Starting phenix.real_space_refine on Tue Apr 29 01:17:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9as8_43808/04_2025/9as8_43808.cif Found real_map, /net/cci-nas-00/data/ceres_data/9as8_43808/04_2025/9as8_43808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9as8_43808/04_2025/9as8_43808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9as8_43808/04_2025/9as8_43808.map" model { file = "/net/cci-nas-00/data/ceres_data/9as8_43808/04_2025/9as8_43808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9as8_43808/04_2025/9as8_43808.cif" } resolution = 2.54 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= 0.115 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 54 5.16 5 C 5286 2.51 5 N 1390 2.21 5 O 1527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8257 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1972 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1645 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 4, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 118 Chain: "C" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2541 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 376 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1708 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'91Q': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.81, per 1000 atoms: 0.70 Number of scatterers: 8257 At special positions: 0 Unit cell: (88, 117.92, 128.48, 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 54 16.00 O 1527 8.00 N 1390 7.00 C 5286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 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=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 991.7 milliseconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 16 sheets defined 38.3% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 81 through 102 removed outlier: 3.548A pdb=" N GLU A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 removed outlier: 3.830A pdb=" N GLN A 106 " --> pdb=" O LYS A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 107 through 127 removed outlier: 3.634A pdb=" N PHE A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 146 through 179 removed outlier: 4.219A pdb=" N VAL A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 187 Processing helix chain 'A' and resid 188 through 208 Processing helix chain 'A' and resid 208 through 215 removed outlier: 4.157A pdb=" N VAL A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 215 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 220 Processing helix chain 'A' and resid 231 through 241 removed outlier: 3.698A pdb=" N SER A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 261 Processing helix chain 'A' and resid 314 through 349 removed outlier: 3.524A pdb=" N GLU A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 3.613A pdb=" N VAL A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 382 removed outlier: 3.611A pdb=" N VAL A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TRP A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 384 through 392 Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.863A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 101 removed outlier: 3.542A pdb=" N ILE B 97 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.977A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.951A pdb=" N ALA B 168 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 164 through 169' Processing helix chain 'B' and resid 184 through 205 removed outlier: 3.587A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 243 Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 10 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 222 through 223 Processing sheet with id=AA2, first strand: chain 'B' and resid 70 through 76 removed outlier: 6.814A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.591A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.591A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.799A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.728A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.654A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.566A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.662A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.660A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 33 through 35 removed outlier: 4.512A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 49 through 51 Processing sheet with id=AB5, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB6, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.743A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.743A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.69 Time building geometry restraints manager: 2.66 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: 2642 1.34 - 1.46: 2030 1.46 - 1.58: 3675 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 8426 Sorted by residual: bond pdb=" N ASP C 247 " pdb=" CA ASP C 247 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.31e-02 5.83e+03 8.24e+00 bond pdb=" N VAL E 137 " pdb=" CA VAL E 137 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.19e-02 7.06e+03 7.89e+00 bond pdb=" N ASP C 163 " pdb=" CA ASP C 163 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.25e-02 6.40e+03 7.85e+00 bond pdb=" N ASP C 333 " pdb=" CA ASP C 333 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.32e-02 5.74e+03 7.52e+00 bond pdb=" N ASN A 384 " pdb=" CA ASN A 384 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.33e-02 5.65e+03 6.45e+00 ... (remaining 8421 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 10956 1.76 - 3.52: 422 3.52 - 5.28: 71 5.28 - 7.03: 22 7.03 - 8.79: 3 Bond angle restraints: 11474 Sorted by residual: angle pdb=" N ASP C 247 " pdb=" CA ASP C 247 " pdb=" C ASP C 247 " ideal model delta sigma weight residual 113.18 104.39 8.79 1.21e+00 6.83e-01 5.28e+01 angle pdb=" CA ASP C 247 " pdb=" CB ASP C 247 " pdb=" CG ASP C 247 " ideal model delta sigma weight residual 112.60 116.81 -4.21 1.00e+00 1.00e+00 1.77e+01 angle pdb=" CA ASP C 333 " pdb=" CB ASP C 333 " pdb=" CG ASP C 333 " ideal model delta sigma weight residual 112.60 116.70 -4.10 1.00e+00 1.00e+00 1.68e+01 angle pdb=" N ASP C 163 " pdb=" CA ASP C 163 " pdb=" C ASP C 163 " ideal model delta sigma weight residual 112.93 108.88 4.05 1.12e+00 7.97e-01 1.31e+01 angle pdb=" C ASP C 247 " pdb=" CA ASP C 247 " pdb=" CB ASP C 247 " ideal model delta sigma weight residual 109.95 117.00 -7.05 1.99e+00 2.53e-01 1.25e+01 ... (remaining 11469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.73: 4553 22.73 - 45.47: 323 45.47 - 68.20: 56 68.20 - 90.93: 4 90.93 - 113.66: 2 Dihedral angle restraints: 4938 sinusoidal: 1746 harmonic: 3192 Sorted by residual: dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 55.46 37.54 1 1.00e+01 1.00e-02 1.99e+01 dihedral pdb=" C2 91Q A 501 " pdb=" C3 91Q A 501 " pdb=" N1 91Q A 501 " pdb=" C4 91Q A 501 " ideal model delta sinusoidal sigma weight residual 73.77 -39.89 113.66 1 3.00e+01 1.11e-03 1.49e+01 dihedral pdb=" C1 91Q A 501 " pdb=" C3 91Q A 501 " pdb=" N1 91Q A 501 " pdb=" C4 91Q A 501 " ideal model delta sinusoidal sigma weight residual 198.00 87.95 110.05 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 4935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 868 0.037 - 0.073: 342 0.073 - 0.110: 94 0.110 - 0.146: 45 0.146 - 0.183: 6 Chirality restraints: 1355 Sorted by residual: chirality pdb=" CA VAL E 137 " pdb=" N VAL E 137 " pdb=" C VAL E 137 " pdb=" CB VAL E 137 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.36e-01 chirality pdb=" CA GLU C 130 " pdb=" N GLU C 130 " pdb=" C GLU C 130 " pdb=" CB GLU C 130 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA GLU E 222 " pdb=" N GLU E 222 " pdb=" C GLU E 222 " pdb=" CB GLU E 222 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 1352 not shown) Planarity restraints: 1445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 141 " -0.066 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO A 142 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 246 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C ASP C 246 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP C 246 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP C 247 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 22 " 0.244 9.50e-02 1.11e+02 1.09e-01 7.38e+00 pdb=" NE ARG C 22 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 22 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 22 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 22 " 0.008 2.00e-02 2.50e+03 ... (remaining 1442 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 603 2.74 - 3.28: 8101 3.28 - 3.82: 13876 3.82 - 4.36: 16844 4.36 - 4.90: 29409 Nonbonded interactions: 68833 Sorted by model distance: nonbonded pdb=" O SER A 392 " pdb=" OG SER A 392 " model vdw 2.198 3.040 nonbonded pdb=" OG SER C 108 " pdb=" OD1 ASP C 154 " model vdw 2.200 3.040 nonbonded pdb=" O ASP C 333 " pdb=" OG SER C 334 " model vdw 2.219 3.040 nonbonded pdb=" O GLY E 9 " pdb=" NH1 ARG E 18 " model vdw 2.296 3.120 nonbonded pdb=" O ARG B 135 " pdb=" ND1 HIS B 209 " model vdw 2.296 3.120 ... (remaining 68828 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: 2.010 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.410 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 : 0.005 0.050 8429 Z= 0.258 Angle : 0.831 8.793 11480 Z= 0.478 Chirality : 0.046 0.183 1355 Planarity : 0.007 0.109 1445 Dihedral : 15.959 113.662 2865 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.71 % Allowed : 22.44 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1080 helix: 1.80 (0.26), residues: 384 sheet: 0.65 (0.30), residues: 280 loop : -0.03 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 336 HIS 0.003 0.001 HIS C 91 PHE 0.021 0.002 PHE E 27 TYR 0.017 0.002 TYR E 59 ARG 0.006 0.001 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.16002 ( 435) hydrogen bonds : angle 6.39517 ( 1224) SS BOND : bond 0.00437 ( 3) SS BOND : angle 0.97567 ( 6) covalent geometry : bond 0.00483 ( 8426) covalent geometry : angle 0.83122 (11474) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 1.220 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 133 average time/residue: 1.3659 time to fit residues: 194.9340 Evaluate side-chains 107 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 21 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 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 106 GLN A 107 ASN B 80 ASN E 13 GLN E 35 HIS E 39 GLN E 167 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.209985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.156255 restraints weight = 7365.093| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.57 r_work: 0.3613 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8429 Z= 0.196 Angle : 0.656 7.052 11480 Z= 0.349 Chirality : 0.045 0.215 1355 Planarity : 0.005 0.073 1445 Dihedral : 6.415 78.050 1180 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.58 % Allowed : 20.80 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.13 (0.25), residues: 1080 helix: 1.80 (0.26), residues: 391 sheet: 0.75 (0.30), residues: 278 loop : -0.20 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 367 HIS 0.012 0.002 HIS B 209 PHE 0.023 0.003 PHE C 151 TYR 0.023 0.003 TYR A 139 ARG 0.005 0.001 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.04547 ( 435) hydrogen bonds : angle 4.93017 ( 1224) SS BOND : bond 0.00766 ( 3) SS BOND : angle 1.07757 ( 6) covalent geometry : bond 0.00436 ( 8426) covalent geometry : angle 0.65549 (11474) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 317 ASN cc_start: 0.6881 (m110) cc_final: 0.6388 (m110) REVERT: A 341 ILE cc_start: 0.5975 (OUTLIER) cc_final: 0.5089 (mp) REVERT: C 79 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7522 (mp) REVERT: C 217 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7418 (pmm) outliers start: 39 outliers final: 17 residues processed: 146 average time/residue: 1.0914 time to fit residues: 170.6079 Evaluate side-chains 119 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN E 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.213659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.161744 restraints weight = 7548.669| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.52 r_work: 0.3685 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8429 Z= 0.110 Angle : 0.537 5.971 11480 Z= 0.283 Chirality : 0.041 0.145 1355 Planarity : 0.004 0.062 1445 Dihedral : 5.927 80.486 1179 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.64 % Allowed : 22.44 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.25), residues: 1080 helix: 2.26 (0.27), residues: 385 sheet: 0.86 (0.30), residues: 266 loop : -0.16 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 169 HIS 0.007 0.001 HIS B 209 PHE 0.016 0.001 PHE C 199 TYR 0.018 0.001 TYR E 59 ARG 0.006 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 435) hydrogen bonds : angle 4.38585 ( 1224) SS BOND : bond 0.00421 ( 3) SS BOND : angle 0.75798 ( 6) covalent geometry : bond 0.00228 ( 8426) covalent geometry : angle 0.53655 (11474) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.7431 (mmt) cc_final: 0.7223 (mmt) REVERT: A 317 ASN cc_start: 0.6774 (m110) cc_final: 0.6382 (m110) REVERT: A 341 ILE cc_start: 0.6002 (OUTLIER) cc_final: 0.5087 (mp) REVERT: B 194 ARG cc_start: 0.6387 (ttt-90) cc_final: 0.5860 (ttm110) REVERT: C 79 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7292 (mp) REVERT: C 138 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: D 22 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6481 (mt-10) REVERT: E 222 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7201 (pp20) outliers start: 31 outliers final: 13 residues processed: 132 average time/residue: 1.1217 time to fit residues: 158.1883 Evaluate side-chains 117 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.0000 chunk 38 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN E 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.212559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.161712 restraints weight = 7478.079| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.60 r_work: 0.3642 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8429 Z= 0.114 Angle : 0.537 6.388 11480 Z= 0.283 Chirality : 0.041 0.142 1355 Planarity : 0.004 0.058 1445 Dihedral : 5.814 76.796 1179 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.47 % Allowed : 22.68 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.52 (0.25), residues: 1080 helix: 2.39 (0.27), residues: 385 sheet: 0.84 (0.30), residues: 266 loop : -0.13 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 63 HIS 0.007 0.001 HIS B 209 PHE 0.016 0.001 PHE C 199 TYR 0.016 0.001 TYR E 59 ARG 0.003 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 435) hydrogen bonds : angle 4.27608 ( 1224) SS BOND : bond 0.00515 ( 3) SS BOND : angle 0.77826 ( 6) covalent geometry : bond 0.00242 ( 8426) covalent geometry : angle 0.53653 (11474) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 317 ASN cc_start: 0.6802 (m110) cc_final: 0.6446 (m110) REVERT: A 341 ILE cc_start: 0.6052 (OUTLIER) cc_final: 0.5113 (mp) REVERT: C 79 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7315 (mp) REVERT: C 138 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7500 (mt-10) REVERT: D 22 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6484 (mt-10) outliers start: 38 outliers final: 18 residues processed: 139 average time/residue: 1.0156 time to fit residues: 151.8958 Evaluate side-chains 123 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.210020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.158564 restraints weight = 7457.045| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.69 r_work: 0.3612 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8429 Z= 0.141 Angle : 0.576 7.768 11480 Z= 0.304 Chirality : 0.042 0.143 1355 Planarity : 0.004 0.054 1445 Dihedral : 5.948 74.561 1179 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.11 % Allowed : 22.56 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.42 (0.25), residues: 1080 helix: 2.30 (0.26), residues: 385 sheet: 0.75 (0.31), residues: 268 loop : -0.15 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 63 HIS 0.008 0.001 HIS B 209 PHE 0.018 0.002 PHE C 199 TYR 0.013 0.002 TYR A 139 ARG 0.005 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 435) hydrogen bonds : angle 4.38320 ( 1224) SS BOND : bond 0.00639 ( 3) SS BOND : angle 0.92201 ( 6) covalent geometry : bond 0.00309 ( 8426) covalent geometry : angle 0.57568 (11474) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.929 Fit side-chains REVERT: A 341 ILE cc_start: 0.6090 (OUTLIER) cc_final: 0.5141 (mp) REVERT: C 79 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7437 (mp) REVERT: C 138 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7546 (mt-10) REVERT: D 22 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6501 (mt-10) outliers start: 35 outliers final: 23 residues processed: 135 average time/residue: 1.0165 time to fit residues: 147.6440 Evaluate side-chains 128 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 107 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 ASN C 239 ASN E 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.210087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.158057 restraints weight = 7442.759| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.66 r_work: 0.3607 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8429 Z= 0.137 Angle : 0.569 6.958 11480 Z= 0.301 Chirality : 0.042 0.182 1355 Planarity : 0.004 0.052 1445 Dihedral : 5.915 75.142 1179 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.94 % Allowed : 22.56 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.39 (0.25), residues: 1080 helix: 2.31 (0.26), residues: 385 sheet: 0.72 (0.30), residues: 268 loop : -0.18 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 63 HIS 0.007 0.001 HIS B 209 PHE 0.018 0.002 PHE C 199 TYR 0.013 0.002 TYR E 178 ARG 0.006 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.03693 ( 435) hydrogen bonds : angle 4.34166 ( 1224) SS BOND : bond 0.00619 ( 3) SS BOND : angle 0.92458 ( 6) covalent geometry : bond 0.00299 ( 8426) covalent geometry : angle 0.56833 (11474) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 0.966 Fit side-chains REVERT: A 203 SER cc_start: 0.5834 (t) cc_final: 0.5452 (m) REVERT: A 341 ILE cc_start: 0.6055 (OUTLIER) cc_final: 0.5134 (mp) REVERT: C 79 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7397 (mp) REVERT: C 138 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7541 (mt-10) REVERT: D 22 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6501 (mt-10) outliers start: 42 outliers final: 25 residues processed: 144 average time/residue: 1.0534 time to fit residues: 163.5264 Evaluate side-chains 135 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 13 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 ASN E 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.205231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.149923 restraints weight = 7509.900| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.82 r_work: 0.3543 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8429 Z= 0.229 Angle : 0.687 9.199 11480 Z= 0.362 Chirality : 0.046 0.239 1355 Planarity : 0.005 0.053 1445 Dihedral : 6.409 74.443 1179 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.47 % Allowed : 23.15 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.13 (0.25), residues: 1080 helix: 1.96 (0.26), residues: 385 sheet: 0.68 (0.30), residues: 285 loop : -0.30 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 63 HIS 0.010 0.002 HIS B 209 PHE 0.023 0.003 PHE C 151 TYR 0.016 0.003 TYR E 103 ARG 0.005 0.001 ARG E 179 Details of bonding type rmsd hydrogen bonds : bond 0.04578 ( 435) hydrogen bonds : angle 4.72865 ( 1224) SS BOND : bond 0.00915 ( 3) SS BOND : angle 1.30189 ( 6) covalent geometry : bond 0.00522 ( 8426) covalent geometry : angle 0.68644 (11474) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.925 Fit side-chains REVERT: A 121 MET cc_start: 0.3863 (tpt) cc_final: 0.3639 (tpp) REVERT: A 147 LEU cc_start: 0.6652 (mm) cc_final: 0.5911 (pp) REVERT: A 203 SER cc_start: 0.5806 (t) cc_final: 0.5384 (m) REVERT: A 341 ILE cc_start: 0.6093 (OUTLIER) cc_final: 0.5656 (mt) REVERT: A 385 LYS cc_start: 0.6882 (tptt) cc_final: 0.6563 (ttmt) REVERT: C 79 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7602 (mp) REVERT: C 138 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: D 22 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6551 (mt-10) outliers start: 38 outliers final: 24 residues processed: 147 average time/residue: 1.0333 time to fit residues: 164.2890 Evaluate side-chains 139 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 ASN E 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.207870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.152368 restraints weight = 7568.927| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.91 r_work: 0.3579 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8429 Z= 0.142 Angle : 0.587 8.190 11480 Z= 0.309 Chirality : 0.042 0.145 1355 Planarity : 0.004 0.048 1445 Dihedral : 6.129 78.845 1179 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.23 % Allowed : 24.21 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.25 (0.25), residues: 1080 helix: 2.16 (0.26), residues: 385 sheet: 0.69 (0.30), residues: 280 loop : -0.30 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 63 HIS 0.008 0.001 HIS B 209 PHE 0.019 0.002 PHE C 151 TYR 0.014 0.002 TYR E 178 ARG 0.006 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 435) hydrogen bonds : angle 4.41633 ( 1224) SS BOND : bond 0.00636 ( 3) SS BOND : angle 0.94997 ( 6) covalent geometry : bond 0.00312 ( 8426) covalent geometry : angle 0.58654 (11474) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.940 Fit side-chains REVERT: A 121 MET cc_start: 0.3854 (tpt) cc_final: 0.3634 (tpp) REVERT: A 147 LEU cc_start: 0.6697 (mm) cc_final: 0.5935 (pp) REVERT: A 203 SER cc_start: 0.5731 (t) cc_final: 0.5405 (m) REVERT: A 341 ILE cc_start: 0.6042 (OUTLIER) cc_final: 0.5415 (mt) REVERT: A 385 LYS cc_start: 0.6852 (tptt) cc_final: 0.6538 (ttmt) REVERT: C 79 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7546 (mp) REVERT: C 138 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: D 22 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6471 (mt-10) outliers start: 36 outliers final: 23 residues processed: 143 average time/residue: 1.0820 time to fit residues: 166.6756 Evaluate side-chains 138 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.208711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.153383 restraints weight = 7587.054| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.91 r_work: 0.3592 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8429 Z= 0.133 Angle : 0.579 7.992 11480 Z= 0.303 Chirality : 0.042 0.141 1355 Planarity : 0.004 0.047 1445 Dihedral : 5.752 77.681 1177 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.88 % Allowed : 25.03 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.34 (0.25), residues: 1080 helix: 2.30 (0.26), residues: 385 sheet: 0.68 (0.30), residues: 280 loop : -0.27 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 63 HIS 0.007 0.001 HIS B 209 PHE 0.017 0.002 PHE C 151 TYR 0.015 0.002 TYR E 178 ARG 0.007 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.03665 ( 435) hydrogen bonds : angle 4.32336 ( 1224) SS BOND : bond 0.00612 ( 3) SS BOND : angle 0.92144 ( 6) covalent geometry : bond 0.00288 ( 8426) covalent geometry : angle 0.57893 (11474) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 0.956 Fit side-chains REVERT: A 80 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6231 (pp) REVERT: A 121 MET cc_start: 0.3917 (tpt) cc_final: 0.3716 (tpp) REVERT: A 147 LEU cc_start: 0.6584 (mm) cc_final: 0.5975 (pp) REVERT: A 203 SER cc_start: 0.5688 (t) cc_final: 0.5374 (m) REVERT: A 341 ILE cc_start: 0.5950 (OUTLIER) cc_final: 0.5344 (mt) REVERT: A 385 LYS cc_start: 0.6829 (tptt) cc_final: 0.6526 (ttmt) REVERT: C 79 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7417 (mp) REVERT: C 101 MET cc_start: 0.8211 (mtp) cc_final: 0.7776 (mpp) REVERT: C 138 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7638 (mt-10) REVERT: D 22 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6478 (mt-10) outliers start: 33 outliers final: 24 residues processed: 135 average time/residue: 1.0069 time to fit residues: 146.3764 Evaluate side-chains 140 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.208085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.152895 restraints weight = 7494.454| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.94 r_work: 0.3592 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8429 Z= 0.145 Angle : 0.599 8.004 11480 Z= 0.313 Chirality : 0.043 0.164 1355 Planarity : 0.004 0.047 1445 Dihedral : 5.803 76.784 1177 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.76 % Allowed : 25.26 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.32 (0.25), residues: 1080 helix: 2.27 (0.26), residues: 385 sheet: 0.67 (0.30), residues: 280 loop : -0.27 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 63 HIS 0.008 0.001 HIS B 209 PHE 0.018 0.002 PHE C 151 TYR 0.013 0.002 TYR E 178 ARG 0.006 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 435) hydrogen bonds : angle 4.38198 ( 1224) SS BOND : bond 0.00650 ( 3) SS BOND : angle 0.99054 ( 6) covalent geometry : bond 0.00320 ( 8426) covalent geometry : angle 0.59825 (11474) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.898 Fit side-chains REVERT: A 80 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6362 (pp) REVERT: A 147 LEU cc_start: 0.6560 (mm) cc_final: 0.6003 (pp) REVERT: A 203 SER cc_start: 0.5710 (t) cc_final: 0.5409 (m) REVERT: A 341 ILE cc_start: 0.5884 (OUTLIER) cc_final: 0.5478 (mt) REVERT: A 385 LYS cc_start: 0.6961 (tptt) cc_final: 0.6652 (tttt) REVERT: C 79 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7455 (mp) REVERT: C 138 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: D 22 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6510 (mt-10) outliers start: 32 outliers final: 25 residues processed: 135 average time/residue: 1.0127 time to fit residues: 146.9238 Evaluate side-chains 139 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 22 GLU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 138 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 37 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.205684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.149952 restraints weight = 7579.163| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.87 r_work: 0.3557 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8429 Z= 0.207 Angle : 0.673 8.469 11480 Z= 0.353 Chirality : 0.045 0.217 1355 Planarity : 0.004 0.048 1445 Dihedral : 6.159 77.081 1177 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.64 % Allowed : 25.50 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.11 (0.25), residues: 1080 helix: 2.01 (0.26), residues: 385 sheet: 0.62 (0.30), residues: 280 loop : -0.35 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 63 HIS 0.009 0.002 HIS B 209 PHE 0.022 0.002 PHE C 151 TYR 0.015 0.002 TYR E 103 ARG 0.005 0.001 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 435) hydrogen bonds : angle 4.65284 ( 1224) SS BOND : bond 0.00854 ( 3) SS BOND : angle 1.27489 ( 6) covalent geometry : bond 0.00470 ( 8426) covalent geometry : angle 0.67253 (11474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8408.73 seconds wall clock time: 144 minutes 54.44 seconds (8694.44 seconds total)