Starting phenix.real_space_refine on Sun Dec 29 17:06:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ruc_24702/12_2024/7ruc_24702.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ruc_24702/12_2024/7ruc_24702.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/cci-nas-00/data/ceres_data/7ruc_24702/12_2024/7ruc_24702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ruc_24702/12_2024/7ruc_24702.map" model { file = "/net/cci-nas-00/data/ceres_data/7ruc_24702/12_2024/7ruc_24702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ruc_24702/12_2024/7ruc_24702.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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 64 5.16 5 C 6835 2.51 5 N 1832 2.21 5 O 2026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10766 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2417 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 18, 'TRANS': 287} Chain breaks: 1 Chain: "B" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2412 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 18, 'TRANS': 286} Chain breaks: 1 Chain: "C" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2175 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain: "D" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 340 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 8, 'TRANS': 34} Chain: "F" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2175 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain: "G" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 790 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 12, 'TRANS': 87} Chain breaks: 1 Chain: "H" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 392 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1952 SG CYS A 283 54.155 67.467 98.552 1.00142.37 S ATOM 1975 SG CYS A 286 55.590 69.741 96.078 1.00127.85 S ATOM 4364 SG CYS B 283 53.181 71.227 98.454 1.00138.48 S ATOM 4387 SG CYS B 286 51.745 68.778 96.011 1.00126.91 S Time building chain proxies: 7.77, per 1000 atoms: 0.72 Number of scatterers: 10766 At special positions: 0 Unit cell: (108.9, 125.4, 113.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 64 16.00 P 6 15.00 Mg 2 11.99 O 2026 8.00 N 1832 7.00 C 6835 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" SG CYS A 283 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 283 " pdb="ZN ZN B 401 " - pdb=" SG CYS A 286 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 286 " Number of angles added : 6 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2554 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 2 sheets defined 70.2% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 22 through 28 Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.592A pdb=" N ALA A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 78 Processing helix chain 'A' and resid 116 through 132 removed outlier: 4.296A pdb=" N ALA A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 152 Processing helix chain 'A' and resid 163 through 187 Proline residue: A 174 - end of helix Processing helix chain 'A' and resid 210 through 232 removed outlier: 3.686A pdb=" N LEU A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 245 through 263 Processing helix chain 'A' and resid 283 through 304 Processing helix chain 'A' and resid 321 through 334 removed outlier: 3.897A pdb=" N GLN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 28 Processing helix chain 'B' and resid 43 through 57 removed outlier: 3.517A pdb=" N ALA B 57 " --> pdb=" O VAL B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 78 Processing helix chain 'B' and resid 116 through 131 removed outlier: 4.975A pdb=" N GLY B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 135 through 152 Processing helix chain 'B' and resid 163 through 190 removed outlier: 3.531A pdb=" N THR B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) Proline residue: B 174 - end of helix Processing helix chain 'B' and resid 211 through 232 removed outlier: 4.251A pdb=" N LYS B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 245 through 263 Processing helix chain 'B' and resid 283 through 304 Processing helix chain 'B' and resid 321 through 334 removed outlier: 4.003A pdb=" N GLN B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 37 removed outlier: 3.941A pdb=" N GLN C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 56 Processing helix chain 'C' and resid 58 through 76 Processing helix chain 'C' and resid 78 through 96 Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 120 through 133 Processing helix chain 'C' and resid 142 through 156 Processing helix chain 'C' and resid 158 through 169 Processing helix chain 'C' and resid 171 through 186 Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 191 through 206 removed outlier: 4.126A pdb=" N VAL C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 223 Processing helix chain 'C' and resid 234 through 250 Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 262 through 267 Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.902A pdb=" N GLU C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY C 285 " --> pdb=" O GLN C 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 1009 through 1014 removed outlier: 4.370A pdb=" N ALA D1013 " --> pdb=" O PRO D1009 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL D1014 " --> pdb=" O TRP D1010 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1009 through 1014' Processing helix chain 'D' and resid 1015 through 1017 No H-bonds generated for 'chain 'D' and resid 1015 through 1017' Processing helix chain 'D' and resid 1018 through 1030 removed outlier: 3.745A pdb=" N ILE D1022 " --> pdb=" O TRP D1018 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN D1023 " --> pdb=" O VAL D1019 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN D1024 " --> pdb=" O PRO D1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1044 Processing helix chain 'F' and resid 21 through 37 Processing helix chain 'F' and resid 38 through 57 Processing helix chain 'F' and resid 58 through 77 Processing helix chain 'F' and resid 78 through 97 Processing helix chain 'F' and resid 101 through 115 Processing helix chain 'F' and resid 119 through 133 removed outlier: 4.081A pdb=" N VAL F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 156 removed outlier: 3.535A pdb=" N HIS F 146 " --> pdb=" O HIS F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 169 Processing helix chain 'F' and resid 172 through 187 Processing helix chain 'F' and resid 188 through 190 No H-bonds generated for 'chain 'F' and resid 188 through 190' Processing helix chain 'F' and resid 191 through 206 removed outlier: 3.798A pdb=" N VAL F 196 " --> pdb=" O VAL F 192 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU F 206 " --> pdb=" O GLN F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 223 removed outlier: 3.586A pdb=" N ALA F 212 " --> pdb=" O ASN F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 248 Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 262 through 267 Processing helix chain 'F' and resid 269 through 284 removed outlier: 4.289A pdb=" N ASN F 273 " --> pdb=" O ASP F 269 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU F 274 " --> pdb=" O PRO F 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 1017 through 1032 removed outlier: 4.732A pdb=" N ILE G1021 " --> pdb=" O GLU G1017 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG G1030 " --> pdb=" O ILE G1026 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS G1031 " --> pdb=" O GLN G1027 " (cutoff:3.500A) Processing helix chain 'G' and resid 1039 through 1044 Processing helix chain 'G' and resid 1062 through 1075 Processing helix chain 'G' and resid 1081 through 1089 removed outlier: 3.841A pdb=" N LEU G1085 " --> pdb=" O SER G1081 " (cutoff:3.500A) Processing helix chain 'G' and resid 1092 through 1111 removed outlier: 4.357A pdb=" N TYR G1098 " --> pdb=" O VAL G1094 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG G1099 " --> pdb=" O GLN G1095 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN G1111 " --> pdb=" O GLN G1107 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 107 removed outlier: 4.329A pdb=" N VAL H 102 " --> pdb=" O LEU H 98 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG H 105 " --> pdb=" O LYS H 101 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS H 106 " --> pdb=" O VAL H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 130 Processing helix chain 'H' and resid 133 through 140 removed outlier: 3.551A pdb=" N ARG H 137 " --> pdb=" O ASP H 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87 removed outlier: 6.470A pdb=" N VAL A 62 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N MET A 97 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE A 64 " --> pdb=" O MET A 97 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 63 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASP A 160 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE A 65 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP A 33 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE A 239 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N PHE A 35 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL A 241 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLY A 37 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ILE A 243 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N ASN A 268 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE A 238 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ILE A 270 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N CYS A 240 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASN A 272 " --> pdb=" O CYS A 240 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N CYS A 242 " --> pdb=" O ASN A 272 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU A 274 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 269 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU A 312 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 271 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 86 through 87 removed outlier: 6.555A pdb=" N VAL B 62 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N MET B 97 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE B 64 " --> pdb=" O MET B 97 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TRP B 33 " --> pdb=" O THR B 237 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE B 239 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE B 35 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL B 241 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLY B 37 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ASN B 268 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 240 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE B 269 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU B 312 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 271 " --> pdb=" O LEU B 312 " (cutoff:3.500A) 651 hydrogen bonds defined for protein. 1947 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: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3527 1.34 - 1.46: 1966 1.46 - 1.58: 5393 1.58 - 1.69: 6 1.69 - 1.81: 106 Bond restraints: 10998 Sorted by residual: bond pdb=" C LEU A 314 " pdb=" N LEU A 315 " ideal model delta sigma weight residual 1.330 1.303 0.027 1.47e-02 4.63e+03 3.26e+00 bond pdb=" CA PRO B 163 " pdb=" C PRO B 163 " ideal model delta sigma weight residual 1.525 1.514 0.012 9.70e-03 1.06e+04 1.49e+00 bond pdb=" O3B ATP B 402 " pdb=" PB ATP B 402 " ideal model delta sigma weight residual 1.592 1.562 0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" C1' ATP B 402 " pdb=" C2' ATP B 402 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.20e-02 6.94e+03 8.73e-01 bond pdb=" C1' ATP A 401 " pdb=" C2' ATP A 401 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.20e-02 6.94e+03 8.51e-01 ... (remaining 10993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 14537 1.40 - 2.79: 248 2.79 - 4.19: 83 4.19 - 5.59: 6 5.59 - 6.98: 8 Bond angle restraints: 14882 Sorted by residual: angle pdb=" N ASP B 116 " pdb=" CA ASP B 116 " pdb=" C ASP B 116 " ideal model delta sigma weight residual 112.97 110.05 2.92 1.06e+00 8.90e-01 7.61e+00 angle pdb=" N SER G1097 " pdb=" CA SER G1097 " pdb=" C SER G1097 " ideal model delta sigma weight residual 111.75 108.44 3.31 1.28e+00 6.10e-01 6.68e+00 angle pdb=" C2' ATP A 401 " pdb=" C3' ATP A 401 " pdb=" O3' ATP A 401 " ideal model delta sigma weight residual 111.83 105.10 6.73 2.67e+00 1.40e-01 6.35e+00 angle pdb=" C1' ATP A 401 " pdb=" C2' ATP A 401 " pdb=" O2' ATP A 401 " ideal model delta sigma weight residual 110.58 103.60 6.98 2.79e+00 1.28e-01 6.25e+00 angle pdb=" C2' ATP B 402 " pdb=" C3' ATP B 402 " pdb=" O3' ATP B 402 " ideal model delta sigma weight residual 111.83 105.29 6.54 2.67e+00 1.40e-01 6.01e+00 ... (remaining 14877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 6045 17.61 - 35.21: 567 35.21 - 52.82: 114 52.82 - 70.43: 28 70.43 - 88.04: 12 Dihedral angle restraints: 6766 sinusoidal: 2838 harmonic: 3928 Sorted by residual: dihedral pdb=" CA LEU A 303 " pdb=" C LEU A 303 " pdb=" N TYR A 304 " pdb=" CA TYR A 304 " ideal model delta harmonic sigma weight residual -180.00 -163.63 -16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU F 181 " pdb=" CG GLU F 181 " pdb=" CD GLU F 181 " pdb=" OE1 GLU F 181 " ideal model delta sinusoidal sigma weight residual 0.00 88.04 -88.04 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CG ARG B 263 " pdb=" CD ARG B 263 " pdb=" NE ARG B 263 " pdb=" CZ ARG B 263 " ideal model delta sinusoidal sigma weight residual 180.00 135.99 44.01 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 6763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1462 0.060 - 0.120: 157 0.120 - 0.180: 12 0.180 - 0.240: 2 0.240 - 0.300: 4 Chirality restraints: 1637 Sorted by residual: chirality pdb=" C2' ATP A 401 " pdb=" C1' ATP A 401 " pdb=" C3' ATP A 401 " pdb=" O2' ATP A 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C2' ATP B 402 " pdb=" C1' ATP B 402 " pdb=" C3' ATP B 402 " pdb=" O2' ATP B 402 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C3' ATP A 401 " pdb=" C2' ATP A 401 " pdb=" C4' ATP A 401 " pdb=" O3' ATP A 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 1634 not shown) Planarity restraints: 1922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 230 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO F 231 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO F 231 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 231 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 122 " -0.132 9.50e-02 1.11e+02 5.95e-02 2.76e+00 pdb=" NE ARG C 122 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG C 122 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 122 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 122 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 197 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C ALA C 197 " -0.026 2.00e-02 2.50e+03 pdb=" O ALA C 197 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN C 198 " 0.009 2.00e-02 2.50e+03 ... (remaining 1919 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 48 2.40 - 3.02: 7471 3.02 - 3.65: 17099 3.65 - 4.27: 24908 4.27 - 4.90: 41551 Nonbonded interactions: 91077 Sorted by model distance: nonbonded pdb=" O2B ATP A 401 " pdb="MG MG A 402 " model vdw 1.772 2.170 nonbonded pdb=" O2G ATP A 401 " pdb="MG MG A 402 " model vdw 1.780 2.170 nonbonded pdb=" O2G ATP B 402 " pdb="MG MG B 403 " model vdw 1.856 2.170 nonbonded pdb=" O2B ATP B 402 " pdb="MG MG B 403 " model vdw 1.858 2.170 nonbonded pdb=" OG1 THR B 45 " pdb="MG MG B 403 " model vdw 1.962 2.170 ... (remaining 91072 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' and (resid 16 through 190 or resid 210 through 339)) selection = (chain 'B' and resid 16 through 339) } ncs_group { reference = chain 'C' 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: 3.230 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: 0.080 Set scattering table: 0.120 Process input model: 30.450 Find NCS groups from input model: 0.410 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.004 0.036 10998 Z= 0.233 Angle : 0.533 6.983 14882 Z= 0.283 Chirality : 0.040 0.300 1637 Planarity : 0.004 0.060 1922 Dihedral : 14.647 88.037 4212 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 1.89 (0.24), residues: 1324 helix: 1.87 (0.18), residues: 861 sheet: 0.70 (0.63), residues: 67 loop : 0.08 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 96 HIS 0.005 0.001 HIS B 71 PHE 0.018 0.001 PHE B 173 TYR 0.024 0.001 TYR G1098 ARG 0.014 0.001 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8479 (tppt) REVERT: A 91 TYR cc_start: 0.8539 (m-80) cc_final: 0.7911 (m-80) REVERT: A 118 MET cc_start: 0.1844 (tpp) cc_final: 0.0711 (tmm) REVERT: A 130 MET cc_start: 0.6357 (mmp) cc_final: 0.5529 (mtp) REVERT: A 140 MET cc_start: 0.6098 (mtm) cc_final: 0.5893 (mtm) REVERT: A 258 GLU cc_start: 0.7352 (tp30) cc_final: 0.7030 (tp30) REVERT: A 323 ASP cc_start: 0.7994 (p0) cc_final: 0.7427 (t0) REVERT: B 140 MET cc_start: 0.6634 (mmp) cc_final: 0.6322 (mmm) REVERT: B 146 MET cc_start: 0.8080 (mtp) cc_final: 0.7871 (mtm) REVERT: C 91 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7913 (mm-30) REVERT: C 102 ASP cc_start: 0.7543 (t70) cc_final: 0.7095 (t0) REVERT: C 156 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7596 (mt-10) REVERT: C 158 ASN cc_start: 0.7803 (t0) cc_final: 0.6970 (t0) REVERT: C 208 ASN cc_start: 0.8714 (t0) cc_final: 0.8273 (t0) REVERT: C 209 LYS cc_start: 0.8882 (ptpt) cc_final: 0.8203 (ttpp) REVERT: C 226 ILE cc_start: 0.7488 (mm) cc_final: 0.7169 (mt) REVERT: C 228 ASP cc_start: 0.7013 (t0) cc_final: 0.6802 (t0) REVERT: D 1043 LEU cc_start: 0.8196 (mm) cc_final: 0.7879 (mm) REVERT: F 208 ASN cc_start: 0.8184 (t0) cc_final: 0.7886 (t0) REVERT: G 1026 ILE cc_start: 0.7820 (mt) cc_final: 0.7008 (mt) REVERT: G 1030 ARG cc_start: 0.7784 (mpp80) cc_final: 0.7498 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2489 time to fit residues: 68.5800 Evaluate side-chains 141 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 326 ASN B 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10998 Z= 0.224 Angle : 0.578 6.449 14882 Z= 0.302 Chirality : 0.042 0.150 1637 Planarity : 0.005 0.052 1922 Dihedral : 8.477 87.798 1513 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.01 % Allowed : 5.57 % Favored : 93.42 % 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: 2.15 (0.24), residues: 1324 helix: 2.03 (0.18), residues: 884 sheet: 0.64 (0.62), residues: 67 loop : 0.18 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 132 HIS 0.004 0.001 HIS A 166 PHE 0.015 0.002 PHE B 173 TYR 0.014 0.002 TYR G1042 ARG 0.009 0.001 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 TYR cc_start: 0.8426 (m-80) cc_final: 0.8098 (m-80) REVERT: A 118 MET cc_start: 0.1818 (tpp) cc_final: 0.0729 (tmm) REVERT: A 323 ASP cc_start: 0.8026 (p0) cc_final: 0.7314 (t0) REVERT: B 19 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7614 (mp0) REVERT: C 91 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7947 (mm-30) REVERT: C 121 GLU cc_start: 0.8146 (tp30) cc_final: 0.7851 (tp30) REVERT: C 158 ASN cc_start: 0.7869 (t0) cc_final: 0.7212 (t0) REVERT: C 208 ASN cc_start: 0.8665 (t0) cc_final: 0.7998 (t0) REVERT: C 226 ILE cc_start: 0.7609 (mm) cc_final: 0.7229 (mt) REVERT: D 1027 GLN cc_start: 0.8191 (mm110) cc_final: 0.7653 (tm-30) REVERT: D 1038 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6758 (mt) REVERT: D 1043 LEU cc_start: 0.8024 (mm) cc_final: 0.7697 (tt) REVERT: F 208 ASN cc_start: 0.8335 (t0) cc_final: 0.8037 (t0) REVERT: G 1030 ARG cc_start: 0.8015 (mpp80) cc_final: 0.7799 (ptm160) outliers start: 12 outliers final: 7 residues processed: 164 average time/residue: 0.2046 time to fit residues: 50.5208 Evaluate side-chains 144 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 1038 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 120 optimal weight: 0.0870 chunk 129 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 326 ASN ** F 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10998 Z= 0.212 Angle : 0.540 5.572 14882 Z= 0.281 Chirality : 0.040 0.175 1637 Planarity : 0.005 0.056 1922 Dihedral : 8.062 88.229 1513 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.43 % Allowed : 7.09 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.24), residues: 1324 helix: 2.00 (0.18), residues: 886 sheet: 0.41 (0.59), residues: 72 loop : 0.26 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1018 HIS 0.005 0.001 HIS B 166 PHE 0.015 0.002 PHE C 242 TYR 0.026 0.002 TYR C 275 ARG 0.006 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1848 (tpp) cc_final: 0.0688 (tmm) REVERT: A 147 ARG cc_start: 0.7356 (ttm110) cc_final: 0.6819 (mtt-85) REVERT: A 297 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8085 (mp) REVERT: A 323 ASP cc_start: 0.8032 (p0) cc_final: 0.7279 (t0) REVERT: B 19 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7609 (mp0) REVERT: C 91 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7898 (mm-30) REVERT: C 121 GLU cc_start: 0.8290 (tp30) cc_final: 0.7928 (tp30) REVERT: C 158 ASN cc_start: 0.7954 (t0) cc_final: 0.7262 (t0) REVERT: C 208 ASN cc_start: 0.8748 (t0) cc_final: 0.8059 (t0) REVERT: C 226 ILE cc_start: 0.7617 (mm) cc_final: 0.7234 (mt) REVERT: C 255 PHE cc_start: 0.8811 (t80) cc_final: 0.8314 (t80) REVERT: D 1038 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6757 (mt) REVERT: D 1042 TYR cc_start: 0.6796 (t80) cc_final: 0.6547 (t80) REVERT: D 1043 LEU cc_start: 0.8049 (mm) cc_final: 0.7703 (tt) REVERT: F 208 ASN cc_start: 0.8349 (t0) cc_final: 0.8055 (t0) outliers start: 17 outliers final: 9 residues processed: 165 average time/residue: 0.2043 time to fit residues: 50.7774 Evaluate side-chains 152 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 1038 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 326 ASN B 308 HIS B 331 GLN F 198 GLN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10998 Z= 0.369 Angle : 0.606 10.668 14882 Z= 0.314 Chirality : 0.043 0.154 1637 Planarity : 0.005 0.053 1922 Dihedral : 7.834 87.958 1513 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.28 % Allowed : 8.61 % Favored : 89.11 % 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: 1.78 (0.23), residues: 1324 helix: 1.73 (0.17), residues: 882 sheet: 0.45 (0.60), residues: 67 loop : 0.11 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 241 HIS 0.006 0.002 HIS C 165 PHE 0.015 0.002 PHE C 188 TYR 0.015 0.002 TYR F 182 ARG 0.006 0.001 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1751 (tpp) cc_final: 0.0660 (tmm) REVERT: A 147 ARG cc_start: 0.7381 (ttm110) cc_final: 0.6892 (mtt-85) REVERT: A 152 MET cc_start: 0.7654 (tmm) cc_final: 0.7422 (tmm) REVERT: A 323 ASP cc_start: 0.8008 (p0) cc_final: 0.7299 (t0) REVERT: B 19 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7533 (mp0) REVERT: B 23 LYS cc_start: 0.8367 (ttpt) cc_final: 0.8072 (ttpt) REVERT: B 82 SER cc_start: 0.8030 (m) cc_final: 0.7710 (p) REVERT: C 91 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7891 (mm-30) REVERT: C 106 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7962 (tm-30) REVERT: C 158 ASN cc_start: 0.7941 (t0) cc_final: 0.7262 (t0) REVERT: C 208 ASN cc_start: 0.8786 (t0) cc_final: 0.8181 (t0) REVERT: C 226 ILE cc_start: 0.7654 (mm) cc_final: 0.7263 (mt) REVERT: C 277 ASP cc_start: 0.8784 (m-30) cc_final: 0.8571 (m-30) REVERT: D 1043 LEU cc_start: 0.8114 (mm) cc_final: 0.7777 (tt) REVERT: F 208 ASN cc_start: 0.8446 (t0) cc_final: 0.8106 (t0) REVERT: F 269 ASP cc_start: 0.7764 (t0) cc_final: 0.7149 (t0) REVERT: G 1042 TYR cc_start: 0.7050 (t80) cc_final: 0.6659 (t80) outliers start: 27 outliers final: 20 residues processed: 167 average time/residue: 0.1994 time to fit residues: 50.5524 Evaluate side-chains 170 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 1014 VAL Chi-restraints excluded: chain G residue 1080 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 0 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1027 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10998 Z= 0.212 Angle : 0.550 13.384 14882 Z= 0.283 Chirality : 0.041 0.208 1637 Planarity : 0.005 0.055 1922 Dihedral : 7.435 78.030 1513 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.77 % Allowed : 10.80 % Favored : 87.43 % 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: 1.88 (0.23), residues: 1324 helix: 1.80 (0.18), residues: 885 sheet: 0.53 (0.61), residues: 67 loop : 0.18 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP F 241 HIS 0.003 0.001 HIS C 165 PHE 0.015 0.001 PHE C 188 TYR 0.014 0.001 TYR A 250 ARG 0.004 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1628 (tpp) cc_final: 0.0503 (tmm) REVERT: A 147 ARG cc_start: 0.7364 (ttm110) cc_final: 0.6866 (mtt-85) REVERT: A 152 MET cc_start: 0.7550 (tmm) cc_final: 0.7269 (tmm) REVERT: A 323 ASP cc_start: 0.8018 (p0) cc_final: 0.7253 (t0) REVERT: B 19 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7493 (mp0) REVERT: C 91 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7882 (mm-30) REVERT: C 106 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7944 (tm-30) REVERT: C 158 ASN cc_start: 0.7928 (t0) cc_final: 0.7254 (t0) REVERT: C 208 ASN cc_start: 0.8782 (t0) cc_final: 0.8097 (t0) REVERT: C 226 ILE cc_start: 0.7638 (mm) cc_final: 0.7242 (mt) REVERT: C 277 ASP cc_start: 0.8810 (m-30) cc_final: 0.8515 (m-30) REVERT: D 1043 LEU cc_start: 0.8068 (mm) cc_final: 0.7530 (tt) REVERT: F 208 ASN cc_start: 0.8423 (t0) cc_final: 0.8097 (t0) REVERT: F 241 TRP cc_start: 0.8356 (t60) cc_final: 0.8120 (t60) REVERT: G 1042 TYR cc_start: 0.6946 (t80) cc_final: 0.6690 (t80) outliers start: 21 outliers final: 16 residues processed: 165 average time/residue: 0.2037 time to fit residues: 51.2019 Evaluate side-chains 162 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain G residue 1089 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10998 Z= 0.322 Angle : 0.588 11.708 14882 Z= 0.302 Chirality : 0.042 0.180 1637 Planarity : 0.005 0.060 1922 Dihedral : 7.266 75.461 1513 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.36 % Allowed : 11.56 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.23), residues: 1324 helix: 1.68 (0.17), residues: 885 sheet: -0.08 (0.55), residues: 78 loop : 0.22 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 241 HIS 0.005 0.001 HIS F 165 PHE 0.021 0.002 PHE C 203 TYR 0.014 0.002 TYR A 250 ARG 0.005 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1593 (tpp) cc_final: 0.0531 (tmm) REVERT: A 127 GLN cc_start: 0.6194 (pt0) cc_final: 0.5601 (mm110) REVERT: A 147 ARG cc_start: 0.7373 (ttm110) cc_final: 0.6895 (mtt-85) REVERT: A 152 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7275 (tmm) REVERT: A 323 ASP cc_start: 0.7975 (p0) cc_final: 0.7261 (t0) REVERT: B 19 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7529 (mp0) REVERT: B 82 SER cc_start: 0.7992 (m) cc_final: 0.7675 (p) REVERT: C 91 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7892 (mm-30) REVERT: C 106 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7931 (tm-30) REVERT: C 158 ASN cc_start: 0.7959 (t0) cc_final: 0.7283 (t0) REVERT: C 208 ASN cc_start: 0.8828 (t0) cc_final: 0.8132 (t0) REVERT: C 226 ILE cc_start: 0.7692 (mm) cc_final: 0.7310 (mt) REVERT: C 277 ASP cc_start: 0.8820 (m-30) cc_final: 0.8412 (m-30) REVERT: D 1043 LEU cc_start: 0.8073 (mm) cc_final: 0.7684 (tt) REVERT: F 208 ASN cc_start: 0.8488 (t0) cc_final: 0.8175 (t0) REVERT: F 241 TRP cc_start: 0.8326 (t60) cc_final: 0.8041 (t60) outliers start: 28 outliers final: 23 residues processed: 167 average time/residue: 0.1997 time to fit residues: 50.1513 Evaluate side-chains 168 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain G residue 1019 VAL Chi-restraints excluded: chain G residue 1089 LEU Chi-restraints excluded: chain G residue 1100 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 ASN A 331 GLN F 198 GLN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1027 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10998 Z= 0.212 Angle : 0.549 11.120 14882 Z= 0.282 Chirality : 0.040 0.180 1637 Planarity : 0.005 0.060 1922 Dihedral : 6.965 67.744 1513 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.28 % Allowed : 12.74 % Favored : 84.98 % 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: 1.83 (0.23), residues: 1324 helix: 1.78 (0.17), residues: 884 sheet: -0.01 (0.56), residues: 78 loop : 0.23 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 241 HIS 0.003 0.001 HIS F 168 PHE 0.023 0.002 PHE F 232 TYR 0.013 0.001 TYR A 250 ARG 0.003 0.000 ARG B 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1519 (tpp) cc_final: 0.0453 (tmm) REVERT: A 127 GLN cc_start: 0.6085 (pt0) cc_final: 0.5501 (mm-40) REVERT: A 147 ARG cc_start: 0.7326 (ttm110) cc_final: 0.6837 (mtt-85) REVERT: A 152 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7221 (tmm) REVERT: A 323 ASP cc_start: 0.7994 (p0) cc_final: 0.7180 (t0) REVERT: B 19 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7510 (mp0) REVERT: B 82 SER cc_start: 0.7975 (m) cc_final: 0.7657 (p) REVERT: C 91 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7838 (mm-30) REVERT: C 121 GLU cc_start: 0.8256 (tp30) cc_final: 0.8005 (tp30) REVERT: C 158 ASN cc_start: 0.7952 (t0) cc_final: 0.7279 (t0) REVERT: C 208 ASN cc_start: 0.8807 (t0) cc_final: 0.8112 (t0) REVERT: C 226 ILE cc_start: 0.7697 (mm) cc_final: 0.7322 (mt) REVERT: C 277 ASP cc_start: 0.8854 (m-30) cc_final: 0.8389 (m-30) REVERT: D 1043 LEU cc_start: 0.8073 (mm) cc_final: 0.7809 (tt) REVERT: F 164 TYR cc_start: 0.8668 (t80) cc_final: 0.8276 (t80) REVERT: F 208 ASN cc_start: 0.8491 (t0) cc_final: 0.8201 (t0) REVERT: F 241 TRP cc_start: 0.8379 (t60) cc_final: 0.8113 (t60) outliers start: 27 outliers final: 21 residues processed: 169 average time/residue: 0.1959 time to fit residues: 50.1944 Evaluate side-chains 168 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain G residue 1019 VAL Chi-restraints excluded: chain G residue 1089 LEU Chi-restraints excluded: chain G residue 1100 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.0040 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 ASN F 238 ASN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10998 Z= 0.235 Angle : 0.561 11.861 14882 Z= 0.287 Chirality : 0.041 0.174 1637 Planarity : 0.005 0.058 1922 Dihedral : 6.901 66.623 1513 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.62 % Allowed : 12.66 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.24), residues: 1324 helix: 1.77 (0.17), residues: 885 sheet: -0.16 (0.56), residues: 80 loop : 0.21 (0.35), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 241 HIS 0.003 0.001 HIS F 165 PHE 0.018 0.002 PHE F 232 TYR 0.013 0.001 TYR A 250 ARG 0.004 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1523 (tpp) cc_final: 0.0458 (tmm) REVERT: A 127 GLN cc_start: 0.6112 (pt0) cc_final: 0.5550 (mm110) REVERT: A 147 ARG cc_start: 0.7326 (ttm110) cc_final: 0.6857 (mtt-85) REVERT: A 152 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7188 (tmm) REVERT: A 323 ASP cc_start: 0.7974 (p0) cc_final: 0.7170 (t0) REVERT: B 19 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7505 (mp0) REVERT: B 82 SER cc_start: 0.7983 (m) cc_final: 0.7660 (p) REVERT: C 91 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7817 (mm-30) REVERT: C 121 GLU cc_start: 0.8297 (tp30) cc_final: 0.8022 (tp30) REVERT: C 158 ASN cc_start: 0.7946 (t0) cc_final: 0.7267 (t0) REVERT: C 208 ASN cc_start: 0.8809 (t0) cc_final: 0.8120 (t0) REVERT: C 226 ILE cc_start: 0.7693 (mm) cc_final: 0.7314 (mt) REVERT: C 277 ASP cc_start: 0.8815 (m-30) cc_final: 0.8336 (m-30) REVERT: F 164 TYR cc_start: 0.8661 (t80) cc_final: 0.8210 (t80) REVERT: F 208 ASN cc_start: 0.8506 (t0) cc_final: 0.8214 (t0) REVERT: F 241 TRP cc_start: 0.8389 (t60) cc_final: 0.8125 (t60) outliers start: 31 outliers final: 26 residues processed: 166 average time/residue: 0.2012 time to fit residues: 50.9628 Evaluate side-chains 168 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain G residue 1014 VAL Chi-restraints excluded: chain G residue 1019 VAL Chi-restraints excluded: chain G residue 1089 LEU Chi-restraints excluded: chain G residue 1100 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.1980 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 125 optimal weight: 0.0000 chunk 76 optimal weight: 0.8980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10998 Z= 0.194 Angle : 0.554 12.444 14882 Z= 0.283 Chirality : 0.040 0.139 1637 Planarity : 0.005 0.057 1922 Dihedral : 6.681 63.278 1513 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.45 % Allowed : 12.91 % Favored : 84.64 % 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: 1.84 (0.24), residues: 1324 helix: 1.81 (0.18), residues: 887 sheet: -0.36 (0.55), residues: 85 loop : 0.26 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 241 HIS 0.003 0.001 HIS C 223 PHE 0.015 0.001 PHE C 203 TYR 0.013 0.001 TYR A 250 ARG 0.003 0.000 ARG C 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1510 (tpp) cc_final: 0.0437 (tmm) REVERT: A 127 GLN cc_start: 0.6136 (pt0) cc_final: 0.5575 (mm110) REVERT: A 147 ARG cc_start: 0.7239 (ttm110) cc_final: 0.6782 (mtt-85) REVERT: A 152 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7181 (tmm) REVERT: A 323 ASP cc_start: 0.7949 (p0) cc_final: 0.7155 (t0) REVERT: B 19 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7513 (mp0) REVERT: C 91 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7821 (mm-30) REVERT: C 121 GLU cc_start: 0.8279 (tp30) cc_final: 0.8015 (tp30) REVERT: C 158 ASN cc_start: 0.7938 (t0) cc_final: 0.7225 (t0) REVERT: C 226 ILE cc_start: 0.7671 (mm) cc_final: 0.7305 (mt) REVERT: C 277 ASP cc_start: 0.8808 (m-30) cc_final: 0.8325 (m-30) REVERT: F 208 ASN cc_start: 0.8486 (t0) cc_final: 0.8195 (t0) REVERT: F 241 TRP cc_start: 0.8383 (t60) cc_final: 0.8148 (t60) outliers start: 29 outliers final: 22 residues processed: 170 average time/residue: 0.1939 time to fit residues: 49.8640 Evaluate side-chains 164 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain G residue 1019 VAL Chi-restraints excluded: chain G residue 1089 LEU Chi-restraints excluded: chain G residue 1100 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.9990 chunk 87 optimal weight: 0.0040 chunk 131 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN F 168 HIS F 261 GLN G1027 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10998 Z= 0.202 Angle : 0.570 12.915 14882 Z= 0.289 Chirality : 0.041 0.253 1637 Planarity : 0.005 0.090 1922 Dihedral : 6.622 63.043 1513 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.28 % Allowed : 13.33 % Favored : 84.39 % 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: 1.80 (0.24), residues: 1324 helix: 1.80 (0.18), residues: 886 sheet: -0.34 (0.55), residues: 85 loop : 0.20 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 241 HIS 0.003 0.001 HIS C 223 PHE 0.014 0.001 PHE C 203 TYR 0.012 0.001 TYR A 250 ARG 0.014 0.000 ARG G1030 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.1523 (tpp) cc_final: 0.0417 (tmm) REVERT: A 125 MET cc_start: 0.5298 (tpt) cc_final: 0.4669 (ptt) REVERT: A 127 GLN cc_start: 0.6176 (pt0) cc_final: 0.5608 (mm110) REVERT: A 147 ARG cc_start: 0.7234 (ttm110) cc_final: 0.6814 (mtt-85) REVERT: A 152 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7214 (tmm) REVERT: A 323 ASP cc_start: 0.7964 (p0) cc_final: 0.7117 (t0) REVERT: B 19 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7514 (mp0) REVERT: C 91 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7789 (mm-30) REVERT: C 121 GLU cc_start: 0.8293 (tp30) cc_final: 0.8022 (tp30) REVERT: C 158 ASN cc_start: 0.7941 (t0) cc_final: 0.7234 (t0) REVERT: C 226 ILE cc_start: 0.7694 (mm) cc_final: 0.7343 (mt) REVERT: C 277 ASP cc_start: 0.8800 (m-30) cc_final: 0.8311 (m-30) REVERT: F 164 TYR cc_start: 0.8684 (t80) cc_final: 0.8376 (t80) REVERT: F 208 ASN cc_start: 0.8487 (t0) cc_final: 0.8199 (t0) REVERT: F 241 TRP cc_start: 0.8386 (t60) cc_final: 0.8150 (t60) outliers start: 27 outliers final: 25 residues processed: 168 average time/residue: 0.2095 time to fit residues: 52.7890 Evaluate side-chains 169 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain D residue 1046 MET Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 276 LEU Chi-restraints excluded: chain G residue 1019 VAL Chi-restraints excluded: chain G residue 1089 LEU Chi-restraints excluded: chain G residue 1100 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN F 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.140418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.102587 restraints weight = 20067.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.102313 restraints weight = 13346.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.102723 restraints weight = 9255.049| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10998 Z= 0.216 Angle : 0.577 13.340 14882 Z= 0.294 Chirality : 0.041 0.239 1637 Planarity : 0.005 0.083 1922 Dihedral : 6.585 62.835 1513 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.45 % Allowed : 13.59 % Favored : 83.97 % 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: 1.78 (0.24), residues: 1324 helix: 1.80 (0.18), residues: 886 sheet: -0.45 (0.55), residues: 86 loop : 0.17 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D1018 HIS 0.003 0.001 HIS C 223 PHE 0.029 0.001 PHE C 112 TYR 0.016 0.002 TYR F 275 ARG 0.009 0.000 ARG A 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2245.92 seconds wall clock time: 42 minutes 48.73 seconds (2568.73 seconds total)