Starting phenix.real_space_refine on Sat Nov 16 00:21:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zh8_60096/11_2024/8zh8_60096.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zh8_60096/11_2024/8zh8_60096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zh8_60096/11_2024/8zh8_60096.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zh8_60096/11_2024/8zh8_60096.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zh8_60096/11_2024/8zh8_60096.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zh8_60096/11_2024/8zh8_60096.cif" } resolution = 3.19 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= -0.001 sd= 1.034 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 68 5.16 5 C 6422 2.51 5 N 1720 2.21 5 O 1838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10048 Number of models: 1 Model: "" Number of chains: 8 Chain: "R" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2635 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 968 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2473 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 88 Chain: "G" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 350 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1704 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 62 Chain: "S" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1730 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "Q" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 187 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.24, per 1000 atoms: 0.62 Number of scatterers: 10048 At special positions: 0 Unit cell: (87.849, 132.795, 148.117, 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 68 16.00 O 1838 8.00 N 1720 7.00 C 6422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 118 " - pdb=" SG CYS R 201 " distance=2.03 Simple disulfide: pdb=" SG CYS R 285 " - pdb=" SG CYS R 327 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.1 seconds 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2456 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 15 sheets defined 37.5% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'R' and resid 7 through 18 removed outlier: 4.108A pdb=" N ARG R 16 " --> pdb=" O SER R 12 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP R 17 " --> pdb=" O ARG R 13 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS R 18 " --> pdb=" O LEU R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 30 Processing helix chain 'R' and resid 41 through 73 removed outlier: 3.506A pdb=" N THR R 71 " --> pdb=" O PHE R 67 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER R 73 " --> pdb=" O VAL R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 77 removed outlier: 3.649A pdb=" N ARG R 77 " --> pdb=" O LYS R 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 74 through 77' Processing helix chain 'R' and resid 78 through 98 Processing helix chain 'R' and resid 98 through 107 Processing helix chain 'R' and resid 113 through 149 removed outlier: 4.019A pdb=" N ILE R 117 " --> pdb=" O GLY R 113 " (cutoff:3.500A) Proline residue: R 122 - end of helix removed outlier: 3.644A pdb=" N THR R 137 " --> pdb=" O ILE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 155 removed outlier: 3.676A pdb=" N LYS R 154 " --> pdb=" O PHE R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 177 removed outlier: 3.599A pdb=" N ALA R 162 " --> pdb=" O THR R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 183 removed outlier: 4.175A pdb=" N HIS R 182 " --> pdb=" O SER R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 195 Processing helix chain 'R' and resid 207 through 223 removed outlier: 3.805A pdb=" N GLN R 211 " --> pdb=" O SER R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 243 Processing helix chain 'R' and resid 264 through 299 removed outlier: 3.814A pdb=" N ALA R 283 " --> pdb=" O VAL R 279 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.579A pdb=" N SER R 299 " --> pdb=" O MET R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 305 Processing helix chain 'R' and resid 306 through 323 Processing helix chain 'R' and resid 323 through 335 Proline residue: R 329 - end of helix Processing helix chain 'R' and resid 336 through 346 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.559A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.987A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.781A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.584A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.649A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 114 through 130 removed outlier: 4.318A pdb=" N GLN A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.890A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 removed outlier: 3.643A pdb=" N TYR A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 204 removed outlier: 4.591A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 243 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.082A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 14 removed outlier: 4.269A pdb=" N GLY Q 14 " --> pdb=" O GLU Q 10 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 184 through 191 Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.926A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.181A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.904A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.085A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.923A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.931A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.036A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.660A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 72 through 76 removed outlier: 3.976A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.724A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.565A pdb=" N THR S 129 " --> pdb=" O ARG S 148 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG S 148 " --> pdb=" O THR S 129 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.837A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1452 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: 3.39 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2254 1.33 - 1.46: 2824 1.46 - 1.58: 5086 1.58 - 1.71: 0 1.71 - 1.84: 101 Bond restraints: 10265 Sorted by residual: bond pdb=" CA PRO R 329 " pdb=" CB PRO R 329 " ideal model delta sigma weight residual 1.534 1.477 0.056 1.52e-02 4.33e+03 1.37e+01 bond pdb=" CA ARG Q 25 " pdb=" C ARG Q 25 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.34e-02 5.57e+03 9.36e+00 bond pdb=" C GLN R 125 " pdb=" O GLN R 125 " ideal model delta sigma weight residual 1.236 1.204 0.033 1.15e-02 7.56e+03 8.21e+00 bond pdb=" C GLN R 125 " pdb=" N SER R 126 " ideal model delta sigma weight residual 1.335 1.298 0.037 1.31e-02 5.83e+03 7.86e+00 bond pdb=" C VAL R 121 " pdb=" N PRO R 122 " ideal model delta sigma weight residual 1.335 1.360 -0.025 1.28e-02 6.10e+03 3.89e+00 ... (remaining 10260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 13498 1.69 - 3.39: 383 3.39 - 5.08: 46 5.08 - 6.77: 12 6.77 - 8.47: 3 Bond angle restraints: 13942 Sorted by residual: angle pdb=" C ASN R 328 " pdb=" N PRO R 329 " pdb=" CA PRO R 329 " ideal model delta sigma weight residual 119.32 114.52 4.80 1.14e+00 7.69e-01 1.77e+01 angle pdb=" C PRO R 329 " pdb=" CA PRO R 329 " pdb=" CB PRO R 329 " ideal model delta sigma weight residual 112.64 106.17 6.47 1.74e+00 3.30e-01 1.38e+01 angle pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta sigma weight residual 120.39 125.45 -5.06 1.39e+00 5.18e-01 1.33e+01 angle pdb=" N SER S 194 " pdb=" CA SER S 194 " pdb=" C SER S 194 " ideal model delta sigma weight residual 108.38 112.67 -4.29 1.35e+00 5.49e-01 1.01e+01 angle pdb=" CA TRP A 96 " pdb=" CB TRP A 96 " pdb=" CG TRP A 96 " ideal model delta sigma weight residual 113.60 119.50 -5.90 1.90e+00 2.77e-01 9.65e+00 ... (remaining 13937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 5496 16.17 - 32.33: 452 32.33 - 48.50: 82 48.50 - 64.66: 13 64.66 - 80.83: 14 Dihedral angle restraints: 6057 sinusoidal: 2247 harmonic: 3810 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -22.52 -63.48 1 1.00e+01 1.00e-02 5.31e+01 dihedral pdb=" CA ARG A 94 " pdb=" C ARG A 94 " pdb=" N LYS A 95 " pdb=" CA LYS A 95 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 6054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1139 0.041 - 0.082: 345 0.082 - 0.123: 95 0.123 - 0.163: 14 0.163 - 0.204: 3 Chirality restraints: 1596 Sorted by residual: chirality pdb=" CA ILE R 199 " pdb=" N ILE R 199 " pdb=" C ILE R 199 " pdb=" CB ILE R 199 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ASN R 328 " pdb=" N ASN R 328 " pdb=" C ASN R 328 " pdb=" CB ASN R 328 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.87e-01 chirality pdb=" CA ILE R 188 " pdb=" N ILE R 188 " pdb=" C ILE R 188 " pdb=" CB ILE R 188 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.52e-01 ... (remaining 1593 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 155 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C ASN B 155 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN B 155 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN B 156 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 328 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C ASN R 328 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN R 328 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO R 329 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 225 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO R 226 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO R 226 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 226 " 0.026 5.00e-02 4.00e+02 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 887 2.75 - 3.28: 9883 3.28 - 3.82: 17145 3.82 - 4.36: 19973 4.36 - 4.90: 34978 Nonbonded interactions: 82866 Sorted by model distance: nonbonded pdb=" OE2 GLU R 142 " pdb=" OH TYR R 157 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR N 117 " pdb=" O CYS B 204 " model vdw 2.218 3.040 nonbonded pdb=" O ASN B 155 " pdb=" ND2 ASN B 155 " model vdw 2.231 3.120 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.237 3.040 nonbonded pdb=" O SER N 63 " pdb=" NH2 ARG N 67 " model vdw 2.239 3.120 ... (remaining 82861 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 25.940 Find NCS groups from input model: 0.140 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 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 : 0.003 0.056 10265 Z= 0.186 Angle : 0.670 8.466 13942 Z= 0.388 Chirality : 0.043 0.204 1596 Planarity : 0.004 0.046 1766 Dihedral : 12.775 80.825 3583 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.57 (0.24), residues: 1294 helix: 1.54 (0.26), residues: 426 sheet: 0.16 (0.29), residues: 330 loop : -0.33 (0.29), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP N 47 HIS 0.006 0.001 HIS B 54 PHE 0.017 0.002 PHE R 314 TYR 0.017 0.001 TYR S 60 ARG 0.005 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 357 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 61 THR cc_start: 0.7475 (t) cc_final: 0.7110 (m) REVERT: A 10 LYS cc_start: 0.7900 (mttp) cc_final: 0.7523 (mttm) REVERT: A 199 ASP cc_start: 0.7787 (p0) cc_final: 0.7091 (p0) outliers start: 1 outliers final: 0 residues processed: 357 average time/residue: 0.2704 time to fit residues: 127.2893 Evaluate side-chains 213 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 0.0060 chunk 117 optimal weight: 0.0770 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 5 ASN R 63 ASN R 81 ASN R 342 ASN B 259 GLN A 130 ASN A 131 ASN A 239 ASN S 82 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10265 Z= 0.201 Angle : 0.665 6.959 13942 Z= 0.349 Chirality : 0.044 0.157 1596 Planarity : 0.005 0.051 1766 Dihedral : 4.454 24.540 1417 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.91 % Allowed : 14.07 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.46 (0.24), residues: 1294 helix: 1.53 (0.26), residues: 427 sheet: 0.06 (0.30), residues: 307 loop : -0.44 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 111 HIS 0.005 0.001 HIS A 209 PHE 0.020 0.002 PHE R 339 TYR 0.021 0.002 TYR S 95 ARG 0.009 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 251 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 335 MET cc_start: 0.6645 (tpp) cc_final: 0.4824 (tpp) REVERT: N 53 GLN cc_start: 0.6088 (OUTLIER) cc_final: 0.5745 (mp10) REVERT: B 260 GLU cc_start: 0.7851 (tp30) cc_final: 0.7536 (tp30) outliers start: 20 outliers final: 8 residues processed: 259 average time/residue: 0.2567 time to fit residues: 90.4605 Evaluate side-chains 218 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 209 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 313 ILE Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain A residue 118 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 117 optimal weight: 0.2980 chunk 126 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 184 GLN A 22 ASN A 131 ASN S 182 ASN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10265 Z= 0.200 Angle : 0.648 7.793 13942 Z= 0.338 Chirality : 0.044 0.261 1596 Planarity : 0.004 0.041 1766 Dihedral : 4.284 20.932 1417 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.06 % Allowed : 15.89 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.44 (0.24), residues: 1294 helix: 1.45 (0.26), residues: 429 sheet: 0.10 (0.29), residues: 320 loop : -0.43 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 111 HIS 0.005 0.001 HIS R 198 PHE 0.040 0.002 PHE R 11 TYR 0.020 0.001 TYR R 194 ARG 0.006 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 237 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 53 GLN cc_start: 0.6238 (OUTLIER) cc_final: 0.5946 (mp10) REVERT: B 78 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6529 (ptpp) REVERT: A 21 LYS cc_start: 0.7226 (ttpp) cc_final: 0.6863 (pttp) REVERT: A 192 PHE cc_start: 0.6455 (t80) cc_final: 0.6228 (t80) REVERT: A 199 ASP cc_start: 0.7530 (p0) cc_final: 0.7014 (p0) outliers start: 32 outliers final: 11 residues processed: 252 average time/residue: 0.2419 time to fit residues: 83.2205 Evaluate side-chains 223 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 201 CYS Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 246 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 56 optimal weight: 0.0060 chunk 78 optimal weight: 30.0000 chunk 117 optimal weight: 0.0870 chunk 124 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN S 39 GLN S 171 GLN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10265 Z= 0.236 Angle : 0.656 9.829 13942 Z= 0.345 Chirality : 0.045 0.341 1596 Planarity : 0.004 0.048 1766 Dihedral : 4.297 21.676 1417 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.49 % Allowed : 19.52 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.50 (0.24), residues: 1294 helix: 1.58 (0.26), residues: 420 sheet: 0.16 (0.29), residues: 317 loop : -0.47 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 111 HIS 0.006 0.001 HIS A 209 PHE 0.023 0.002 PHE R 314 TYR 0.015 0.002 TYR A 170 ARG 0.006 0.001 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 53 GLN cc_start: 0.6747 (mp10) cc_final: 0.6456 (mp10) REVERT: N 80 TYR cc_start: 0.6847 (m-80) cc_final: 0.6193 (m-10) REVERT: A 21 LYS cc_start: 0.7316 (ttpp) cc_final: 0.6928 (pttp) outliers start: 26 outliers final: 12 residues processed: 232 average time/residue: 0.2489 time to fit residues: 78.6072 Evaluate side-chains 209 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain S residue 2 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 293 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN A 131 ASN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 220 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10265 Z= 0.251 Angle : 0.663 10.236 13942 Z= 0.347 Chirality : 0.045 0.368 1596 Planarity : 0.004 0.051 1766 Dihedral : 4.281 22.220 1417 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.97 % Allowed : 20.96 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.54 (0.24), residues: 1294 helix: 1.68 (0.26), residues: 419 sheet: 0.15 (0.28), residues: 336 loop : -0.49 (0.29), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.052 0.002 PHE R 11 TYR 0.014 0.002 TYR N 95 ARG 0.004 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 15 LEU cc_start: 0.8299 (mm) cc_final: 0.7875 (mp) REVERT: N 53 GLN cc_start: 0.6737 (mp10) cc_final: 0.6472 (mp10) REVERT: A 195 LYS cc_start: 0.8346 (tptp) cc_final: 0.8145 (tptp) outliers start: 31 outliers final: 16 residues processed: 229 average time/residue: 0.2461 time to fit residues: 77.0739 Evaluate side-chains 211 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 201 CYS Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 203 THR 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: 10.0000 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 30 optimal weight: 0.4980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 0.0070 chunk 10 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 120 optimal weight: 0.9980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 156 GLN R 198 HIS B 54 HIS ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN A 131 ASN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10265 Z= 0.189 Angle : 0.658 10.700 13942 Z= 0.342 Chirality : 0.044 0.317 1596 Planarity : 0.004 0.050 1766 Dihedral : 4.222 24.573 1417 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.06 % Allowed : 20.57 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.71 (0.24), residues: 1294 helix: 1.81 (0.27), residues: 419 sheet: 0.37 (0.30), residues: 302 loop : -0.43 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 181 HIS 0.005 0.001 HIS A 209 PHE 0.030 0.001 PHE R 339 TYR 0.024 0.001 TYR N 115 ARG 0.009 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 219 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 53 GLN cc_start: 0.6668 (mp10) cc_final: 0.6429 (mp10) REVERT: A 199 ASP cc_start: 0.7487 (p0) cc_final: 0.7128 (p0) outliers start: 32 outliers final: 17 residues processed: 241 average time/residue: 0.2527 time to fit residues: 83.8614 Evaluate side-chains 211 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 201 CYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 77 optimal weight: 30.0000 chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 156 GLN ** R 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10265 Z= 0.246 Angle : 0.720 14.240 13942 Z= 0.366 Chirality : 0.044 0.174 1596 Planarity : 0.004 0.050 1766 Dihedral : 4.253 23.901 1417 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.97 % Allowed : 22.01 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.66 (0.24), residues: 1294 helix: 1.73 (0.26), residues: 423 sheet: 0.28 (0.29), residues: 317 loop : -0.43 (0.28), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 169 HIS 0.005 0.001 HIS A 209 PHE 0.022 0.002 PHE R 339 TYR 0.031 0.002 TYR N 115 ARG 0.007 0.001 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 267 LYS cc_start: 0.7984 (mmmt) cc_final: 0.7720 (mmmt) REVERT: N 53 GLN cc_start: 0.6773 (mp10) cc_final: 0.6561 (mp10) REVERT: B 336 LEU cc_start: 0.7570 (tp) cc_final: 0.7282 (tp) outliers start: 31 outliers final: 26 residues processed: 215 average time/residue: 0.2564 time to fit residues: 74.8081 Evaluate side-chains 217 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 184 GLN Chi-restraints excluded: chain R residue 201 CYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 275 MET Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 156 GLN R 185 GLN A 101 ASN A 123 ASN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10265 Z= 0.287 Angle : 0.740 13.538 13942 Z= 0.377 Chirality : 0.044 0.170 1596 Planarity : 0.004 0.050 1766 Dihedral : 4.381 26.596 1417 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.83 % Allowed : 22.11 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.61 (0.25), residues: 1294 helix: 1.67 (0.26), residues: 423 sheet: 0.08 (0.28), residues: 334 loop : -0.32 (0.29), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 332 HIS 0.005 0.001 HIS A 209 PHE 0.034 0.002 PHE R 11 TYR 0.020 0.002 TYR N 80 ARG 0.007 0.001 ARG R 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 267 LYS cc_start: 0.8030 (mmmt) cc_final: 0.7804 (mmmt) REVERT: B 262 MET cc_start: 0.5300 (tpp) cc_final: 0.5050 (tpp) REVERT: B 336 LEU cc_start: 0.7617 (tp) cc_final: 0.7354 (tp) outliers start: 40 outliers final: 27 residues processed: 217 average time/residue: 0.2651 time to fit residues: 77.2239 Evaluate side-chains 206 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 156 GLN Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 178 SER Chi-restraints excluded: chain R residue 201 CYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 69 optimal weight: 0.0970 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 overall best weight: 1.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 156 GLN ** R 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10265 Z= 0.245 Angle : 0.750 13.761 13942 Z= 0.380 Chirality : 0.044 0.173 1596 Planarity : 0.004 0.051 1766 Dihedral : 4.397 33.714 1417 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.78 % Allowed : 23.06 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.53 (0.24), residues: 1294 helix: 1.52 (0.26), residues: 426 sheet: 0.07 (0.28), residues: 336 loop : -0.31 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 111 HIS 0.005 0.001 HIS A 209 PHE 0.039 0.002 PHE R 11 TYR 0.035 0.002 TYR N 115 ARG 0.014 0.001 ARG R 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 262 MET cc_start: 0.5237 (tpp) cc_final: 0.5015 (tpp) REVERT: B 336 LEU cc_start: 0.7589 (tp) cc_final: 0.7344 (tp) outliers start: 29 outliers final: 26 residues processed: 203 average time/residue: 0.2805 time to fit residues: 77.5708 Evaluate side-chains 204 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 156 GLN Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 178 SER Chi-restraints excluded: chain R residue 201 CYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 10.0000 chunk 58 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 81 optimal weight: 0.0570 chunk 109 optimal weight: 0.7980 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 156 GLN ** R 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10265 Z= 0.238 Angle : 0.764 15.285 13942 Z= 0.384 Chirality : 0.044 0.182 1596 Planarity : 0.004 0.069 1766 Dihedral : 4.369 32.260 1417 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.58 % Allowed : 23.54 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.45 (0.24), residues: 1294 helix: 1.38 (0.26), residues: 432 sheet: 0.13 (0.28), residues: 333 loop : -0.39 (0.29), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 181 HIS 0.004 0.001 HIS A 209 PHE 0.049 0.002 PHE R 11 TYR 0.036 0.002 TYR N 115 ARG 0.009 0.001 ARG Q 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2588 Ramachandran restraints generated. 1294 Oldfield, 0 Emsley, 1294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 68 PHE cc_start: 0.6571 (m-10) cc_final: 0.6354 (m-80) REVERT: B 336 LEU cc_start: 0.7623 (tp) cc_final: 0.7394 (tp) outliers start: 27 outliers final: 23 residues processed: 207 average time/residue: 0.2452 time to fit residues: 68.6527 Evaluate side-chains 199 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 155 TRP Chi-restraints excluded: chain R residue 156 GLN Chi-restraints excluded: chain R residue 169 VAL Chi-restraints excluded: chain R residue 178 SER Chi-restraints excluded: chain R residue 201 CYS Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 235 SER Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain A residue 99 CYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 PHE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 156 GLN ** R 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 219 GLN ** 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 = 0.4074 r_free = 0.4074 target = 0.118437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.095991 restraints weight = 26684.116| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 4.19 r_work: 0.3537 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.6003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10265 Z= 0.217 Angle : 0.744 14.079 13942 Z= 0.376 Chirality : 0.044 0.185 1596 Planarity : 0.004 0.050 1766 Dihedral : 4.342 31.116 1417 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.49 % Allowed : 24.11 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.51 (0.24), residues: 1294 helix: 1.43 (0.26), residues: 428 sheet: 0.18 (0.29), residues: 317 loop : -0.35 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 181 HIS 0.004 0.001 HIS A 209 PHE 0.058 0.002 PHE R 339 TYR 0.034 0.001 TYR N 115 ARG 0.009 0.001 ARG S 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2702.93 seconds wall clock time: 49 minutes 52.10 seconds (2992.10 seconds total)