Starting phenix.real_space_refine on Sun May 11 16:44:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9as8_43808/05_2025/9as8_43808.cif Found real_map, /net/cci-nas-00/data/ceres_data/9as8_43808/05_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_43808/05_2025/9as8_43808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9as8_43808/05_2025/9as8_43808.map" model { file = "/net/cci-nas-00/data/ceres_data/9as8_43808/05_2025/9as8_43808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9as8_43808/05_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-5687/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: 5.76, 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: 2.21 Conformation dependent library (CDL) restraints added in 980.9 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: 0.98 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: 2.55 Time building geometry restraints manager: 2.48 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: 1.860 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.350 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.170 ------------------------------------------------------------------------------- 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 : 0.947 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 133 average time/residue: 1.1295 time to fit residues: 160.7630 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 : 0.894 ------------------------------------------------------------------------------- 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 = 77)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.158766 restraints weight = 7365.095| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.53 r_work: 0.3618 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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: 0.6908 (m110) cc_final: 0.6429 (m110) REVERT: A 341 ILE cc_start: 0.5903 (OUTLIER) cc_final: 0.5039 (mp) REVERT: C 79 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7524 (mp) REVERT: C 217 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7430 (pmm) outliers start: 39 outliers final: 17 residues processed: 146 average time/residue: 1.0482 time to fit residues: 164.0229 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 : 0.876 ------------------------------------------------------------------------------- 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: 0.1980 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 45 optimal weight: 0.0060 chunk 6 optimal weight: 0.0870 chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 = 0.4349 r_free = 0.4349 target = 0.214157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.167444 restraints weight = 7549.424| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 1.52 r_work: 0.3673 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8429 Z= 0.106 Angle : 0.532 5.790 11480 Z= 0.280 Chirality : 0.041 0.145 1355 Planarity : 0.004 0.063 1445 Dihedral : 5.911 80.662 1179 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.53 % Allowed : 22.68 % Favored : 73.80 % 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: 1.44 (0.25), residues: 1080 helix: 2.27 (0.27), residues: 385 sheet: 0.86 (0.30), residues: 266 loop : -0.15 (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 0.005 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 435) hydrogen bonds : angle 4.38235 ( 1224) SS BOND : bond 0.00464 ( 3) SS BOND : angle 0.74769 ( 6) covalent geometry : bond 0.00217 ( 8426) covalent geometry : angle 0.53170 (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 143 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 317 ASN cc_start: 0.6788 (m110) cc_final: 0.6391 (m110) REVERT: A 341 ILE cc_start: 0.6054 (OUTLIER) cc_final: 0.5129 (mp) REVERT: B 10 LYS cc_start: 0.7609 (ttpp) cc_final: 0.7266 (mttp) REVERT: B 194 ARG cc_start: 0.6424 (ttt-90) cc_final: 0.5906 (ttm110) REVERT: C 79 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7266 (mp) REVERT: C 138 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: C 217 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7301 (pmm) REVERT: D 22 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6527 (mt-10) REVERT: E 222 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7186 (pp20) outliers start: 30 outliers final: 13 residues processed: 134 average time/residue: 1.0799 time to fit residues: 154.9411 Evaluate side-chains 118 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 217 MET 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: 0.0050 chunk 38 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- 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 = 0.4317 r_free = 0.4317 target = 0.210330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.159268 restraints weight = 7455.117| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.59 r_work: 0.3602 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2226 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= 0.146 Angle : 0.577 6.825 11480 Z= 0.305 Chirality : 0.042 0.152 1355 Planarity : 0.004 0.058 1445 Dihedral : 6.016 76.197 1179 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.58 % Allowed : 22.21 % Favored : 73.21 % 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: 1.38 (0.25), residues: 1080 helix: 2.27 (0.27), residues: 385 sheet: 0.74 (0.30), residues: 278 loop : -0.19 (0.29), residues: 417 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 0.017 0.002 TYR E 59 ARG 0.003 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.03836 ( 435) hydrogen bonds : angle 4.47413 ( 1224) SS BOND : bond 0.00662 ( 3) SS BOND : angle 0.96641 ( 6) covalent geometry : bond 0.00321 ( 8426) covalent geometry : angle 0.57664 (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 151 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 110 ASN cc_start: 0.6057 (OUTLIER) cc_final: 0.5814 (m-40) REVERT: A 203 SER cc_start: 0.5874 (t) cc_final: 0.5445 (m) REVERT: A 317 ASN cc_start: 0.6858 (m110) cc_final: 0.6473 (m110) REVERT: A 341 ILE cc_start: 0.6018 (OUTLIER) cc_final: 0.5100 (mp) REVERT: C 79 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7444 (mp) REVERT: C 138 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7557 (mt-10) REVERT: C 217 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7320 (pmm) REVERT: D 22 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6541 (mt-10) outliers start: 39 outliers final: 19 residues processed: 140 average time/residue: 1.0154 time to fit residues: 152.7517 Evaluate side-chains 128 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN 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 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 173 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 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: 2.9990 chunk 79 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.210994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.161816 restraints weight = 7453.506| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.58 r_work: 0.3632 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8429 Z= 0.126 Angle : 0.553 7.469 11480 Z= 0.292 Chirality : 0.041 0.142 1355 Planarity : 0.004 0.054 1445 Dihedral : 5.907 76.228 1179 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.47 % Allowed : 22.44 % Favored : 73.09 % 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: 1.45 (0.25), residues: 1080 helix: 2.32 (0.26), residues: 385 sheet: 0.80 (0.31), residues: 266 loop : -0.16 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 63 HIS 0.007 0.001 HIS B 209 PHE 0.017 0.002 PHE C 199 TYR 0.016 0.002 TYR E 59 ARG 0.006 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 435) hydrogen bonds : angle 4.33389 ( 1224) SS BOND : bond 0.00571 ( 3) SS BOND : angle 0.88360 ( 6) covalent geometry : bond 0.00270 ( 8426) covalent geometry : angle 0.55287 (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 146 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 341 ILE cc_start: 0.6054 (OUTLIER) cc_final: 0.5116 (mp) REVERT: C 79 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7376 (mp) REVERT: C 138 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: D 22 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6505 (mt-10) outliers start: 38 outliers final: 22 residues processed: 138 average time/residue: 1.0515 time to fit residues: 155.5955 Evaluate side-chains 130 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 56 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 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 = 0.4297 r_free = 0.4297 target = 0.208025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.156743 restraints weight = 7431.595| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.56 r_work: 0.3583 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8429 Z= 0.168 Angle : 0.612 7.294 11480 Z= 0.324 Chirality : 0.043 0.186 1355 Planarity : 0.004 0.051 1445 Dihedral : 6.136 74.315 1179 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.94 % Allowed : 22.68 % 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: 1.29 (0.25), residues: 1080 helix: 2.19 (0.26), residues: 385 sheet: 0.66 (0.30), residues: 281 loop : -0.21 (0.30), residues: 414 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 0.020 0.002 PHE C 199 TYR 0.018 0.002 TYR E 59 ARG 0.005 0.001 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 435) hydrogen bonds : angle 4.54282 ( 1224) SS BOND : bond 0.00746 ( 3) SS BOND : angle 1.13913 ( 6) covalent geometry : bond 0.00375 ( 8426) covalent geometry : angle 0.61210 (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 155 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 0.897 Fit side-chains REVERT: A 203 SER cc_start: 0.5811 (t) cc_final: 0.5438 (m) REVERT: A 341 ILE cc_start: 0.6040 (OUTLIER) cc_final: 0.5394 (mt) REVERT: C 79 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7536 (mp) REVERT: C 138 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: D 22 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6500 (mt-10) outliers start: 42 outliers final: 25 residues processed: 144 average time/residue: 1.0663 time to fit residues: 164.3858 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 : 0.825 ------------------------------------------------------------------------------- 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 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 208 GLU 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: 6.9990 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.208469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.156885 restraints weight = 7492.487| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.54 r_work: 0.3614 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8429 Z= 0.157 Angle : 0.598 8.570 11480 Z= 0.316 Chirality : 0.043 0.163 1355 Planarity : 0.004 0.049 1445 Dihedral : 5.863 75.971 1177 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.47 % Allowed : 23.50 % Favored : 72.03 % 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: 1.28 (0.25), residues: 1080 helix: 2.26 (0.26), residues: 385 sheet: 0.65 (0.30), residues: 276 loop : -0.31 (0.29), residues: 419 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 199 TYR 0.019 0.002 TYR E 59 ARG 0.006 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 435) hydrogen bonds : angle 4.43278 ( 1224) SS BOND : bond 0.00672 ( 3) SS BOND : angle 1.06887 ( 6) covalent geometry : bond 0.00349 ( 8426) covalent geometry : angle 0.59751 (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 149 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 1.009 Fit side-chains REVERT: A 147 LEU cc_start: 0.6592 (mm) cc_final: 0.5927 (pp) REVERT: A 203 SER cc_start: 0.5801 (t) cc_final: 0.5449 (m) REVERT: A 341 ILE cc_start: 0.6026 (OUTLIER) cc_final: 0.5402 (mt) REVERT: A 385 LYS cc_start: 0.6853 (tptt) cc_final: 0.6542 (ttmt) REVERT: C 79 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7487 (mp) REVERT: C 138 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: D 22 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6490 (mt-10) outliers start: 38 outliers final: 26 residues processed: 141 average time/residue: 1.0193 time to fit residues: 154.5881 Evaluate side-chains 137 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 47 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 73 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.211364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.162829 restraints weight = 7547.167| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.56 r_work: 0.3638 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8429 Z= 0.111 Angle : 0.542 7.624 11480 Z= 0.284 Chirality : 0.041 0.143 1355 Planarity : 0.004 0.047 1445 Dihedral : 5.537 76.900 1177 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.88 % Allowed : 24.32 % Favored : 71.80 % 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: 1.47 (0.25), residues: 1080 helix: 2.49 (0.26), residues: 385 sheet: 0.68 (0.30), residues: 267 loop : -0.20 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 63 HIS 0.006 0.001 HIS B 209 PHE 0.016 0.001 PHE C 199 TYR 0.016 0.001 TYR E 59 ARG 0.006 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 435) hydrogen bonds : angle 4.16215 ( 1224) SS BOND : bond 0.00455 ( 3) SS BOND : angle 0.76701 ( 6) covalent geometry : bond 0.00234 ( 8426) covalent geometry : angle 0.54163 (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 145 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.881 Fit side-chains REVERT: A 80 LEU cc_start: 0.6291 (OUTLIER) cc_final: 0.5884 (pp) REVERT: A 135 ILE cc_start: 0.6986 (OUTLIER) cc_final: 0.6662 (mm) REVERT: A 147 LEU cc_start: 0.6604 (mm) cc_final: 0.6009 (pp) REVERT: A 203 SER cc_start: 0.5794 (t) cc_final: 0.5469 (m) REVERT: A 341 ILE cc_start: 0.5987 (OUTLIER) cc_final: 0.5369 (mt) REVERT: A 385 LYS cc_start: 0.6883 (tptt) cc_final: 0.6571 (ttmt) REVERT: C 79 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7331 (mp) REVERT: C 101 MET cc_start: 0.8210 (mtp) cc_final: 0.7797 (mpp) REVERT: C 138 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7539 (mt-10) REVERT: D 22 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6453 (mt-10) outliers start: 33 outliers final: 23 residues processed: 138 average time/residue: 0.9925 time to fit residues: 147.6421 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 : 0.897 ------------------------------------------------------------------------------- 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 135 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 25 CYS 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 177 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 156 SER Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 208 GLU 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: 0.9990 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.0020 chunk 52 optimal weight: 1.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.210788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.163074 restraints weight = 7559.275| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.51 r_work: 0.3627 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8429 Z= 0.120 Angle : 0.560 7.756 11480 Z= 0.294 Chirality : 0.041 0.146 1355 Planarity : 0.004 0.046 1445 Dihedral : 5.517 74.617 1177 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.76 % Allowed : 24.44 % Favored : 71.80 % 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: 1.51 (0.25), residues: 1080 helix: 2.48 (0.26), residues: 385 sheet: 0.73 (0.30), residues: 272 loop : -0.17 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 63 HIS 0.006 0.001 HIS B 209 PHE 0.016 0.002 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 0.03458 ( 435) hydrogen bonds : angle 4.18729 ( 1224) SS BOND : bond 0.00516 ( 3) SS BOND : angle 0.84532 ( 6) covalent geometry : bond 0.00258 ( 8426) covalent geometry : angle 0.55958 (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 138 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 106 time to evaluate : 0.952 Fit side-chains REVERT: A 80 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6102 (pp) REVERT: A 147 LEU cc_start: 0.6697 (mm) cc_final: 0.6098 (pp) REVERT: A 203 SER cc_start: 0.5804 (t) cc_final: 0.5489 (m) REVERT: A 341 ILE cc_start: 0.6090 (OUTLIER) cc_final: 0.5440 (mt) REVERT: A 385 LYS cc_start: 0.6848 (tptt) cc_final: 0.6541 (ttmt) REVERT: C 79 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7378 (mp) REVERT: C 101 MET cc_start: 0.8248 (mtp) cc_final: 0.7831 (mpp) REVERT: C 138 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: D 15 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6700 (tp) REVERT: D 22 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6490 (mt-10) outliers start: 32 outliers final: 20 residues processed: 132 average time/residue: 1.0425 time to fit residues: 148.0138 Evaluate side-chains 130 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU 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 29 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 15 LEU 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 156 SER Chi-restraints excluded: chain E residue 201 THR 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: 0.4980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.210870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.164539 restraints weight = 7478.978| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.39 r_work: 0.3648 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8429 Z= 0.120 Angle : 0.554 7.690 11480 Z= 0.291 Chirality : 0.042 0.324 1355 Planarity : 0.004 0.046 1445 Dihedral : 5.485 73.810 1177 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.64 % Allowed : 25.03 % Favored : 71.33 % 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: 1.54 (0.25), residues: 1080 helix: 2.54 (0.26), residues: 385 sheet: 0.72 (0.30), residues: 272 loop : -0.17 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 63 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 0.03430 ( 435) hydrogen bonds : angle 4.15248 ( 1224) SS BOND : bond 0.00478 ( 3) SS BOND : angle 0.81428 ( 6) covalent geometry : bond 0.00258 ( 8426) covalent geometry : angle 0.55339 (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 141 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.833 Fit side-chains REVERT: A 80 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6202 (pp) REVERT: A 147 LEU cc_start: 0.6552 (mm) cc_final: 0.6042 (pp) REVERT: A 203 SER cc_start: 0.5841 (t) cc_final: 0.5526 (m) REVERT: A 341 ILE cc_start: 0.6173 (OUTLIER) cc_final: 0.5225 (mp) REVERT: A 385 LYS cc_start: 0.6857 (tptt) cc_final: 0.6548 (ttmt) REVERT: C 79 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7363 (mp) REVERT: C 101 MET cc_start: 0.8240 (mtp) cc_final: 0.7831 (mpp) REVERT: C 138 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: D 15 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6731 (tp) REVERT: D 22 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6515 (mt-10) outliers start: 31 outliers final: 21 residues processed: 136 average time/residue: 1.0265 time to fit residues: 150.0610 Evaluate side-chains 132 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU 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 29 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 15 LEU 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 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: 4.9990 chunk 103 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.4299 r_free = 0.4299 target = 0.207243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.151388 restraints weight = 7547.160| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.91 r_work: 0.3559 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8429 Z= 0.191 Angle : 0.644 8.248 11480 Z= 0.340 Chirality : 0.046 0.395 1355 Planarity : 0.004 0.047 1445 Dihedral : 5.943 73.274 1177 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.76 % Allowed : 24.91 % Favored : 71.33 % 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: 1.27 (0.25), residues: 1080 helix: 2.21 (0.26), residues: 385 sheet: 0.66 (0.30), residues: 280 loop : -0.30 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 63 HIS 0.009 0.002 HIS B 209 PHE 0.020 0.002 PHE C 199 TYR 0.023 0.002 TYR E 59 ARG 0.006 0.001 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 435) hydrogen bonds : angle 4.51634 ( 1224) SS BOND : bond 0.00767 ( 3) SS BOND : angle 1.15865 ( 6) covalent geometry : bond 0.00433 ( 8426) covalent geometry : angle 0.64378 (11474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7686.24 seconds wall clock time: 132 minutes 36.88 seconds (7956.88 seconds total)