Starting phenix.real_space_refine on Sat Jul 4 10:42:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sii_25142/07_2026/7sii_25142_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sii_25142/07_2026/7sii_25142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sii_25142/07_2026/7sii_25142_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sii_25142/07_2026/7sii_25142_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sii_25142/07_2026/7sii_25142.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sii_25142/07_2026/7sii_25142.map" } resolution = 3.45 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= 0.006 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: 8 Type Number sf(0) Gaussians P 4 5.49 5 S 52 5.16 5 Cl 2 4.86 5 C 6580 2.51 5 N 1820 2.21 5 O 1834 1.98 5 F 8 1.80 5 H 10184 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20484 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5112 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 18, 'TRANS': 305} Chain breaks: 2 Chain: "B" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 5051 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 17, 'TRANS': 301} Chain breaks: 3 Chain: "C" Number of atoms: 5112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5112 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 18, 'TRANS': 305} Chain breaks: 2 Chain: "D" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 5051 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 17, 'TRANS': 301} Chain breaks: 3 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'9IM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'9IM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'1SY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.22, per 1000 atoms: 0.16 Number of scatterers: 20484 At special positions: 0 Unit cell: (93.96, 98.28, 105.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 2 17.00 S 52 16.00 P 4 15.00 F 8 9.00 O 1834 8.00 N 1820 7.00 C 6580 6.00 H 10184 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 533.4 milliseconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 64.9% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 16 through 37 Processing helix chain 'A' and resid 39 through 70 removed outlier: 3.882A pdb=" N THR A 43 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 91 through 109 Processing helix chain 'A' and resid 116 through 135 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.776A pdb=" N GLY A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 186 Proline residue: A 173 - end of helix removed outlier: 4.247A pdb=" N GLN A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.646A pdb=" N ALA A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 removed outlier: 3.761A pdb=" N GLN A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 302 Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.646A pdb=" N GLN A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 37 Processing helix chain 'B' and resid 39 through 70 removed outlier: 3.513A pdb=" N THR B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 78 Processing helix chain 'B' and resid 80 through 90 Processing helix chain 'B' and resid 91 through 109 Processing helix chain 'B' and resid 117 through 135 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 155 through 167 Processing helix chain 'B' and resid 167 through 186 Proline residue: B 173 - end of helix removed outlier: 4.256A pdb=" N GLN B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALA B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 262 through 274 removed outlier: 3.748A pdb=" N GLN B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 301 Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.793A pdb=" N GLN B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 37 Processing helix chain 'C' and resid 39 through 70 removed outlier: 3.882A pdb=" N THR C 43 " --> pdb=" O PRO C 39 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU C 68 " --> pdb=" O CYS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 109 Processing helix chain 'C' and resid 116 through 135 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 154 through 167 removed outlier: 3.776A pdb=" N GLY C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 186 Proline residue: C 173 - end of helix removed outlier: 4.247A pdb=" N GLN C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA C 177 " --> pdb=" O PRO C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 removed outlier: 3.646A pdb=" N ALA C 215 " --> pdb=" O ASN C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 274 removed outlier: 3.762A pdb=" N GLN C 266 " --> pdb=" O ALA C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 302 Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.646A pdb=" N GLN C 335 " --> pdb=" O ARG C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 37 Processing helix chain 'D' and resid 39 through 70 removed outlier: 3.513A pdb=" N THR D 43 " --> pdb=" O PRO D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 78 Processing helix chain 'D' and resid 80 through 90 Processing helix chain 'D' and resid 91 through 109 Processing helix chain 'D' and resid 117 through 135 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 155 through 167 Processing helix chain 'D' and resid 167 through 186 Proline residue: D 173 - end of helix removed outlier: 4.256A pdb=" N GLN D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA D 177 " --> pdb=" O PRO D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 216 Processing helix chain 'D' and resid 262 through 274 removed outlier: 3.748A pdb=" N GLN D 266 " --> pdb=" O ALA D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 301 Processing helix chain 'D' and resid 324 through 335 removed outlier: 3.793A pdb=" N GLN D 335 " --> pdb=" O ARG D 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 223 removed outlier: 6.925A pdb=" N ILE A 244 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 255 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU A 249 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ARG A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU A 198 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE A 312 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE A 200 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N TYR A 314 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 202 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 232 removed outlier: 6.490A pdb=" N GLN A 228 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 239 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLY A 230 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP A 237 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 219 through 224 removed outlier: 6.929A pdb=" N ILE B 244 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER B 243 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU B 259 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 245 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS B 257 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLU B 249 " --> pdb=" O ARG B 253 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ARG B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU B 198 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B 312 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE B 200 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N TYR B 314 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU B 202 " --> pdb=" O TYR B 314 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 228 through 232 removed outlier: 6.697A pdb=" N ARG B 232 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LYS B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 219 through 223 removed outlier: 6.924A pdb=" N ILE C 244 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY C 255 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU C 249 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ARG C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU C 198 " --> pdb=" O ARG C 310 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE C 312 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE C 200 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N TYR C 314 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU C 202 " --> pdb=" O TYR C 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 228 through 232 removed outlier: 6.491A pdb=" N GLN C 228 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL C 239 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLY C 230 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP C 237 " --> pdb=" O GLY C 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 219 through 224 removed outlier: 6.929A pdb=" N ILE D 244 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER D 243 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU D 259 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR D 245 " --> pdb=" O CYS D 257 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS D 257 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU D 249 " --> pdb=" O ARG D 253 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ARG D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU D 198 " --> pdb=" O ARG D 310 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE D 312 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE D 200 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N TYR D 314 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU D 202 " --> pdb=" O TYR D 314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 228 through 232 removed outlier: 6.697A pdb=" N ARG D 232 " --> pdb=" O LYS D 236 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LYS D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1896 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: 4.27 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10144 1.03 - 1.23: 44 1.23 - 1.42: 4450 1.42 - 1.61: 6018 1.61 - 1.81: 74 Bond restraints: 20730 Sorted by residual: bond pdb=" C5 1SY D 401 " pdb=" N7 1SY D 401 " ideal model delta sigma weight residual 1.370 1.572 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C5 1SY B 401 " pdb=" N7 1SY B 401 " ideal model delta sigma weight residual 1.370 1.572 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C38 1SY B 401 " pdb=" O43 1SY B 401 " ideal model delta sigma weight residual 1.225 1.396 -0.171 2.00e-02 2.50e+03 7.32e+01 bond pdb=" C38 1SY D 401 " pdb=" O43 1SY D 401 " ideal model delta sigma weight residual 1.225 1.395 -0.170 2.00e-02 2.50e+03 7.27e+01 bond pdb=" C40 1SY D 401 " pdb=" N42 1SY D 401 " ideal model delta sigma weight residual 1.367 1.530 -0.163 2.00e-02 2.50e+03 6.67e+01 ... (remaining 20725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 37246 3.36 - 6.71: 105 6.71 - 10.07: 13 10.07 - 13.43: 4 13.43 - 16.78: 12 Bond angle restraints: 37380 Sorted by residual: angle pdb=" C34 1SY B 401 " pdb=" N33 1SY B 401 " pdb=" C36 1SY B 401 " ideal model delta sigma weight residual 105.30 122.08 -16.78 3.00e+00 1.11e-01 3.13e+01 angle pdb=" C34 1SY D 401 " pdb=" N33 1SY D 401 " pdb=" C36 1SY D 401 " ideal model delta sigma weight residual 105.30 122.04 -16.74 3.00e+00 1.11e-01 3.11e+01 angle pdb=" O17 1SY B 401 " pdb=" P18 1SY B 401 " pdb=" O20 1SY B 401 " ideal model delta sigma weight residual 100.83 117.53 -16.70 3.00e+00 1.11e-01 3.10e+01 angle pdb=" O17 1SY D 401 " pdb=" P18 1SY D 401 " pdb=" O20 1SY D 401 " ideal model delta sigma weight residual 100.83 117.46 -16.63 3.00e+00 1.11e-01 3.07e+01 angle pdb=" C4 1SY B 401 " pdb=" N9 1SY B 401 " pdb=" C8 1SY B 401 " ideal model delta sigma weight residual 106.31 122.87 -16.56 3.00e+00 1.11e-01 3.05e+01 ... (remaining 37375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 8944 17.67 - 35.33: 602 35.33 - 53.00: 221 53.00 - 70.67: 44 70.67 - 88.33: 5 Dihedral angle restraints: 9816 sinusoidal: 5476 harmonic: 4340 Sorted by residual: dihedral pdb=" CA ARG A 284 " pdb=" CB ARG A 284 " pdb=" CG ARG A 284 " pdb=" CD ARG A 284 " ideal model delta sinusoidal sigma weight residual -180.00 -120.96 -59.04 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG C 284 " pdb=" CB ARG C 284 " pdb=" CG ARG C 284 " pdb=" CD ARG C 284 " ideal model delta sinusoidal sigma weight residual -180.00 -121.02 -58.98 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N ARG D 238 " pdb=" CA ARG D 238 " pdb=" CB ARG D 238 " pdb=" CG ARG D 238 " ideal model delta sinusoidal sigma weight residual -60.00 -116.20 56.20 3 1.50e+01 4.44e-03 9.39e+00 ... (remaining 9813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1435 0.056 - 0.111: 138 0.111 - 0.167: 15 0.167 - 0.222: 2 0.222 - 0.278: 4 Chirality restraints: 1594 Sorted by residual: chirality pdb=" C2' 1SY D 401 " pdb=" C1' 1SY D 401 " pdb=" C3' 1SY D 401 " pdb=" O2' 1SY D 401 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C2' 1SY B 401 " pdb=" C1' 1SY B 401 " pdb=" C3' 1SY B 401 " pdb=" O2' 1SY B 401 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C22 1SY D 401 " pdb=" C21 1SY D 401 " pdb=" C24 1SY D 401 " pdb=" O23 1SY D 401 " both_signs ideal model delta sigma weight residual False -2.70 -2.45 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 1591 not shown) Planarity restraints: 3020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 72 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C HIS B 72 " -0.020 2.00e-02 2.50e+03 pdb=" O HIS B 72 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE B 73 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 72 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C HIS D 72 " 0.020 2.00e-02 2.50e+03 pdb=" O HIS D 72 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE D 73 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 140 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO B 141 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 141 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 141 " -0.015 5.00e-02 4.00e+02 ... (remaining 3017 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 785 2.17 - 2.77: 39642 2.77 - 3.38: 58113 3.38 - 3.99: 72331 3.99 - 4.60: 115888 Nonbonded interactions: 286759 Sorted by model distance: nonbonded pdb=" OE1 GLU A 38 " pdb=" H GLU A 38 " model vdw 1.557 2.450 nonbonded pdb=" OE1 GLU C 38 " pdb=" H GLU C 38 " model vdw 1.558 2.450 nonbonded pdb=" O ILE C 73 " pdb=" H GLY C 79 " model vdw 1.640 2.450 nonbonded pdb=" O ILE A 73 " pdb=" H GLY A 79 " model vdw 1.640 2.450 nonbonded pdb=" O TYR A 245 " pdb=" HG1 THR A 256 " model vdw 1.656 2.450 ... (remaining 286754 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.350 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: 0.160 Extract box with map and model: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.260 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 0.009 0.202 10546 Z= 0.426 Angle : 0.827 16.784 14350 Z= 0.340 Chirality : 0.036 0.278 1594 Planarity : 0.003 0.026 1816 Dihedral : 13.003 88.332 3992 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.21 % Allowed : 4.97 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.94 (0.25), residues: 1258 helix: 3.56 (0.18), residues: 730 sheet: -0.09 (0.43), residues: 144 loop : -0.56 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 178 TYR 0.010 0.001 TYR A 106 PHE 0.009 0.001 PHE B 291 TRP 0.006 0.001 TRP C 161 HIS 0.003 0.001 HIS C 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00862 / 0.43 (10546) covalent geometry : angle 0.82670 / 0.34 (14350) hydrogen bonds : bond 0.13219 / 9.49 ( 636) hydrogen bonds : angle 6.50405 / 4.82 ( 1896) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 HIS cc_start: 0.7093 (t-90) cc_final: 0.6844 (m170) REVERT: A 236 LYS cc_start: 0.8114 (mmmm) cc_final: 0.7605 (mtpp) REVERT: B 66 LEU cc_start: 0.8651 (tt) cc_final: 0.8415 (tp) REVERT: B 86 ARG cc_start: 0.8248 (ttt90) cc_final: 0.7884 (ttm-80) REVERT: B 91 CYS cc_start: 0.7624 (t) cc_final: 0.7258 (t) REVERT: B 238 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.6095 (tmm-80) REVERT: C 41 GLU cc_start: 0.6950 (tm-30) cc_final: 0.6643 (tm-30) REVERT: C 106 TYR cc_start: 0.8495 (t80) cc_final: 0.8264 (t80) REVERT: C 185 HIS cc_start: 0.7084 (t-90) cc_final: 0.6682 (m170) REVERT: C 236 LYS cc_start: 0.8062 (mmmm) cc_final: 0.7732 (mtpp) REVERT: C 289 LYS cc_start: 0.8860 (mttp) cc_final: 0.8566 (mttm) REVERT: D 66 LEU cc_start: 0.8635 (tt) cc_final: 0.8391 (tp) REVERT: D 86 ARG cc_start: 0.8271 (ttt90) cc_final: 0.7878 (ttm-80) REVERT: D 91 CYS cc_start: 0.7592 (t) cc_final: 0.7224 (t) REVERT: D 238 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.6030 (tmm-80) REVERT: D 240 TYR cc_start: 0.8969 (m-80) cc_final: 0.7567 (m-80) outliers start: 24 outliers final: 8 residues processed: 211 average time/residue: 0.2133 time to fit residues: 64.6733 Evaluate side-chains 161 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 266 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.117191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.098343 restraints weight = 44656.714| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.45 r_work: 0.2991 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10546 Z= 0.158 Angle : 0.539 5.111 14350 Z= 0.275 Chirality : 0.036 0.146 1594 Planarity : 0.004 0.036 1816 Dihedral : 6.921 52.803 1626 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.57 % Allowed : 8.66 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.55 (0.25), residues: 1258 helix: 3.14 (0.18), residues: 764 sheet: -0.15 (0.43), residues: 144 loop : -0.94 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.013 0.001 TYR C 106 PHE 0.009 0.001 PHE B 279 TRP 0.009 0.001 TRP B 161 HIS 0.004 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (10546) covalent geometry : angle 0.53921 / 0.27 (14350) hydrogen bonds : bond 0.04069 / 2.84 ( 636) hydrogen bonds : angle 5.00153 / 3.72 ( 1896) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8846 (tmm) cc_final: 0.8524 (tmm) REVERT: A 185 HIS cc_start: 0.7724 (t-90) cc_final: 0.6933 (m170) REVERT: A 236 LYS cc_start: 0.8310 (mmmm) cc_final: 0.7809 (mtpp) REVERT: A 240 TYR cc_start: 0.8118 (m-80) cc_final: 0.7880 (m-80) REVERT: A 260 GLU cc_start: 0.8822 (pt0) cc_final: 0.8592 (pt0) REVERT: B 86 ARG cc_start: 0.8761 (ttt90) cc_final: 0.8381 (ttm-80) REVERT: C 185 HIS cc_start: 0.7739 (t-90) cc_final: 0.6880 (m170) REVERT: C 236 LYS cc_start: 0.8320 (mmmm) cc_final: 0.7839 (mtpp) REVERT: C 240 TYR cc_start: 0.8121 (m-80) cc_final: 0.7901 (m-80) REVERT: D 86 ARG cc_start: 0.8788 (ttt90) cc_final: 0.8420 (ttm-80) outliers start: 17 outliers final: 11 residues processed: 175 average time/residue: 0.2152 time to fit residues: 55.1161 Evaluate side-chains 158 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 263 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 114 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.120890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.102023 restraints weight = 42968.651| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.30 r_work: 0.3056 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10546 Z= 0.145 Angle : 0.504 4.321 14350 Z= 0.257 Chirality : 0.035 0.141 1594 Planarity : 0.004 0.039 1816 Dihedral : 5.961 46.487 1612 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.38 % Allowed : 10.22 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.52 (0.24), residues: 1258 helix: 3.04 (0.18), residues: 776 sheet: 0.09 (0.44), residues: 144 loop : -1.03 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.011 0.001 TYR C 106 PHE 0.011 0.001 PHE B 105 TRP 0.008 0.001 TRP D 161 HIS 0.003 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10546) covalent geometry : angle 0.50445 / 0.26 (14350) hydrogen bonds : bond 0.03871 / 2.70 ( 636) hydrogen bonds : angle 4.72082 / 3.51 ( 1896) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7210 (tm-30) REVERT: A 120 MET cc_start: 0.8951 (tmm) cc_final: 0.8730 (tmm) REVERT: A 185 HIS cc_start: 0.7707 (t-90) cc_final: 0.7021 (m90) REVERT: A 240 TYR cc_start: 0.8187 (m-80) cc_final: 0.7911 (m-80) REVERT: B 86 ARG cc_start: 0.8744 (ttt90) cc_final: 0.8363 (ttm-80) REVERT: C 185 HIS cc_start: 0.7733 (t-90) cc_final: 0.6956 (m90) REVERT: C 240 TYR cc_start: 0.8194 (m-80) cc_final: 0.7904 (m-80) REVERT: D 86 ARG cc_start: 0.8781 (ttt90) cc_final: 0.8404 (ttm-80) outliers start: 15 outliers final: 15 residues processed: 165 average time/residue: 0.1882 time to fit residues: 46.0122 Evaluate side-chains 165 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 296 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 104 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.100671 restraints weight = 45459.401| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.50 r_work: 0.3074 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10546 Z= 0.223 Angle : 0.560 4.452 14350 Z= 0.288 Chirality : 0.037 0.144 1594 Planarity : 0.004 0.044 1816 Dihedral : 6.497 46.483 1612 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.03 % Allowed : 10.87 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.24), residues: 1258 helix: 2.76 (0.18), residues: 776 sheet: 0.06 (0.44), residues: 150 loop : -1.19 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.014 0.001 TYR C 106 PHE 0.020 0.002 PHE A 221 TRP 0.009 0.001 TRP B 161 HIS 0.003 0.001 HIS C 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (10546) covalent geometry : angle 0.56006 / 0.29 (14350) hydrogen bonds : bond 0.04144 / 2.85 ( 636) hydrogen bonds : angle 4.80918 / 3.56 ( 1896) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7406 (tm-30) REVERT: A 185 HIS cc_start: 0.7742 (t-90) cc_final: 0.6996 (m170) REVERT: A 237 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7526 (t0) REVERT: A 240 TYR cc_start: 0.8228 (m-80) cc_final: 0.7861 (m-80) REVERT: B 86 ARG cc_start: 0.8854 (ttt90) cc_final: 0.8464 (ttm-80) REVERT: C 185 HIS cc_start: 0.7814 (t-90) cc_final: 0.7016 (m90) REVERT: C 240 TYR cc_start: 0.8213 (m-80) cc_final: 0.7861 (m-80) REVERT: D 86 ARG cc_start: 0.8863 (ttt90) cc_final: 0.8474 (ttm-80) outliers start: 22 outliers final: 20 residues processed: 161 average time/residue: 0.2209 time to fit residues: 51.4766 Evaluate side-chains 164 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 296 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 33 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.123686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.103585 restraints weight = 44610.819| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.48 r_work: 0.3093 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10546 Z= 0.118 Angle : 0.485 3.942 14350 Z= 0.245 Chirality : 0.034 0.140 1594 Planarity : 0.004 0.043 1816 Dihedral : 5.661 45.114 1612 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.30 % Allowed : 10.87 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.25), residues: 1258 helix: 3.06 (0.18), residues: 770 sheet: 0.08 (0.45), residues: 140 loop : -0.94 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 197 TYR 0.010 0.001 TYR C 106 PHE 0.012 0.001 PHE A 221 TRP 0.007 0.001 TRP A 161 HIS 0.002 0.000 HIS C 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (10546) covalent geometry : angle 0.48506 / 0.25 (14350) hydrogen bonds : bond 0.03592 / 2.49 ( 636) hydrogen bonds : angle 4.46907 / 3.33 ( 1896) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7370 (tm-30) REVERT: A 185 HIS cc_start: 0.7805 (t-90) cc_final: 0.6937 (m90) REVERT: A 240 TYR cc_start: 0.8189 (m-80) cc_final: 0.7961 (m-80) REVERT: B 86 ARG cc_start: 0.8810 (ttt90) cc_final: 0.8417 (ttm-80) REVERT: C 185 HIS cc_start: 0.7854 (t-90) cc_final: 0.6948 (m170) REVERT: C 240 TYR cc_start: 0.8158 (m-80) cc_final: 0.7950 (m-80) REVERT: D 86 ARG cc_start: 0.8814 (ttt90) cc_final: 0.8422 (ttm-80) outliers start: 25 outliers final: 20 residues processed: 173 average time/residue: 0.2155 time to fit residues: 54.0146 Evaluate side-chains 167 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 296 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 105 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.123146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.103049 restraints weight = 45019.295| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.48 r_work: 0.3084 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10546 Z= 0.143 Angle : 0.494 4.080 14350 Z= 0.249 Chirality : 0.034 0.139 1594 Planarity : 0.004 0.042 1816 Dihedral : 5.513 44.921 1610 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.58 % Allowed : 11.14 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.53 (0.24), residues: 1258 helix: 3.05 (0.18), residues: 770 sheet: 0.02 (0.45), residues: 140 loop : -0.90 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.010 0.001 TYR C 106 PHE 0.011 0.001 PHE B 105 TRP 0.007 0.001 TRP D 161 HIS 0.002 0.001 HIS C 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (10546) covalent geometry : angle 0.49380 / 0.25 (14350) hydrogen bonds : bond 0.03610 / 2.50 ( 636) hydrogen bonds : angle 4.45696 / 3.32 ( 1896) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7423 (tm-30) REVERT: A 185 HIS cc_start: 0.7792 (t-90) cc_final: 0.6949 (m170) REVERT: A 240 TYR cc_start: 0.8206 (m-80) cc_final: 0.7961 (m-80) REVERT: B 86 ARG cc_start: 0.8818 (ttt90) cc_final: 0.8424 (ttm-80) REVERT: B 104 TYR cc_start: 0.7952 (t80) cc_final: 0.7641 (t80) REVERT: C 185 HIS cc_start: 0.7806 (t-90) cc_final: 0.6980 (m170) REVERT: C 240 TYR cc_start: 0.8185 (m-80) cc_final: 0.7957 (m-80) REVERT: D 86 ARG cc_start: 0.8819 (ttt90) cc_final: 0.8424 (ttm-80) outliers start: 28 outliers final: 22 residues processed: 165 average time/residue: 0.2250 time to fit residues: 53.2354 Evaluate side-chains 171 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 296 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 41 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.121812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.101618 restraints weight = 45011.184| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.50 r_work: 0.3056 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10546 Z= 0.197 Angle : 0.527 4.876 14350 Z= 0.269 Chirality : 0.035 0.140 1594 Planarity : 0.004 0.043 1816 Dihedral : 5.761 45.223 1607 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.49 % Allowed : 11.42 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.36 (0.24), residues: 1258 helix: 2.92 (0.18), residues: 770 sheet: -0.05 (0.46), residues: 140 loop : -0.96 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.010 0.001 TYR A 199 PHE 0.009 0.001 PHE B 105 TRP 0.007 0.001 TRP B 161 HIS 0.002 0.001 HIS C 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (10546) covalent geometry : angle 0.52713 / 0.27 (14350) hydrogen bonds : bond 0.03892 / 2.68 ( 636) hydrogen bonds : angle 4.60202 / 3.41 ( 1896) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 HIS cc_start: 0.7822 (t-90) cc_final: 0.7019 (m170) REVERT: B 86 ARG cc_start: 0.8833 (ttt90) cc_final: 0.8435 (ttm-80) REVERT: C 185 HIS cc_start: 0.7819 (t-90) cc_final: 0.6954 (m170) REVERT: C 306 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7454 (pp30) REVERT: D 86 ARG cc_start: 0.8826 (ttt90) cc_final: 0.8415 (ttm-80) outliers start: 27 outliers final: 18 residues processed: 161 average time/residue: 0.2053 time to fit residues: 47.4371 Evaluate side-chains 164 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 296 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 110 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.122505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.102460 restraints weight = 44987.408| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.48 r_work: 0.3095 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10546 Z= 0.162 Angle : 0.507 4.173 14350 Z= 0.257 Chirality : 0.035 0.140 1594 Planarity : 0.004 0.043 1816 Dihedral : 5.544 44.577 1607 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.39 % Allowed : 12.34 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.42 (0.25), residues: 1258 helix: 2.98 (0.18), residues: 770 sheet: -0.10 (0.46), residues: 140 loop : -0.95 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.013 0.001 TYR C 106 PHE 0.008 0.001 PHE B 105 TRP 0.010 0.001 TRP B 34 HIS 0.002 0.001 HIS C 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (10546) covalent geometry : angle 0.50741 / 0.26 (14350) hydrogen bonds : bond 0.03740 / 2.59 ( 636) hydrogen bonds : angle 4.51610 / 3.36 ( 1896) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 HIS cc_start: 0.7783 (t-90) cc_final: 0.6971 (m170) REVERT: B 86 ARG cc_start: 0.8804 (ttt90) cc_final: 0.8399 (ttm-80) REVERT: B 150 LYS cc_start: 0.8991 (ttpt) cc_final: 0.8625 (ttmt) REVERT: C 185 HIS cc_start: 0.7952 (t-90) cc_final: 0.7088 (m170) REVERT: C 237 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7204 (t0) REVERT: D 86 ARG cc_start: 0.8800 (ttt90) cc_final: 0.8390 (ttm-80) REVERT: D 150 LYS cc_start: 0.8976 (ttpt) cc_final: 0.8608 (ttmt) outliers start: 26 outliers final: 21 residues processed: 162 average time/residue: 0.2183 time to fit residues: 50.2454 Evaluate side-chains 167 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 296 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 45 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.123757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.103796 restraints weight = 44788.548| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.47 r_work: 0.3093 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10546 Z= 0.120 Angle : 0.487 4.282 14350 Z= 0.246 Chirality : 0.034 0.137 1594 Planarity : 0.004 0.043 1816 Dihedral : 5.293 44.222 1607 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.93 % Allowed : 12.43 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.25), residues: 1258 helix: 3.07 (0.18), residues: 770 sheet: -0.12 (0.46), residues: 140 loop : -0.84 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 197 TYR 0.012 0.001 TYR C 106 PHE 0.009 0.001 PHE B 105 TRP 0.010 0.001 TRP B 34 HIS 0.002 0.000 HIS C 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (10546) covalent geometry : angle 0.48704 / 0.25 (14350) hydrogen bonds : bond 0.03565 / 2.47 ( 636) hydrogen bonds : angle 4.38359 / 3.27 ( 1896) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 HIS cc_start: 0.7770 (t-90) cc_final: 0.6958 (m170) REVERT: B 86 ARG cc_start: 0.8792 (ttt90) cc_final: 0.8383 (ttm-80) REVERT: B 104 TYR cc_start: 0.7960 (t80) cc_final: 0.7636 (t80) REVERT: B 150 LYS cc_start: 0.8983 (ttpt) cc_final: 0.8614 (ttmt) REVERT: C 185 HIS cc_start: 0.7811 (t-90) cc_final: 0.7068 (m170) REVERT: D 86 ARG cc_start: 0.8788 (ttt90) cc_final: 0.8372 (ttm-80) REVERT: D 150 LYS cc_start: 0.8977 (ttpt) cc_final: 0.8611 (ttmt) outliers start: 21 outliers final: 19 residues processed: 161 average time/residue: 0.2221 time to fit residues: 50.6205 Evaluate side-chains 166 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 296 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 81 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 31 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.124631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104565 restraints weight = 44820.158| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.50 r_work: 0.3108 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10546 Z= 0.111 Angle : 0.479 4.373 14350 Z= 0.241 Chirality : 0.034 0.138 1594 Planarity : 0.004 0.043 1816 Dihedral : 4.859 43.590 1605 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.93 % Allowed : 12.62 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.69 (0.25), residues: 1258 helix: 3.16 (0.18), residues: 772 sheet: -0.13 (0.45), residues: 140 loop : -0.71 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.011 0.001 TYR C 106 PHE 0.009 0.001 PHE A 221 TRP 0.012 0.001 TRP B 34 HIS 0.003 0.000 HIS C 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (10546) covalent geometry : angle 0.47869 / 0.24 (14350) hydrogen bonds : bond 0.03390 / 2.35 ( 636) hydrogen bonds : angle 4.25024 / 3.18 ( 1896) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 HIS cc_start: 0.7888 (t-90) cc_final: 0.7048 (m170) REVERT: B 86 ARG cc_start: 0.8780 (ttt90) cc_final: 0.8368 (ttm-80) REVERT: B 104 TYR cc_start: 0.7954 (t80) cc_final: 0.7653 (t80) REVERT: C 185 HIS cc_start: 0.7799 (t-90) cc_final: 0.7078 (m170) REVERT: C 237 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7090 (t0) REVERT: D 86 ARG cc_start: 0.8781 (ttt90) cc_final: 0.8362 (ttm-80) outliers start: 21 outliers final: 20 residues processed: 163 average time/residue: 0.2050 time to fit residues: 47.7322 Evaluate side-chains 169 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 GLN Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 296 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.123969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103925 restraints weight = 44687.910| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.49 r_work: 0.3092 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10546 Z= 0.142 Angle : 0.494 6.203 14350 Z= 0.251 Chirality : 0.034 0.138 1594 Planarity : 0.004 0.043 1816 Dihedral : 5.066 43.560 1605 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.93 % Allowed : 12.71 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 2.64 (0.25), residues: 1258 helix: 3.12 (0.18), residues: 772 sheet: -0.17 (0.45), residues: 140 loop : -0.73 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.012 0.001 TYR C 106 PHE 0.008 0.001 PHE B 105 TRP 0.011 0.001 TRP B 34 HIS 0.002 0.000 HIS C 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (10546) covalent geometry : angle 0.49408 / 0.25 (14350) hydrogen bonds : bond 0.03511 / 2.43 ( 636) hydrogen bonds : angle 4.32293 / 3.22 ( 1896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4009.58 seconds wall clock time: 68 minutes 47.12 seconds (4127.12 seconds total)