Starting phenix.real_space_refine on Sat Jul 4 11:25:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8flm_29282/07_2026/8flm_29282_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8flm_29282/07_2026/8flm_29282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8flm_29282/07_2026/8flm_29282_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8flm_29282/07_2026/8flm_29282_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8flm_29282/07_2026/8flm_29282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8flm_29282/07_2026/8flm_29282.map" } resolution = 2.9 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= 0.003 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 6532 2.51 5 N 1790 2.21 5 O 1824 1.98 5 F 8 1.80 5 H 10060 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 20272 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5013 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 17, 'TRANS': 300} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 5013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5013 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 17, 'TRANS': 300} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 5013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5013 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 17, 'TRANS': 300} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 5013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 5013 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 17, 'TRANS': 300} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'Y6H': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'1SY': 1, '9IM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'9IM': 1, 'Y6H': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 3.28, per 1000 atoms: 0.16 Number of scatterers: 20272 At special positions: 0 Unit cell: (89.64, 98.28, 104.76, 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 1824 8.00 N 1790 7.00 C 6532 6.00 H 10060 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: 1.98 Conformation dependent library (CDL) restraints added in 533.7 milliseconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 64.3% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 16 through 37 Processing helix chain 'A' and resid 39 through 70 removed outlier: 3.730A pdb=" N GLU A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 91 through 109 Processing helix chain 'A' and resid 117 through 134 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.977A pdb=" N GLY A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 167 " --> pdb=" O TYR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 186 Proline residue: A 173 - end of helix removed outlier: 4.376A pdb=" N GLN A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ALA A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.760A pdb=" N ALA A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 280 through 302 Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.676A 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: 3.710A pdb=" N GLU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 77 Processing helix chain 'B' and resid 80 through 89 Processing helix chain 'B' and resid 91 through 109 Processing helix chain 'B' and resid 117 through 134 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 154 through 165 removed outlier: 4.035A pdb=" N GLY B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 186 Proline residue: B 173 - end of helix removed outlier: 4.402A pdb=" N GLN B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ALA B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 removed outlier: 3.650A pdb=" N ALA B 215 " --> pdb=" O ASN B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 273 Processing helix chain 'B' and resid 280 through 301 Processing helix chain 'B' and resid 324 through 334 Processing helix chain 'C' and resid 16 through 37 Processing helix chain 'C' and resid 39 through 70 removed outlier: 3.725A pdb=" N GLU C 68 " --> pdb=" O CYS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 77 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 109 Processing helix chain 'C' and resid 117 through 134 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 154 through 167 removed outlier: 3.746A pdb=" N GLY C 158 " --> pdb=" O ASN C 154 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 167 " --> pdb=" O TYR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 186 Proline residue: C 173 - end of helix removed outlier: 4.512A pdb=" N GLN C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ALA C 177 " --> pdb=" O PRO C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 216 removed outlier: 3.530A pdb=" N ALA C 215 " --> pdb=" O ASN C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 removed outlier: 3.527A pdb=" N THR C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 301 removed outlier: 3.502A pdb=" N ASP C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.552A 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: 3.713A pdb=" N GLU D 68 " --> pdb=" O CYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 77 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 134 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 154 through 165 removed outlier: 4.033A pdb=" N GLY D 158 " --> pdb=" O ASN D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 186 Proline residue: D 173 - end of helix removed outlier: 4.383A pdb=" N GLN D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA D 177 " --> pdb=" O PRO D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 216 removed outlier: 3.606A pdb=" N ALA D 215 " --> pdb=" O ASN D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 273 Processing helix chain 'D' and resid 280 through 301 Processing helix chain 'D' and resid 324 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 224 removed outlier: 6.753A pdb=" N ILE A 244 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N SER A 243 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A 259 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLU A 249 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU A 198 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE A 312 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE A 200 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N TYR A 314 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.440A 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: 6.596A pdb=" N GLN A 228 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 239 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLY A 230 " --> pdb=" O ASP A 237 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 219 through 224 removed outlier: 7.084A pdb=" N ILE B 244 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N SER B 243 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 259 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU B 249 " --> pdb=" O ARG B 253 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ARG B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 200 " --> pdb=" O ARG B 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 228 through 232 removed outlier: 6.754A pdb=" N ARG B 232 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 5.460A 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 224 removed outlier: 6.997A pdb=" N ILE C 244 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N SER C 243 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 259 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLU C 249 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ARG C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU C 198 " --> pdb=" O ARG C 310 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE C 312 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE C 200 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N TYR C 314 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 6.335A 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: 6.649A pdb=" N GLN C 228 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL C 239 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLY C 230 " --> pdb=" O ASP C 237 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 219 through 224 removed outlier: 7.035A pdb=" N ILE D 244 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N SER D 243 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU D 259 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLU D 249 " --> pdb=" O ARG D 253 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ARG D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU D 198 " --> pdb=" O ARG D 310 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ILE D 312 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE D 200 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N TYR D 314 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 6.468A 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: 6.400A pdb=" N GLN D 228 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL D 239 " --> pdb=" O GLN D 228 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLY D 230 " --> pdb=" O ASP D 237 " (cutoff:3.500A) 629 hydrogen bonds defined for protein. 1875 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: 4.44 Time building geometry restraints manager: 2.67 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: 10020 1.03 - 1.23: 46 1.23 - 1.42: 4389 1.42 - 1.61: 5981 1.61 - 1.81: 70 Bond restraints: 20506 Sorted by residual: bond pdb=" C40 1SY B 401 " pdb=" N39 1SY B 401 " ideal model delta sigma weight residual 1.304 1.429 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C40 1SY D 401 " pdb=" N39 1SY D 401 " ideal model delta sigma weight residual 1.304 1.429 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C16 9IM B 402 " pdb=" N06 9IM B 402 " ideal model delta sigma weight residual 1.393 1.518 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C16 9IM C 402 " pdb=" N06 9IM C 402 " ideal model delta sigma weight residual 1.393 1.516 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C36 1SY D 401 " pdb=" N42 1SY D 401 " ideal model delta sigma weight residual 1.357 1.472 -0.115 2.00e-02 2.50e+03 3.28e+01 ... (remaining 20501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.14: 36914 6.14 - 12.28: 33 12.28 - 18.42: 13 18.42 - 24.55: 0 24.55 - 30.69: 4 Bond angle restraints: 36964 Sorted by residual: angle pdb=" C18 Y6H C 401 " pdb=" C19 Y6H C 401 " pdb=" C21 Y6H C 401 " ideal model delta sigma weight residual 111.16 141.85 -30.69 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C18 Y6H A 401 " pdb=" C19 Y6H A 401 " pdb=" C21 Y6H A 401 " ideal model delta sigma weight residual 111.16 141.63 -30.47 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C20 Y6H C 401 " pdb=" C19 Y6H C 401 " pdb=" C22 Y6H C 401 " ideal model delta sigma weight residual 108.62 138.35 -29.73 3.00e+00 1.11e-01 9.82e+01 angle pdb=" C20 Y6H A 401 " pdb=" C19 Y6H A 401 " pdb=" C22 Y6H A 401 " ideal model delta sigma weight residual 108.62 138.08 -29.46 3.00e+00 1.11e-01 9.65e+01 angle pdb=" O19 1SY B 401 " pdb=" P18 1SY B 401 " pdb=" O44 1SY B 401 " ideal model delta sigma weight residual 123.21 104.87 18.34 3.00e+00 1.11e-01 3.74e+01 ... (remaining 36959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.86: 8689 20.86 - 41.71: 764 41.71 - 62.57: 268 62.57 - 83.43: 23 83.43 - 104.28: 8 Dihedral angle restraints: 9752 sinusoidal: 5488 harmonic: 4264 Sorted by residual: dihedral pdb=" C18 Y6H A 401 " pdb=" C24 Y6H A 401 " pdb=" O23 Y6H A 401 " pdb=" C25 Y6H A 401 " ideal model delta sinusoidal sigma weight residual -58.10 46.18 -104.28 1 3.00e+01 1.11e-03 1.33e+01 dihedral pdb=" C18 Y6H A 401 " pdb=" C28 Y6H A 401 " pdb=" O29 Y6H A 401 " pdb=" C25 Y6H A 401 " ideal model delta sinusoidal sigma weight residual -58.49 35.93 -94.42 1 3.00e+01 1.11e-03 1.15e+01 dihedral pdb=" CA ASP C 205 " pdb=" CB ASP C 205 " pdb=" CG ASP C 205 " pdb=" OD1 ASP C 205 " ideal model delta sinusoidal sigma weight residual -30.00 -88.00 58.00 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 9749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1302 0.043 - 0.086: 208 0.086 - 0.130: 64 0.130 - 0.173: 4 0.173 - 0.216: 4 Chirality restraints: 1582 Sorted by residual: 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 -2.48 -0.22 2.00e-01 2.50e+01 1.16e+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 -2.54 -0.20 2.00e-01 2.50e+01 1.02e+00 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 -2.54 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1579 not shown) Planarity restraints: 2980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 301 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" CG ASP B 301 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASP B 301 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP B 301 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 301 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C ASP B 301 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP B 301 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA B 302 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 73 " 0.006 2.00e-02 2.50e+03 1.28e-02 1.63e+00 pdb=" C ILE D 73 " -0.022 2.00e-02 2.50e+03 pdb=" O ILE D 73 " 0.008 2.00e-02 2.50e+03 pdb=" N HIS D 74 " 0.007 2.00e-02 2.50e+03 ... (remaining 2977 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1853 2.22 - 2.82: 43140 2.82 - 3.41: 55381 3.41 - 4.01: 73890 4.01 - 4.60: 113761 Nonbonded interactions: 288025 Sorted by model distance: nonbonded pdb=" HE ARG C 197 " pdb=" OD1 ASN C 307 " model vdw 1.625 2.450 nonbonded pdb=" HH TYR A 245 " pdb=" O GLY B 234 " model vdw 1.631 2.450 nonbonded pdb=" HE ARG A 197 " pdb=" OD1 ASN A 307 " model vdw 1.640 2.450 nonbonded pdb=" OD1 ASP A 223 " pdb=" H LYS A 224 " model vdw 1.662 2.450 nonbonded pdb="HH11 ARG C 220 " pdb=" OE2 GLU C 246 " model vdw 1.686 2.450 ... (remaining 288020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 335) selection = (chain 'B' and resid 4 through 335) selection = (chain 'C' and resid 4 through 335) selection = (chain 'D' and resid 4 through 335) } 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: 0.760 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: 0.130 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.980 Find NCS groups from input model: 0.360 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:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 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 : 0.007 0.125 10446 Z= 0.346 Angle : 1.026 30.693 14216 Z= 0.401 Chirality : 0.037 0.216 1582 Planarity : 0.003 0.030 1788 Dihedral : 17.938 104.282 4012 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.94 % Allowed : 23.22 % Favored : 75.84 % 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: 1.55 (0.25), residues: 1240 helix: 2.18 (0.19), residues: 736 sheet: -1.09 (0.49), residues: 96 loop : -0.58 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 281 TYR 0.008 0.001 TYR C 46 PHE 0.010 0.001 PHE C 105 TRP 0.014 0.001 TRP C 119 HIS 0.002 0.000 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00699 / 0.35 (10446) covalent geometry : angle 1.02574 / 0.40 (14216) hydrogen bonds : bond 0.14702 / 10.43 ( 629) hydrogen bonds : angle 6.41331 / 4.87 ( 1875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.538 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 65 average time/residue: 0.6925 time to fit residues: 51.6211 Evaluate side-chains 59 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 213 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.0670 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.096383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.077351 restraints weight = 49496.671| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.13 r_work: 0.2923 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10446 Z= 0.107 Angle : 0.509 5.143 14216 Z= 0.255 Chirality : 0.035 0.152 1582 Planarity : 0.004 0.033 1788 Dihedral : 5.470 47.728 1665 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.50 % Allowed : 21.54 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.68 (0.25), residues: 1240 helix: 2.37 (0.19), residues: 756 sheet: -0.98 (0.50), residues: 96 loop : -0.92 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 331 TYR 0.009 0.001 TYR C 199 PHE 0.008 0.001 PHE D 221 TRP 0.008 0.001 TRP D 161 HIS 0.002 0.001 HIS B 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (10446) covalent geometry : angle 0.50924 / 0.25 (14216) hydrogen bonds : bond 0.04205 / 2.95 ( 629) hydrogen bonds : angle 4.80167 / 3.65 ( 1875) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.549 Fit side-chains REVERT: A 197 ARG cc_start: 0.7834 (mtt90) cc_final: 0.7412 (mtt180) REVERT: A 223 ASP cc_start: 0.8085 (t0) cc_final: 0.7662 (t0) REVERT: C 120 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6216 (mtt) REVERT: D 99 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7882 (mp) REVERT: D 271 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8826 (ttm) outliers start: 16 outliers final: 3 residues processed: 74 average time/residue: 0.8925 time to fit residues: 73.7683 Evaluate side-chains 61 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 271 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 GLN ** C 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.093047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.073689 restraints weight = 49968.706| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.14 r_work: 0.2853 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10446 Z= 0.212 Angle : 0.556 5.066 14216 Z= 0.279 Chirality : 0.037 0.145 1582 Planarity : 0.004 0.026 1788 Dihedral : 5.288 42.873 1657 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.53 % Allowed : 20.69 % Favored : 76.78 % 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: 1.47 (0.24), residues: 1240 helix: 2.16 (0.19), residues: 760 sheet: -0.99 (0.51), residues: 96 loop : -0.94 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 331 TYR 0.012 0.001 TYR A 163 PHE 0.015 0.002 PHE C 105 TRP 0.013 0.002 TRP D 161 HIS 0.005 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (10446) covalent geometry : angle 0.55595 / 0.28 (14216) hydrogen bonds : bond 0.04961 / 3.49 ( 629) hydrogen bonds : angle 4.91076 / 3.74 ( 1875) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 56 time to evaluate : 0.584 Fit side-chains REVERT: A 197 ARG cc_start: 0.7887 (mtt90) cc_final: 0.7340 (mtt180) REVERT: A 223 ASP cc_start: 0.8147 (t0) cc_final: 0.7655 (t0) REVERT: B 99 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7791 (mp) REVERT: C 143 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7646 (mt-10) REVERT: D 99 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7811 (mp) REVERT: D 297 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7774 (m-30) outliers start: 27 outliers final: 7 residues processed: 70 average time/residue: 0.6173 time to fit residues: 50.3579 Evaluate side-chains 65 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 250 ASN Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain D residue 297 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 86 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN ** C 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.092706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.073547 restraints weight = 50064.166| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.13 r_work: 0.2851 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10446 Z= 0.203 Angle : 0.544 5.083 14216 Z= 0.274 Chirality : 0.037 0.142 1582 Planarity : 0.004 0.028 1788 Dihedral : 5.148 39.600 1657 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.72 % Allowed : 20.22 % Favored : 77.06 % 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: 1.39 (0.24), residues: 1240 helix: 2.13 (0.19), residues: 760 sheet: -1.05 (0.50), residues: 96 loop : -1.05 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 331 TYR 0.010 0.001 TYR A 106 PHE 0.018 0.002 PHE C 105 TRP 0.012 0.002 TRP D 161 HIS 0.004 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (10446) covalent geometry : angle 0.54351 / 0.27 (14216) hydrogen bonds : bond 0.04784 / 3.36 ( 629) hydrogen bonds : angle 4.83207 / 3.68 ( 1875) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 56 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 223 ASP cc_start: 0.8165 (t0) cc_final: 0.7660 (t0) REVERT: B 99 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7780 (mp) REVERT: C 99 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7541 (tp) REVERT: C 120 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6346 (mtt) REVERT: C 143 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: D 99 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7799 (mp) REVERT: D 143 GLU cc_start: 0.8241 (tp30) cc_final: 0.7866 (mm-30) outliers start: 29 outliers final: 13 residues processed: 73 average time/residue: 0.6098 time to fit residues: 51.7159 Evaluate side-chains 71 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 250 ASN Chi-restraints excluded: chain D residue 297 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 110 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 GLN ** C 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.093321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.074134 restraints weight = 49747.249| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.13 r_work: 0.2862 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10446 Z= 0.171 Angle : 0.520 5.096 14216 Z= 0.262 Chirality : 0.036 0.142 1582 Planarity : 0.004 0.030 1788 Dihedral : 4.971 34.945 1657 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.34 % Allowed : 20.97 % Favored : 76.69 % 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: 1.54 (0.24), residues: 1240 helix: 2.26 (0.19), residues: 760 sheet: -1.08 (0.50), residues: 96 loop : -1.00 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 331 TYR 0.009 0.001 TYR A 106 PHE 0.015 0.002 PHE C 105 TRP 0.011 0.001 TRP D 161 HIS 0.003 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (10446) covalent geometry : angle 0.51997 / 0.26 (14216) hydrogen bonds : bond 0.04518 / 3.16 ( 629) hydrogen bonds : angle 4.72012 / 3.59 ( 1875) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 223 ASP cc_start: 0.8184 (t0) cc_final: 0.7682 (t0) REVERT: B 99 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7773 (mp) REVERT: C 99 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7578 (tp) REVERT: C 120 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6309 (mtt) REVERT: C 143 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7621 (mt-10) REVERT: D 99 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7797 (mp) REVERT: D 143 GLU cc_start: 0.8234 (tp30) cc_final: 0.7792 (mm-30) outliers start: 25 outliers final: 13 residues processed: 74 average time/residue: 0.6474 time to fit residues: 55.4474 Evaluate side-chains 76 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 250 ASN Chi-restraints excluded: chain D residue 297 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.094141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.074929 restraints weight = 49509.469| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.13 r_work: 0.2876 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10446 Z= 0.140 Angle : 0.499 5.110 14216 Z= 0.251 Chirality : 0.035 0.144 1582 Planarity : 0.004 0.031 1788 Dihedral : 4.774 33.949 1657 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.62 % Allowed : 21.16 % Favored : 76.22 % 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: 1.74 (0.25), residues: 1240 helix: 2.45 (0.19), residues: 756 sheet: -1.05 (0.50), residues: 96 loop : -0.93 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 331 TYR 0.009 0.001 TYR D 106 PHE 0.013 0.001 PHE C 105 TRP 0.011 0.001 TRP B 161 HIS 0.002 0.000 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (10446) covalent geometry : angle 0.49912 / 0.25 (14216) hydrogen bonds : bond 0.04219 / 2.95 ( 629) hydrogen bonds : angle 4.61105 / 3.51 ( 1875) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 19 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7673 (mp10) REVERT: A 223 ASP cc_start: 0.8201 (t0) cc_final: 0.7697 (t0) REVERT: B 99 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7780 (mp) REVERT: B 106 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7901 (t80) REVERT: C 99 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7573 (tp) REVERT: C 143 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7640 (mt-10) REVERT: C 223 ASP cc_start: 0.8057 (t0) cc_final: 0.7691 (t0) REVERT: D 99 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7804 (mp) REVERT: D 143 GLU cc_start: 0.8207 (tp30) cc_final: 0.7780 (mm-30) outliers start: 28 outliers final: 13 residues processed: 79 average time/residue: 0.8260 time to fit residues: 73.4515 Evaluate side-chains 77 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 250 ASN Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 250 ASN Chi-restraints excluded: chain D residue 297 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.094831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.075670 restraints weight = 49564.539| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.13 r_work: 0.2890 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10446 Z= 0.118 Angle : 0.489 6.449 14216 Z= 0.245 Chirality : 0.034 0.144 1582 Planarity : 0.004 0.032 1788 Dihedral : 4.608 32.487 1657 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.87 % Allowed : 21.72 % Favored : 76.40 % 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: 1.93 (0.25), residues: 1240 helix: 2.60 (0.19), residues: 756 sheet: -1.04 (0.50), residues: 96 loop : -0.84 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 334 TYR 0.008 0.001 TYR B 106 PHE 0.011 0.001 PHE A 105 TRP 0.010 0.001 TRP B 161 HIS 0.002 0.000 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (10446) covalent geometry : angle 0.48853 / 0.24 (14216) hydrogen bonds : bond 0.03964 / 2.77 ( 629) hydrogen bonds : angle 4.49459 / 3.42 ( 1875) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 19 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7612 (mp10) REVERT: A 220 ARG cc_start: 0.8647 (mtp85) cc_final: 0.8414 (mtp85) REVERT: A 223 ASP cc_start: 0.8209 (t0) cc_final: 0.7703 (t0) REVERT: B 99 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7773 (mp) REVERT: B 106 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7903 (t80) REVERT: C 99 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7456 (mt) REVERT: C 120 MET cc_start: 0.6870 (mtt) cc_final: 0.6226 (mmt) REVERT: C 143 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7669 (mt-10) REVERT: C 220 ARG cc_start: 0.8106 (mtp85) cc_final: 0.7881 (mtp85) REVERT: C 223 ASP cc_start: 0.8048 (t0) cc_final: 0.7695 (t0) REVERT: D 99 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7816 (mp) REVERT: D 119 TRP cc_start: 0.8703 (t60) cc_final: 0.8267 (t60) REVERT: D 143 GLU cc_start: 0.8148 (tp30) cc_final: 0.7896 (mp0) outliers start: 20 outliers final: 7 residues processed: 75 average time/residue: 0.8710 time to fit residues: 73.3895 Evaluate side-chains 71 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 297 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 120 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.094910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.075724 restraints weight = 49575.849| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.13 r_work: 0.2894 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10446 Z= 0.125 Angle : 0.492 5.153 14216 Z= 0.246 Chirality : 0.035 0.142 1582 Planarity : 0.004 0.032 1788 Dihedral : 4.564 30.264 1657 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.69 % Allowed : 22.28 % Favored : 76.03 % 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: 2.02 (0.25), residues: 1240 helix: 2.65 (0.19), residues: 760 sheet: -1.05 (0.50), residues: 96 loop : -0.77 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 331 TYR 0.008 0.001 TYR B 106 PHE 0.011 0.001 PHE C 105 TRP 0.010 0.001 TRP B 161 HIS 0.002 0.000 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (10446) covalent geometry : angle 0.49151 / 0.25 (14216) hydrogen bonds : bond 0.03952 / 2.76 ( 629) hydrogen bonds : angle 4.47050 / 3.40 ( 1875) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 19 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7630 (mp10) REVERT: A 99 LEU cc_start: 0.7891 (tt) cc_final: 0.7527 (mt) REVERT: A 220 ARG cc_start: 0.8672 (mtp85) cc_final: 0.8434 (mtp85) REVERT: A 223 ASP cc_start: 0.8235 (t0) cc_final: 0.7725 (t0) REVERT: B 99 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7793 (mp) REVERT: B 106 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7903 (t80) REVERT: C 99 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7478 (mt) REVERT: C 143 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: C 223 ASP cc_start: 0.8079 (t0) cc_final: 0.7749 (t0) REVERT: D 99 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7803 (mp) REVERT: D 119 TRP cc_start: 0.8712 (t60) cc_final: 0.8267 (t60) REVERT: D 143 GLU cc_start: 0.8167 (tp30) cc_final: 0.7781 (mm-30) outliers start: 18 outliers final: 6 residues processed: 74 average time/residue: 0.8458 time to fit residues: 70.3368 Evaluate side-chains 71 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 297 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.095709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.076579 restraints weight = 48934.745| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.11 r_work: 0.2909 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10446 Z= 0.110 Angle : 0.481 5.317 14216 Z= 0.240 Chirality : 0.034 0.144 1582 Planarity : 0.003 0.033 1788 Dihedral : 4.398 27.706 1657 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.22 % Allowed : 22.66 % Favored : 76.12 % 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: 2.15 (0.25), residues: 1240 helix: 2.73 (0.19), residues: 764 sheet: -1.03 (0.50), residues: 96 loop : -0.67 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 331 TYR 0.009 0.001 TYR B 261 PHE 0.010 0.001 PHE C 105 TRP 0.009 0.001 TRP B 161 HIS 0.002 0.000 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10446) covalent geometry : angle 0.48066 / 0.24 (14216) hydrogen bonds : bond 0.03754 / 2.63 ( 629) hydrogen bonds : angle 4.37859 / 3.33 ( 1875) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 19 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7624 (mp10) REVERT: A 99 LEU cc_start: 0.7897 (tt) cc_final: 0.7568 (mt) REVERT: A 223 ASP cc_start: 0.8254 (t0) cc_final: 0.7755 (t0) REVERT: B 99 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7804 (mp) REVERT: B 106 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.7893 (t80) REVERT: C 99 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7479 (mt) REVERT: C 143 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7652 (mt-10) REVERT: C 223 ASP cc_start: 0.8085 (t0) cc_final: 0.7753 (t0) REVERT: D 99 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7798 (mp) REVERT: D 106 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7847 (t80) REVERT: D 119 TRP cc_start: 0.8695 (t60) cc_final: 0.8282 (t60) REVERT: D 143 GLU cc_start: 0.8165 (tp30) cc_final: 0.7785 (mm-30) outliers start: 13 outliers final: 5 residues processed: 68 average time/residue: 0.8931 time to fit residues: 67.9851 Evaluate side-chains 68 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 297 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.093932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.074726 restraints weight = 49764.728| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.13 r_work: 0.2873 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10446 Z= 0.163 Angle : 0.514 5.566 14216 Z= 0.258 Chirality : 0.036 0.144 1582 Planarity : 0.004 0.034 1788 Dihedral : 4.687 25.594 1656 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.22 % Allowed : 22.47 % Favored : 76.31 % 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: 2.00 (0.25), residues: 1240 helix: 2.62 (0.19), residues: 760 sheet: -1.02 (0.49), residues: 96 loop : -0.74 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 253 TYR 0.010 0.001 TYR C 163 PHE 0.015 0.002 PHE C 105 TRP 0.011 0.001 TRP D 161 HIS 0.003 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (10446) covalent geometry : angle 0.51370 / 0.26 (14216) hydrogen bonds : bond 0.04248 / 2.97 ( 629) hydrogen bonds : angle 4.53586 / 3.45 ( 1875) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Residue TYR 186 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 19 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7725 (mp10) REVERT: A 99 LEU cc_start: 0.7911 (tt) cc_final: 0.7554 (mt) REVERT: A 223 ASP cc_start: 0.8240 (t0) cc_final: 0.7728 (t0) REVERT: B 99 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7809 (mp) REVERT: B 106 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.7900 (t80) REVERT: C 99 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7509 (mt) REVERT: C 143 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7652 (mt-10) REVERT: C 223 ASP cc_start: 0.8137 (t0) cc_final: 0.7787 (t0) REVERT: D 99 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7827 (mp) REVERT: D 106 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7875 (t80) REVERT: D 143 GLU cc_start: 0.8179 (tp30) cc_final: 0.7912 (mp0) outliers start: 13 outliers final: 5 residues processed: 65 average time/residue: 0.6842 time to fit residues: 51.4749 Evaluate side-chains 72 residues out of total 1076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 TYR Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 106 TYR Chi-restraints excluded: chain D residue 297 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 119 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.094146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.074960 restraints weight = 49633.156| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.12 r_work: 0.2879 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10446 Z= 0.150 Angle : 0.503 5.194 14216 Z= 0.252 Chirality : 0.035 0.143 1582 Planarity : 0.004 0.032 1788 Dihedral : 4.597 25.101 1656 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.03 % Allowed : 22.57 % Favored : 76.40 % 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: 2.00 (0.25), residues: 1240 helix: 2.62 (0.19), residues: 760 sheet: -1.00 (0.49), residues: 96 loop : -0.76 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 331 TYR 0.010 0.001 TYR D 106 PHE 0.013 0.002 PHE C 105 TRP 0.009 0.001 TRP B 161 HIS 0.003 0.000 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (10446) covalent geometry : angle 0.50256 / 0.25 (14216) hydrogen bonds : bond 0.04148 / 2.90 ( 629) hydrogen bonds : angle 4.51784 / 3.44 ( 1875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4823.97 seconds wall clock time: 82 minutes 43.15 seconds (4963.15 seconds total)