 118 through 125 removed outlier: 4.294A pdb=" N HIS F 125 " --> pdb=" O GLN F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 139 Processing helix chain 'F' and resid 148 through 152 Processing helix chain 'F' and resid 157 through 160 No H-bonds generated for 'chain 'F' and resid 157 through 160' Processing helix chain 'F' and resid 166 through 181 removed outlier: 6.441A pdb=" N THR F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ARG F 179 " --> pdb=" O TYR F 175 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 196 removed outlier: 3.605A pdb=" N VAL F 192 " --> pdb=" O ASN F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 218 Processing helix chain 'F' and resid 244 through 248 removed outlier: 3.906A pdb=" N ARG F 247 " --> pdb=" O ASP F 244 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG F 248 " --> pdb=" O LEU F 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 244 through 248' Processing helix chain 'F' and resid 277 through 280 removed outlier: 3.888A pdb=" N LEU F 280 " --> pdb=" O PRO F 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 277 through 280' Processing helix chain 'F' and resid 293 through 299 Processing helix chain 'F' and resid 307 through 313 Processing sheet with id=AA1, first strand: chain 'C' and resid 153 through 156 Processing sheet with id=AA2, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AA3, first strand: chain 'C' and resid 265 through 268 removed outlier: 6.400A pdb=" N VAL C 304 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 322 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 335 through 338 removed outlier: 3.558A pdb=" N LEU C 338 " --> pdb=" O PHE D 225 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL D 185 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 161 through 162 Processing sheet with id=AA6, first strand: chain 'D' and resid 265 through 268 removed outlier: 6.477A pdb=" N VAL D 304 " --> pdb=" O LEU D 266 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE D 268 " --> pdb=" O LEU D 302 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU D 302 " --> pdb=" O PHE D 268 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 153 through 156 removed outlier: 6.431A pdb=" N VAL E 184 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 161 through 162 Processing sheet with id=AA9, first strand: chain 'E' and resid 265 through 268 removed outlier: 7.050A pdb=" N VAL E 304 " --> pdb=" O LEU E 266 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE E 268 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU E 302 " --> pdb=" O PHE E 268 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 335 through 338 removed outlier: 6.599A pdb=" N VAL F 185 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 161 through 162 Processing sheet with id=AB3, first strand: chain 'F' and resid 265 through 268 removed outlier: 6.477A pdb=" N VAL F 304 " --> pdb=" O LEU F 266 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE F 268 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU F 302 " --> pdb=" O PHE F 268 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1461 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: 3.07 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2676 1.33 - 1.45: 1999 1.45 - 1.57: 6143 1.57 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 10916 Sorted by residual: bond pdb=" N ILE E 318 " pdb=" CA ILE E 318 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.22e-02 6.72e+03 1.11e+01 bond pdb=" N THR B 136 " pdb=" CA THR B 136 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.41e-02 5.03e+03 8.86e+00 bond pdb=" N VAL F 237 " pdb=" CA VAL F 237 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.52e+00 bond pdb=" N VAL E 237 " pdb=" CA VAL E 237 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.24e+00 bond pdb=" N LEU B 135 " pdb=" CA LEU B 135 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.20e-02 6.94e+03 7.64e+00 ... (remaining 10911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 14260 2.61 - 5.22: 409 5.22 - 7.83: 50 7.83 - 10.45: 20 10.45 - 13.06: 1 Bond angle restraints: 14740 Sorted by residual: angle pdb=" N PRO B 137 " pdb=" CA PRO B 137 " pdb=" C PRO B 137 " ideal model delta sigma weight residual 111.38 124.44 -13.06 1.59e+00 3.96e-01 6.74e+01 angle pdb=" N THR A 136 " pdb=" CA THR A 136 " pdb=" C THR A 136 " ideal model delta sigma weight residual 112.35 120.21 -7.86 1.34e+00 5.57e-01 3.44e+01 angle pdb=" N LEU B 135 " pdb=" CA LEU B 135 " pdb=" C LEU B 135 " ideal model delta sigma weight residual 111.14 116.67 -5.53 1.08e+00 8.57e-01 2.62e+01 angle pdb=" C VAL F 237 " pdb=" N GLY F 238 " pdb=" CA GLY F 238 " ideal model delta sigma weight residual 121.35 126.61 -5.26 1.03e+00 9.43e-01 2.61e+01 angle pdb=" N THR B 136 " pdb=" CA THR B 136 " pdb=" C THR B 136 " ideal model delta sigma weight residual 109.81 119.87 -10.06 2.21e+00 2.05e-01 2.07e+01 ... (remaining 14735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 6197 15.22 - 30.44: 319 30.44 - 45.66: 105 45.66 - 60.88: 10 60.88 - 76.10: 5 Dihedral angle restraints: 6636 sinusoidal: 2701 harmonic: 3935 Sorted by residual: dihedral pdb=" CA ASN C 258 " pdb=" C ASN C 258 " pdb=" N GLY C 259 " pdb=" CA GLY C 259 " ideal model delta harmonic sigma weight residual 180.00 -153.30 -26.70 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA THR A 136 " pdb=" C THR A 136 " pdb=" N PRO A 137 " pdb=" CA PRO A 137 " ideal model delta harmonic sigma weight residual -180.00 -158.09 -21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ASP C 244 " pdb=" C ASP C 244 " pdb=" N LEU C 245 " pdb=" CA LEU C 245 " ideal model delta harmonic sigma weight residual 180.00 160.36 19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 6633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1329 0.068 - 0.136: 287 0.136 - 0.204: 41 0.204 - 0.272: 7 0.272 - 0.340: 3 Chirality restraints: 1667 Sorted by residual: chirality pdb=" CA THR B 136 " pdb=" N THR B 136 " pdb=" C THR B 136 " pdb=" CB THR B 136 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CB ILE A 60 " pdb=" CA ILE A 60 " pdb=" CG1 ILE A 60 " pdb=" CG2 ILE A 60 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA PRO B 137 " pdb=" N PRO B 137 " pdb=" C PRO B 137 " pdb=" CB PRO B 137 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 1664 not shown) Planarity restraints: 1905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 234 " -0.026 2.00e-02 2.50e+03 5.13e-02 2.64e+01 pdb=" C ARG F 234 " 0.089 2.00e-02 2.50e+03 pdb=" O ARG F 234 " -0.034 2.00e-02 2.50e+03 pdb=" N PRO F 235 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 234 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ARG D 234 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG D 234 " 0.024 2.00e-02 2.50e+03 pdb=" N PRO D 235 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 234 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C ARG C 234 " -0.062 2.00e-02 2.50e+03 pdb=" O ARG C 234 " 0.023 2.00e-02 2.50e+03 pdb=" N PRO C 235 " 0.021 2.00e-02 2.50e+03 ... (remaining 1902 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3271 2.83 - 3.35: 10026 3.35 - 3.87: 17028 3.87 - 4.38: 19296 4.38 - 4.90: 33141 Nonbonded interactions: 82762 Sorted by model distance: nonbonded pdb=" ND2 ASN A 93 " pdb=" O PHE A 155 " model vdw 2.315 3.120 nonbonded pdb=" O LEU C 135 " pdb=" OG1 THR C 138 " model vdw 2.317 3.040 nonbonded pdb=" NH2 ARG A 47 " pdb=" OE1 GLN C 80 " model vdw 2.327 3.120 nonbonded pdb=" O ALA B 122 " pdb=" OG1 THR B 125 " model vdw 2.346 3.040 nonbonded pdb=" NE2 HIS D 240 " pdb=" OE2 GLU D 292 " model vdw 2.350 3.120 ... (remaining 82757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 39 through 161) } ncs_group { reference = (chain 'C' and (resid 52 through 98 or resid 117 through 405)) selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 26.280 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.009 0.078 10916 Z= 0.572 Angle : 1.051 13.058 14740 Z= 0.572 Chirality : 0.060 0.340 1667 Planarity : 0.007 0.065 1905 Dihedral : 10.801 76.103 4102 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.68 % Allowed : 4.32 % Favored : 95.00 % 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: -2.46 (0.18), residues: 1341 helix: -1.40 (0.17), residues: 649 sheet: -1.78 (0.75), residues: 40 loop : -1.80 (0.19), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP A 127 HIS 0.019 0.004 HIS B 118 PHE 0.029 0.004 PHE C 299 TYR 0.025 0.003 TYR E 288 ARG 0.013 0.001 ARG F 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 265 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: B 49 GLU cc_start: 0.8073 (tt0) cc_final: 0.7807 (tt0) REVERT: C 357 MET cc_start: 0.7518 (mpm) cc_final: 0.7210 (mpm) REVERT: D 193 THR cc_start: 0.9013 (p) cc_final: 0.8807 (p) REVERT: E 151 LYS cc_start: 0.8013 (tmtm) cc_final: 0.7097 (mptt) REVERT: E 199 ASP cc_start: 0.5846 (t0) cc_final: 0.5142 (p0) REVERT: E 311 MET cc_start: 0.9238 (ttp) cc_final: 0.8990 (ttm) outliers start: 8 outliers final: 1 residues processed: 273 average time/residue: 0.3382 time to fit residues: 117.6671 Evaluate side-chains 135 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 237 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 133 HIS B 118 HIS B 133 HIS C 92 GLN C 297 ASN C 340 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 ASN D 345 ASN E 52 ASN E 125 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN E 297 ASN E 340 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 HIS F 239 GLN F 297 ASN F 345 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10916 Z= 0.297 Angle : 0.654 8.663 14740 Z= 0.340 Chirality : 0.044 0.168 1667 Planarity : 0.005 0.045 1905 Dihedral : 5.153 25.288 1478 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.64 % Allowed : 8.64 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.33 (0.22), residues: 1341 helix: 0.84 (0.20), residues: 643 sheet: -1.01 (0.83), residues: 40 loop : -1.25 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 372 HIS 0.005 0.001 HIS F 201 PHE 0.021 0.002 PHE C 225 TYR 0.015 0.002 TYR E 189 ARG 0.006 0.001 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 145 time to evaluate : 1.355 Fit side-chains revert: symmetry clash REVERT: B 113 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8611 (tp) REVERT: C 237 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8370 (p) REVERT: C 311 MET cc_start: 0.8767 (ttp) cc_final: 0.8562 (ttt) REVERT: C 357 MET cc_start: 0.7394 (mpm) cc_final: 0.7137 (mpm) REVERT: E 151 LYS cc_start: 0.8083 (tmtm) cc_final: 0.7092 (mmtt) REVERT: E 199 ASP cc_start: 0.5649 (t0) cc_final: 0.5081 (p0) REVERT: F 181 MET cc_start: 0.9248 (tpt) cc_final: 0.8899 (tpt) outliers start: 43 outliers final: 22 residues processed: 178 average time/residue: 0.2207 time to fit residues: 56.6177 Evaluate side-chains 142 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 120 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 HIS C 92 GLN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10916 Z= 0.400 Angle : 0.668 6.894 14740 Z= 0.347 Chirality : 0.046 0.185 1667 Planarity : 0.005 0.044 1905 Dihedral : 5.043 27.113 1478 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.56 % Allowed : 10.92 % Favored : 85.52 % 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: 0.38 (0.22), residues: 1341 helix: 1.64 (0.21), residues: 631 sheet: -1.42 (1.02), residues: 20 loop : -1.06 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 372 HIS 0.009 0.002 HIS B 89 PHE 0.022 0.003 PHE F 265 TYR 0.017 0.002 TYR D 279 ARG 0.006 0.001 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 119 time to evaluate : 1.271 Fit side-chains REVERT: B 114 ASP cc_start: 0.8271 (m-30) cc_final: 0.8068 (m-30) REVERT: D 239 GLN cc_start: 0.7895 (tp40) cc_final: 0.7583 (tp-100) REVERT: D 297 ASN cc_start: 0.8172 (m110) cc_final: 0.7841 (m-40) REVERT: E 151 LYS cc_start: 0.8105 (tmtm) cc_final: 0.7057 (mmtt) REVERT: E 199 ASP cc_start: 0.5923 (t0) cc_final: 0.5177 (p0) REVERT: E 204 ILE cc_start: 0.7093 (mp) cc_final: 0.6757 (pt) REVERT: F 226 ASP cc_start: 0.7478 (m-30) cc_final: 0.7056 (m-30) REVERT: F 338 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8837 (pp) outliers start: 42 outliers final: 29 residues processed: 153 average time/residue: 0.2038 time to fit residues: 46.4219 Evaluate side-chains 136 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 106 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10916 Z= 0.289 Angle : 0.602 9.107 14740 Z= 0.310 Chirality : 0.043 0.180 1667 Planarity : 0.004 0.040 1905 Dihedral : 4.856 26.948 1478 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.90 % Allowed : 11.35 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.23), residues: 1341 helix: 1.94 (0.21), residues: 639 sheet: -1.70 (0.96), residues: 20 loop : -0.91 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 372 HIS 0.004 0.001 HIS B 89 PHE 0.016 0.002 PHE C 225 TYR 0.013 0.001 TYR B 51 ARG 0.004 0.001 ARG C 347 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 116 time to evaluate : 1.324 Fit side-chains REVERT: A 160 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8314 (p90) REVERT: D 239 GLN cc_start: 0.7919 (tp40) cc_final: 0.7588 (tp-100) REVERT: D 297 ASN cc_start: 0.8146 (m110) cc_final: 0.7927 (m-40) REVERT: E 151 LYS cc_start: 0.8083 (tmtm) cc_final: 0.7022 (mmtt) REVERT: E 199 ASP cc_start: 0.6110 (t0) cc_final: 0.5359 (p0) REVERT: E 204 ILE cc_start: 0.7030 (mp) cc_final: 0.6795 (pt) REVERT: F 196 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7692 (tp30) REVERT: F 226 ASP cc_start: 0.7406 (m-30) cc_final: 0.6958 (m-30) REVERT: F 338 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8833 (pp) outliers start: 46 outliers final: 32 residues processed: 152 average time/residue: 0.2071 time to fit residues: 47.0654 Evaluate side-chains 144 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 110 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 229 CYS Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 95 optimal weight: 0.0570 chunk 53 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 211 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10916 Z= 0.315 Angle : 0.607 9.338 14740 Z= 0.311 Chirality : 0.043 0.184 1667 Planarity : 0.004 0.041 1905 Dihedral : 4.736 26.326 1477 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.98 % Allowed : 12.45 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.97 (0.23), residues: 1341 helix: 2.18 (0.21), residues: 635 sheet: -1.78 (0.92), residues: 20 loop : -0.80 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 372 HIS 0.006 0.001 HIS B 89 PHE 0.016 0.002 PHE F 265 TYR 0.023 0.002 TYR B 51 ARG 0.004 0.000 ARG C 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 110 time to evaluate : 1.271 Fit side-chains REVERT: A 130 GLU cc_start: 0.8766 (tp30) cc_final: 0.7924 (tp30) REVERT: A 160 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8387 (p90) REVERT: D 297 ASN cc_start: 0.8146 (m110) cc_final: 0.7839 (m-40) REVERT: E 151 LYS cc_start: 0.8121 (tmtm) cc_final: 0.7001 (mmtt) REVERT: E 199 ASP cc_start: 0.6214 (t0) cc_final: 0.5491 (p0) REVERT: E 204 ILE cc_start: 0.7101 (mp) cc_final: 0.6829 (pt) REVERT: F 196 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7761 (tp30) REVERT: F 226 ASP cc_start: 0.7435 (m-30) cc_final: 0.6977 (m-30) REVERT: F 338 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8847 (pp) outliers start: 47 outliers final: 30 residues processed: 150 average time/residue: 0.1979 time to fit residues: 43.9516 Evaluate side-chains 137 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 105 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 229 CYS Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 0.0870 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10916 Z= 0.185 Angle : 0.547 8.756 14740 Z= 0.279 Chirality : 0.041 0.184 1667 Planarity : 0.004 0.042 1905 Dihedral : 4.457 25.027 1477 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.30 % Allowed : 13.72 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.26 (0.23), residues: 1341 helix: 2.45 (0.21), residues: 633 sheet: -1.81 (0.87), residues: 20 loop : -0.66 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 372 HIS 0.004 0.001 HIS E 70 PHE 0.014 0.001 PHE C 225 TYR 0.024 0.001 TYR B 51 ARG 0.003 0.000 ARG C 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 117 time to evaluate : 1.225 Fit side-chains REVERT: D 297 ASN cc_start: 0.8048 (m110) cc_final: 0.7717 (m-40) REVERT: E 151 LYS cc_start: 0.8145 (tmtm) cc_final: 0.7030 (mmtt) REVERT: E 199 ASP cc_start: 0.6221 (t0) cc_final: 0.5495 (p0) REVERT: F 196 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7761 (tp30) REVERT: F 338 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8810 (pp) outliers start: 39 outliers final: 28 residues processed: 148 average time/residue: 0.2076 time to fit residues: 44.8485 Evaluate side-chains 137 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 229 CYS Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 128 optimal weight: 0.2980 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10916 Z= 0.168 Angle : 0.536 9.820 14740 Z= 0.271 Chirality : 0.041 0.188 1667 Planarity : 0.003 0.044 1905 Dihedral : 4.304 23.703 1477 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.05 % Allowed : 15.07 % Favored : 81.88 % 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: 1.36 (0.24), residues: 1341 helix: 2.49 (0.21), residues: 641 sheet: -1.84 (0.83), residues: 20 loop : -0.59 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 372 HIS 0.004 0.001 HIS E 70 PHE 0.013 0.001 PHE C 225 TYR 0.024 0.001 TYR B 51 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 115 time to evaluate : 1.289 Fit side-chains revert: symmetry clash REVERT: D 166 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7003 (tm-30) REVERT: D 195 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8350 (tt) REVERT: D 297 ASN cc_start: 0.8053 (m110) cc_final: 0.7772 (m-40) REVERT: E 151 LYS cc_start: 0.8153 (tmtm) cc_final: 0.7054 (mmtt) REVERT: E 199 ASP cc_start: 0.6262 (t0) cc_final: 0.5595 (p0) REVERT: F 338 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8741 (pp) REVERT: F 341 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6271 (mmt-90) outliers start: 36 outliers final: 28 residues processed: 144 average time/residue: 0.2318 time to fit residues: 47.9986 Evaluate side-chains 141 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 160 PHE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 229 CYS Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 341 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 87 optimal weight: 0.0060 chunk 63 optimal weight: 0.7980 chunk 11 optimal weight: 0.0470 chunk 100 optimal weight: 2.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10916 Z= 0.141 Angle : 0.530 10.737 14740 Z= 0.268 Chirality : 0.040 0.193 1667 Planarity : 0.004 0.045 1905 Dihedral : 4.135 22.323 1477 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.22 % Allowed : 14.82 % Favored : 81.96 % 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: 1.51 (0.24), residues: 1341 helix: 2.59 (0.21), residues: 641 sheet: -1.84 (0.81), residues: 20 loop : -0.49 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 372 HIS 0.004 0.001 HIS E 70 PHE 0.013 0.001 PHE C 225 TYR 0.020 0.001 TYR B 51 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 132 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8100 (tptm) cc_final: 0.7840 (tptm) REVERT: D 195 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8411 (tt) REVERT: D 297 ASN cc_start: 0.7960 (m110) cc_final: 0.7728 (m-40) REVERT: E 151 LYS cc_start: 0.8056 (tmtm) cc_final: 0.6994 (mmtt) REVERT: E 199 ASP cc_start: 0.6315 (t0) cc_final: 0.5688 (p0) REVERT: F 260 GLU cc_start: 0.7891 (pm20) cc_final: 0.7462 (mp0) REVERT: F 338 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8686 (pp) REVERT: F 341 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.6213 (mmt-90) outliers start: 38 outliers final: 27 residues processed: 162 average time/residue: 0.2259 time to fit residues: 52.7871 Evaluate side-chains 150 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 341 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10916 Z= 0.346 Angle : 0.632 10.359 14740 Z= 0.321 Chirality : 0.044 0.184 1667 Planarity : 0.004 0.045 1905 Dihedral : 4.450 25.204 1477 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.88 % Allowed : 15.50 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.23), residues: 1341 helix: 2.49 (0.21), residues: 636 sheet: -1.90 (0.80), residues: 20 loop : -0.50 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 146 HIS 0.007 0.001 HIS A 139 PHE 0.016 0.002 PHE C 225 TYR 0.025 0.002 TYR B 51 ARG 0.006 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 112 time to evaluate : 1.251 Fit side-chains REVERT: A 45 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8435 (tm) REVERT: B 84 TYR cc_start: 0.8814 (m-80) cc_final: 0.8404 (m-80) REVERT: C 181 MET cc_start: 0.9205 (mmm) cc_final: 0.8953 (tpt) REVERT: D 272 MET cc_start: 0.7816 (mmp) cc_final: 0.7440 (mmp) REVERT: D 297 ASN cc_start: 0.8089 (m110) cc_final: 0.7859 (m-40) REVERT: E 151 LYS cc_start: 0.8090 (tmtm) cc_final: 0.7046 (mmtt) REVERT: E 199 ASP cc_start: 0.6432 (t0) cc_final: 0.5746 (p0) REVERT: F 196 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7871 (tp30) REVERT: F 226 ASP cc_start: 0.7456 (m-30) cc_final: 0.6950 (m-30) REVERT: F 338 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8654 (pp) REVERT: F 341 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.6488 (mmt-90) outliers start: 34 outliers final: 27 residues processed: 140 average time/residue: 0.2207 time to fit residues: 44.4461 Evaluate side-chains 140 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 229 CYS Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 341 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 87 optimal weight: 0.4980 chunk 132 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10916 Z= 0.213 Angle : 0.583 11.254 14740 Z= 0.295 Chirality : 0.042 0.187 1667 Planarity : 0.004 0.043 1905 Dihedral : 4.331 23.914 1477 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.88 % Allowed : 15.50 % Favored : 81.63 % 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: 1.50 (0.23), residues: 1341 helix: 2.56 (0.21), residues: 636 sheet: -1.97 (0.77), residues: 20 loop : -0.44 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 146 HIS 0.004 0.001 HIS E 70 PHE 0.014 0.001 PHE C 225 TYR 0.032 0.001 TYR B 51 ARG 0.005 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 115 time to evaluate : 1.354 Fit side-chains REVERT: B 84 TYR cc_start: 0.8755 (m-80) cc_final: 0.8347 (m-80) REVERT: C 181 MET cc_start: 0.9138 (mmm) cc_final: 0.8900 (tpt) REVERT: C 367 MET cc_start: 0.8936 (tpp) cc_final: 0.8651 (tpp) REVERT: D 195 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8367 (tt) REVERT: D 272 MET cc_start: 0.7757 (mmp) cc_final: 0.7423 (mmp) REVERT: D 297 ASN cc_start: 0.8008 (m110) cc_final: 0.7748 (m-40) REVERT: E 151 LYS cc_start: 0.8091 (tmtm) cc_final: 0.7051 (mmtt) REVERT: E 199 ASP cc_start: 0.6455 (t0) cc_final: 0.5754 (p0) REVERT: F 196 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7771 (tp30) REVERT: F 260 GLU cc_start: 0.7985 (pm20) cc_final: 0.7437 (mp0) REVERT: F 338 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8683 (pp) REVERT: F 341 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.6324 (mmt-90) outliers start: 34 outliers final: 28 residues processed: 141 average time/residue: 0.2208 time to fit residues: 44.6273 Evaluate side-chains 142 residues out of total 1183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 111 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 212 CYS Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 229 CYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 258 ASN Chi-restraints excluded: chain E residue 392 VAL Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 229 CYS Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 338 LEU Chi-restraints excluded: chain F residue 341 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 6 optimal weight: 0.0370 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.125520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.097327 restraints weight = 19163.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.097987 restraints weight = 12958.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.098398 restraints weight = 11192.517| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10916 Z= 0.152 Angle : 0.553 11.293 14740 Z= 0.276 Chirality : 0.041 0.189 1667 Planarity : 0.004 0.043 1905 Dihedral : 4.076 22.013 1477 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.62 % Allowed : 15.83 % Favored : 81.54 % 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: 1.57 (0.24), residues: 1341 helix: 2.60 (0.21), residues: 642 sheet: -2.14 (0.79), residues: 20 loop : -0.40 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 146 HIS 0.004 0.001 HIS E 70 PHE 0.012 0.001 PHE C 225 TYR 0.029 0.001 TYR B 51 ARG 0.005 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2029.15 seconds wall clock time: 37 minutes 8.07 seconds (2228.07 seconds total)