Starting phenix.real_space_refine on Wed Sep 17 10:54:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9as8_43808/09_2025/9as8_43808.cif Found real_map, /net/cci-nas-00/data/ceres_data/9as8_43808/09_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_43808/09_2025/9as8_43808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9as8_43808/09_2025/9as8_43808.map" model { file = "/net/cci-nas-00/data/ceres_data/9as8_43808/09_2025/9as8_43808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9as8_43808/09_2025/9as8_43808.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 3, 'ASP:plan': 5, 'GLU:plan': 2} 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: {'GLU:plan': 8, 'ARG:plan': 9, 'GLN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 6, 'TYR:plan': 1} 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: {'ARG:plan': 6, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN: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: {'ARG:plan': 1, 'GLU: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: {'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG: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: 2.30, per 1000 atoms: 0.28 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: 0.72 Conformation dependent library (CDL) restraints added in 524.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.40 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: 1.42 Time building geometry restraints manager: 0.99 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: 2.330 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.100 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.510 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG C 49 TYR 0.017 0.002 TYR E 59 PHE 0.021 0.002 PHE E 27 TRP 0.029 0.002 TRP A 336 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 8426) covalent geometry : angle 0.83122 (11474) SS BOND : bond 0.00437 ( 3) SS BOND : angle 0.97567 ( 6) hydrogen bonds : bond 0.16002 ( 435) hydrogen bonds : angle 6.39517 ( 1224) *********************** 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 : 0.362 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 133 average time/residue: 0.5460 time to fit residues: 77.4448 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 : 0.287 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 183 HIS A 317 ASN B 80 ASN E 13 GLN E 35 HIS E 39 GLN E 167 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.216667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.167802 restraints weight = 7505.250| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.51 r_work: 0.3673 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8429 Z= 0.118 Angle : 0.556 5.787 11480 Z= 0.294 Chirality : 0.042 0.148 1355 Planarity : 0.004 0.074 1445 Dihedral : 5.987 82.356 1180 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.76 % Allowed : 20.92 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.25), residues: 1080 helix: 2.14 (0.26), residues: 391 sheet: 0.82 (0.30), residues: 284 loop : -0.07 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 194 TYR 0.020 0.002 TYR A 139 PHE 0.016 0.002 PHE C 199 TRP 0.014 0.002 TRP C 297 HIS 0.007 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8426) covalent geometry : angle 0.55589 (11474) SS BOND : bond 0.00537 ( 3) SS BOND : angle 0.75184 ( 6) hydrogen bonds : bond 0.03768 ( 435) hydrogen bonds : angle 4.58909 ( 1224) *********************** 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 150 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 MET cc_start: 0.6302 (mtm) cc_final: 0.5747 (ttp) REVERT: A 317 ASN cc_start: 0.6967 (m-40) cc_final: 0.6477 (m110) REVERT: A 341 ILE cc_start: 0.6070 (OUTLIER) cc_final: 0.5188 (mp) REVERT: B 10 LYS cc_start: 0.7751 (ttpp) cc_final: 0.7392 (mttp) REVERT: B 128 ILE cc_start: 0.7234 (mt) cc_final: 0.6988 (pt) REVERT: C 79 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7200 (mp) REVERT: C 234 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8647 (m-80) outliers start: 32 outliers final: 17 residues processed: 142 average time/residue: 0.5311 time to fit residues: 80.7038 Evaluate side-chains 121 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 18 MET 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 79 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 138 GLU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 247 ASP 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 95 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 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 = 0.4293 r_free = 0.4293 target = 0.207356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.161131 restraints weight = 7470.325| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.35 r_work: 0.3596 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8429 Z= 0.216 Angle : 0.674 6.976 11480 Z= 0.359 Chirality : 0.046 0.227 1355 Planarity : 0.005 0.063 1445 Dihedral : 6.482 76.176 1179 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.70 % Allowed : 21.62 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.25), residues: 1080 helix: 1.80 (0.26), residues: 390 sheet: 0.67 (0.30), residues: 278 loop : -0.28 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 67 TYR 0.021 0.003 TYR E 59 PHE 0.024 0.003 PHE A 332 TRP 0.016 0.002 TRP A 151 HIS 0.012 0.002 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 8426) covalent geometry : angle 0.67323 (11474) SS BOND : bond 0.00813 ( 3) SS BOND : angle 1.23810 ( 6) hydrogen bonds : bond 0.04748 ( 435) hydrogen bonds : angle 4.94213 ( 1224) *********************** 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 150 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 110 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 220 LYS cc_start: 0.4628 (OUTLIER) cc_final: 0.4353 (ttmm) REVERT: A 317 ASN cc_start: 0.6921 (m-40) cc_final: 0.6512 (m110) REVERT: A 341 ILE cc_start: 0.6016 (OUTLIER) cc_final: 0.5115 (mp) REVERT: C 79 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7583 (mp) REVERT: C 219 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7660 (mmt90) REVERT: D 22 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6660 (mt-10) outliers start: 40 outliers final: 17 residues processed: 138 average time/residue: 0.5779 time to fit residues: 85.0005 Evaluate side-chains 125 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 220 LYS 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 196 THR Chi-restraints excluded: chain C residue 219 ARG 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 30 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 16 optimal weight: 0.1980 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 90 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN C 237 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 = 0.4311 r_free = 0.4311 target = 0.209626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.158256 restraints weight = 7612.665| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.59 r_work: 0.3614 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2388 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= 0.141 Angle : 0.577 7.075 11480 Z= 0.305 Chirality : 0.042 0.142 1355 Planarity : 0.004 0.058 1445 Dihedral : 6.163 79.461 1179 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.94 % Allowed : 22.33 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.25), residues: 1080 helix: 2.16 (0.27), residues: 384 sheet: 0.70 (0.30), residues: 278 loop : -0.28 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 194 TYR 0.020 0.002 TYR E 59 PHE 0.019 0.002 PHE C 151 TRP 0.014 0.002 TRP C 63 HIS 0.009 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8426) covalent geometry : angle 0.57671 (11474) SS BOND : bond 0.00621 ( 3) SS BOND : angle 0.96459 ( 6) hydrogen bonds : bond 0.03839 ( 435) hydrogen bonds : angle 4.51482 ( 1224) *********************** 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 149 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 107 time to evaluate : 0.354 Fit side-chains REVERT: A 220 LYS cc_start: 0.4543 (OUTLIER) cc_final: 0.4295 (ttmm) REVERT: A 341 ILE cc_start: 0.5978 (OUTLIER) cc_final: 0.5356 (mt) REVERT: C 79 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7463 (mp) REVERT: C 138 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7530 (mt-10) outliers start: 42 outliers final: 19 residues processed: 140 average time/residue: 0.5722 time to fit residues: 85.5038 Evaluate side-chains 123 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 220 LYS 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 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 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 70 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4295 r_free = 0.4295 target = 0.208096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.158705 restraints weight = 7559.258| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.45 r_work: 0.3601 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8429 Z= 0.162 Angle : 0.603 6.655 11480 Z= 0.320 Chirality : 0.043 0.164 1355 Planarity : 0.004 0.053 1445 Dihedral : 5.947 76.934 1177 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.82 % Allowed : 22.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.25), residues: 1080 helix: 2.05 (0.27), residues: 385 sheet: 0.65 (0.30), residues: 278 loop : -0.28 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 194 TYR 0.020 0.002 TYR E 59 PHE 0.021 0.002 PHE C 151 TRP 0.015 0.002 TRP C 63 HIS 0.008 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8426) covalent geometry : angle 0.60244 (11474) SS BOND : bond 0.00703 ( 3) SS BOND : angle 1.05295 ( 6) hydrogen bonds : bond 0.04021 ( 435) hydrogen bonds : angle 4.55931 ( 1224) *********************** 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 154 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 0.342 Fit side-chains REVERT: A 110 ASN cc_start: 0.6226 (OUTLIER) cc_final: 0.6007 (m-40) REVERT: A 203 SER cc_start: 0.5867 (t) cc_final: 0.5425 (m) REVERT: A 220 LYS cc_start: 0.4723 (OUTLIER) cc_final: 0.4439 (mtmm) REVERT: A 341 ILE cc_start: 0.5996 (OUTLIER) cc_final: 0.5382 (mt) REVERT: A 385 LYS cc_start: 0.6879 (tptt) cc_final: 0.6616 (ttmt) REVERT: C 79 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7510 (mp) REVERT: C 138 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: D 22 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6528 (mt-10) outliers start: 41 outliers final: 22 residues processed: 145 average time/residue: 0.5540 time to fit residues: 85.8763 Evaluate side-chains 135 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 220 LYS 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 222 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4309 r_free = 0.4309 target = 0.209433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.158429 restraints weight = 7393.488| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.54 r_work: 0.3622 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2694 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= 0.135 Angle : 0.567 6.252 11480 Z= 0.301 Chirality : 0.042 0.142 1355 Planarity : 0.004 0.051 1445 Dihedral : 5.799 77.686 1177 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.47 % Allowed : 23.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.26), residues: 1080 helix: 2.25 (0.27), residues: 385 sheet: 0.68 (0.30), residues: 282 loop : -0.23 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 194 TYR 0.018 0.002 TYR E 59 PHE 0.018 0.002 PHE C 151 TRP 0.014 0.002 TRP C 63 HIS 0.007 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8426) covalent geometry : angle 0.56681 (11474) SS BOND : bond 0.00568 ( 3) SS BOND : angle 0.91147 ( 6) hydrogen bonds : bond 0.03710 ( 435) hydrogen bonds : angle 4.36839 ( 1224) *********************** 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 151 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 0.274 Fit side-chains REVERT: A 203 SER cc_start: 0.5804 (t) cc_final: 0.5387 (m) REVERT: A 220 LYS cc_start: 0.4678 (OUTLIER) cc_final: 0.4419 (mtmm) REVERT: A 341 ILE cc_start: 0.5995 (OUTLIER) cc_final: 0.5378 (mt) REVERT: A 385 LYS cc_start: 0.6855 (tptt) cc_final: 0.6568 (ttmt) REVERT: C 79 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7434 (mp) REVERT: C 138 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7535 (mt-10) REVERT: D 22 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6499 (mt-10) outliers start: 38 outliers final: 24 residues processed: 142 average time/residue: 0.5436 time to fit residues: 82.4523 Evaluate side-chains 134 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 220 LYS 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 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 156 SER Chi-restraints excluded: chain E residue 201 THR 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 94 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.205057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.149815 restraints weight = 7518.089| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.85 r_work: 0.3537 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8429 Z= 0.224 Angle : 0.673 7.992 11480 Z= 0.358 Chirality : 0.046 0.248 1355 Planarity : 0.005 0.049 1445 Dihedral : 6.240 76.396 1177 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.23 % Allowed : 24.32 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.25), residues: 1080 helix: 1.93 (0.26), residues: 385 sheet: 0.63 (0.30), residues: 287 loop : -0.34 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 194 TYR 0.022 0.003 TYR E 59 PHE 0.024 0.003 PHE C 151 TRP 0.018 0.002 TRP C 63 HIS 0.009 0.002 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 8426) covalent geometry : angle 0.67275 (11474) SS BOND : bond 0.00840 ( 3) SS BOND : angle 1.27561 ( 6) hydrogen bonds : bond 0.04548 ( 435) hydrogen bonds : angle 4.73554 ( 1224) *********************** 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 151 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 0.334 Fit side-chains REVERT: A 203 SER cc_start: 0.5804 (t) cc_final: 0.5418 (m) REVERT: A 220 LYS cc_start: 0.4708 (OUTLIER) cc_final: 0.4415 (mtmm) REVERT: A 341 ILE cc_start: 0.6053 (OUTLIER) cc_final: 0.5610 (mt) REVERT: A 385 LYS cc_start: 0.6831 (tptt) cc_final: 0.6525 (ttmt) REVERT: C 79 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7629 (mp) REVERT: C 138 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: D 22 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6535 (mt-10) outliers start: 36 outliers final: 25 residues processed: 141 average time/residue: 0.5726 time to fit residues: 86.0166 Evaluate side-chains 136 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LYS 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 184 THR Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 243 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 84 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 74 optimal weight: 0.2980 chunk 64 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 26 optimal weight: 0.0870 chunk 73 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- 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 = 0.4317 r_free = 0.4317 target = 0.210402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.163624 restraints weight = 7530.228| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.42 r_work: 0.3647 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8429 Z= 0.114 Angle : 0.544 5.911 11480 Z= 0.288 Chirality : 0.041 0.143 1355 Planarity : 0.004 0.046 1445 Dihedral : 5.726 80.561 1177 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.06 % Allowed : 25.73 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.26), residues: 1080 helix: 2.36 (0.26), residues: 385 sheet: 0.75 (0.30), residues: 279 loop : -0.27 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 194 TYR 0.016 0.001 TYR E 59 PHE 0.016 0.001 PHE C 199 TRP 0.012 0.002 TRP C 63 HIS 0.006 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 8426) covalent geometry : angle 0.54431 (11474) SS BOND : bond 0.00455 ( 3) SS BOND : angle 0.79585 ( 6) hydrogen bonds : bond 0.03424 ( 435) hydrogen bonds : angle 4.23954 ( 1224) *********************** 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 140 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.352 Fit side-chains REVERT: A 147 LEU cc_start: 0.6363 (mm) cc_final: 0.5938 (pp) REVERT: A 203 SER cc_start: 0.5836 (t) cc_final: 0.5524 (m) REVERT: A 220 LYS cc_start: 0.4788 (OUTLIER) cc_final: 0.4516 (mtmm) REVERT: A 341 ILE cc_start: 0.6052 (OUTLIER) cc_final: 0.5624 (mt) REVERT: A 385 LYS cc_start: 0.6867 (tptt) cc_final: 0.6568 (ttmt) REVERT: C 101 MET cc_start: 0.8140 (mtp) cc_final: 0.7706 (mpp) REVERT: C 138 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: D 22 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6483 (mt-10) outliers start: 26 outliers final: 17 residues processed: 135 average time/residue: 0.5446 time to fit residues: 78.6145 Evaluate side-chains 129 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 341 ILE 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 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 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 48 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.4285 r_free = 0.4285 target = 0.205813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.149761 restraints weight = 7489.536| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.85 r_work: 0.3544 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8429 Z= 0.203 Angle : 0.655 9.107 11480 Z= 0.346 Chirality : 0.045 0.222 1355 Planarity : 0.004 0.047 1445 Dihedral : 6.104 76.830 1177 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.64 % Allowed : 25.62 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.25), residues: 1080 helix: 2.10 (0.26), residues: 385 sheet: 0.68 (0.30), residues: 287 loop : -0.34 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 194 TYR 0.021 0.002 TYR E 59 PHE 0.023 0.002 PHE C 151 TRP 0.016 0.002 TRP C 63 HIS 0.009 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 8426) covalent geometry : angle 0.65442 (11474) SS BOND : bond 0.00788 ( 3) SS BOND : angle 1.22674 ( 6) hydrogen bonds : bond 0.04333 ( 435) hydrogen bonds : angle 4.61923 ( 1224) *********************** 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 142 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.331 Fit side-chains REVERT: A 121 MET cc_start: 0.3835 (tpt) cc_final: 0.3623 (tpp) REVERT: A 147 LEU cc_start: 0.6296 (mm) cc_final: 0.5863 (pp) REVERT: A 203 SER cc_start: 0.5802 (t) cc_final: 0.5432 (m) REVERT: A 220 LYS cc_start: 0.4769 (OUTLIER) cc_final: 0.4478 (mtmm) REVERT: A 341 ILE cc_start: 0.6055 (OUTLIER) cc_final: 0.5616 (mt) REVERT: A 385 LYS cc_start: 0.6896 (tptt) cc_final: 0.6599 (tttt) REVERT: C 138 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: D 22 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6564 (mt-10) outliers start: 31 outliers final: 22 residues processed: 136 average time/residue: 0.5521 time to fit residues: 80.2256 Evaluate side-chains 134 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 341 ILE 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 138 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 184 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 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 72 optimal weight: 2.9990 chunk 6 optimal weight: 0.0010 chunk 81 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 62 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 = 0.210207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.155967 restraints weight = 7461.040| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.83 r_work: 0.3616 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8429 Z= 0.111 Angle : 0.549 7.318 11480 Z= 0.288 Chirality : 0.042 0.181 1355 Planarity : 0.004 0.045 1445 Dihedral : 5.660 80.248 1177 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.59 % Allowed : 26.67 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.25), residues: 1080 helix: 2.41 (0.26), residues: 385 sheet: 0.73 (0.30), residues: 279 loop : -0.27 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 194 TYR 0.017 0.001 TYR E 59 PHE 0.016 0.001 PHE C 199 TRP 0.013 0.002 TRP C 63 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8426) covalent geometry : angle 0.54861 (11474) SS BOND : bond 0.00423 ( 3) SS BOND : angle 0.77366 ( 6) hydrogen bonds : bond 0.03360 ( 435) hydrogen bonds : angle 4.22346 ( 1224) ********************** 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 127 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.317 Fit side-chains REVERT: A 96 ILE cc_start: 0.5204 (OUTLIER) cc_final: 0.4692 (pt) REVERT: A 147 LEU cc_start: 0.6198 (mm) cc_final: 0.5976 (pp) REVERT: A 203 SER cc_start: 0.5735 (t) cc_final: 0.5417 (m) REVERT: A 220 LYS cc_start: 0.4691 (OUTLIER) cc_final: 0.4463 (mtmm) REVERT: A 341 ILE cc_start: 0.5991 (OUTLIER) cc_final: 0.5574 (mt) REVERT: C 101 MET cc_start: 0.8156 (mtp) cc_final: 0.7722 (mpp) REVERT: C 138 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7663 (mt-10) outliers start: 22 outliers final: 17 residues processed: 123 average time/residue: 0.5409 time to fit residues: 71.2191 Evaluate side-chains 126 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 341 ILE 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 138 GLU 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 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 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 83 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.206391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.150385 restraints weight = 7515.068| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.92 r_work: 0.3554 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8429 Z= 0.186 Angle : 0.641 8.772 11480 Z= 0.337 Chirality : 0.044 0.207 1355 Planarity : 0.004 0.046 1445 Dihedral : 5.996 76.327 1177 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.06 % Allowed : 26.44 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.25), residues: 1080 helix: 2.23 (0.26), residues: 385 sheet: 0.68 (0.30), residues: 287 loop : -0.31 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 194 TYR 0.021 0.002 TYR E 59 PHE 0.022 0.002 PHE C 151 TRP 0.017 0.002 TRP C 63 HIS 0.008 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8426) covalent geometry : angle 0.64091 (11474) SS BOND : bond 0.00745 ( 3) SS BOND : angle 1.16897 ( 6) hydrogen bonds : bond 0.04163 ( 435) hydrogen bonds : angle 4.54495 ( 1224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4195.40 seconds wall clock time: 72 minutes 11.12 seconds (4331.12 seconds total)