Starting phenix.real_space_refine on Wed Sep 17 12:31:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rql_19445/09_2025/8rql_19445.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rql_19445/09_2025/8rql_19445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rql_19445/09_2025/8rql_19445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rql_19445/09_2025/8rql_19445.map" model { file = "/net/cci-nas-00/data/ceres_data/8rql_19445/09_2025/8rql_19445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rql_19445/09_2025/8rql_19445.cif" } resolution = 3.03 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= -0.001 sd= 0.033 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: 5 Type Number sf(0) Gaussians S 55 5.16 5 C 5537 2.51 5 N 1460 2.21 5 O 1588 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8646 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2142 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 3, 'TRANS': 274} Chain breaks: 3 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "A" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1683 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2572 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 55} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1755 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'FLF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.11, per 1000 atoms: 0.24 Number of scatterers: 8646 At special positions: 0 Unit cell: (87.556, 119.77, 123.074, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 F 6 9.00 O 1588 8.00 N 1460 7.00 C 5537 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 543.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 40.1% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'R' and resid 3 through 38 removed outlier: 4.341A pdb=" N THR R 10 " --> pdb=" O LYS R 6 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE R 11 " --> pdb=" O SER R 7 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP R 34 " --> pdb=" O VAL R 30 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TRP R 35 " --> pdb=" O ASN R 31 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL R 36 " --> pdb=" O CYS R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 69 removed outlier: 3.628A pdb=" N SER R 57 " --> pdb=" O ILE R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 77 removed outlier: 3.805A pdb=" N PHE R 76 " --> pdb=" O PHE R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 112 removed outlier: 3.971A pdb=" N PHE R 95 " --> pdb=" O VAL R 91 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA R 100 " --> pdb=" O SER R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 125 Processing helix chain 'R' and resid 125 through 158 removed outlier: 3.921A pdb=" N VAL R 130 " --> pdb=" O VAL R 126 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU R 131 " --> pdb=" O LYS R 127 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU R 134 " --> pdb=" O VAL R 130 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE R 152 " --> pdb=" O ILE R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 183 Processing helix chain 'R' and resid 187 through 212 removed outlier: 3.524A pdb=" N LEU R 200 " --> pdb=" O ALA R 196 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU R 201 " --> pdb=" O MET R 197 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE R 203 " --> pdb=" O LEU R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 253 Processing helix chain 'R' and resid 260 through 282 removed outlier: 3.547A pdb=" N LEU R 264 " --> pdb=" O ASN R 260 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR R 272 " --> pdb=" O MET R 268 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 3.836A pdb=" N SER R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS R 278 " --> pdb=" O SER R 274 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL R 279 " --> pdb=" O CYS R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 303 Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 96 through 102 removed outlier: 3.594A pdb=" N GLU A 101 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP A 102 " --> pdb=" O CYS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 removed outlier: 4.242A pdb=" N HIS A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 removed outlier: 3.872A pdb=" N SER A 135 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR A 136 " --> pdb=" O TYR A 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 132 through 136' Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.655A pdb=" N GLU A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 170 through 185 removed outlier: 4.105A pdb=" N LEU A 185 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 227 Processing helix chain 'B' and resid 21 through 42 removed outlier: 3.757A pdb=" N ARG B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.523A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.867A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.538A pdb=" N LYS A 54 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A 73 " --> pdb=" O LYS A 54 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU A 36 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N CYS A 105 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 109 through 111 Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 68 Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 80 removed outlier: 6.767A pdb=" N ALA B 90 " --> pdb=" O TYR B 76 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N MET B 78 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 88 " --> pdb=" O MET B 78 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TRP B 80 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU B 86 " --> pdb=" O TRP B 80 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP B 100 " --> pdb=" O LYS B 106 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LYS B 106 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 117 through 122 removed outlier: 4.507A pdb=" N GLY B 133 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASN B 142 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 152 " --> pdb=" O ASN B 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 163 through 168 removed outlier: 4.406A pdb=" N THR B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP B 187 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLN B 193 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 204 through 209 removed outlier: 3.851A pdb=" N GLN B 237 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASP B 229 " --> pdb=" O CYS B 235 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N CYS B 235 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 246 through 251 removed outlier: 6.898A pdb=" N ASP B 271 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLU B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 290 through 295 removed outlier: 6.526A pdb=" N GLY B 305 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL B 293 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B 303 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE B 295 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU B 301 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N CYS B 311 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL B 324 " --> pdb=" O CYS B 311 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B 313 " --> pdb=" O ALA B 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.835A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 4.065A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 4.065A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1384 1.32 - 1.44: 2482 1.44 - 1.56: 4878 1.56 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 8824 Sorted by residual: bond pdb=" N FLF R 401 " pdb=" C1' FLF R 401 " ideal model delta sigma weight residual 1.377 1.451 -0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" N FLF R 401 " pdb=" C6 FLF R 401 " ideal model delta sigma weight residual 1.378 1.450 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" N ILE R 179 " pdb=" CA ILE R 179 " ideal model delta sigma weight residual 1.460 1.502 -0.043 1.21e-02 6.83e+03 1.24e+01 bond pdb=" N ILE R 148 " pdb=" CA ILE R 148 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.06e-02 8.90e+03 8.95e+00 bond pdb=" C ASN R 149 " pdb=" O ASN R 149 " ideal model delta sigma weight residual 1.234 1.195 0.039 1.35e-02 5.49e+03 8.39e+00 ... (remaining 8819 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 11904 2.66 - 5.32: 58 5.32 - 7.98: 3 7.98 - 10.64: 2 10.64 - 13.30: 2 Bond angle restraints: 11969 Sorted by residual: angle pdb=" N ILE R 145 " pdb=" CA ILE R 145 " pdb=" C ILE R 145 " ideal model delta sigma weight residual 110.62 102.10 8.52 1.14e+00 7.69e-01 5.58e+01 angle pdb=" N ILE R 148 " pdb=" CA ILE R 148 " pdb=" C ILE R 148 " ideal model delta sigma weight residual 112.98 107.36 5.62 1.25e+00 6.40e-01 2.02e+01 angle pdb=" C2 FLF R 401 " pdb=" C1 FLF R 401 " pdb=" C7 FLF R 401 " ideal model delta sigma weight residual 118.34 105.04 13.30 3.00e+00 1.11e-01 1.96e+01 angle pdb=" N ILE R 179 " pdb=" CA ILE R 179 " pdb=" CB ILE R 179 " ideal model delta sigma weight residual 110.58 117.02 -6.44 1.50e+00 4.44e-01 1.84e+01 angle pdb=" CA ALA R 146 " pdb=" C ALA R 146 " pdb=" O ALA R 146 " ideal model delta sigma weight residual 121.07 116.50 4.57 1.10e+00 8.26e-01 1.73e+01 ... (remaining 11964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 4756 17.54 - 35.09: 354 35.09 - 52.63: 48 52.63 - 70.17: 4 70.17 - 87.72: 4 Dihedral angle restraints: 5166 sinusoidal: 1907 harmonic: 3259 Sorted by residual: dihedral pdb=" CB CYS S 22 " pdb=" SG CYS S 22 " pdb=" SG CYS S 96 " pdb=" CB CYS S 96 " ideal model delta sinusoidal sigma weight residual 93.00 62.33 30.67 1 1.00e+01 1.00e-02 1.34e+01 dihedral pdb=" CA PHE A 76 " pdb=" C PHE A 76 " pdb=" N LYS A 77 " pdb=" CA LYS A 77 " ideal model delta harmonic sigma weight residual 180.00 163.44 16.56 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ARG R 83 " pdb=" CB ARG R 83 " pdb=" CG ARG R 83 " pdb=" CD ARG R 83 " ideal model delta sinusoidal sigma weight residual 180.00 120.78 59.22 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 974 0.033 - 0.065: 281 0.065 - 0.098: 78 0.098 - 0.131: 48 0.131 - 0.164: 3 Chirality restraints: 1384 Sorted by residual: chirality pdb=" CB ILE R 148 " pdb=" CA ILE R 148 " pdb=" CG1 ILE R 148 " pdb=" CG2 ILE R 148 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CA ILE R 145 " pdb=" N ILE R 145 " pdb=" C ILE R 145 " pdb=" CB ILE R 145 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CB ILE R 179 " pdb=" CA ILE R 179 " pdb=" CG1 ILE R 179 " pdb=" CG2 ILE R 179 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 1381 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN R 144 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C ASN R 144 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN R 144 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE R 145 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 145 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C ILE R 145 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE R 145 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA R 146 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET R 81 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C MET R 81 " -0.028 2.00e-02 2.50e+03 pdb=" O MET R 81 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE R 82 " 0.009 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 127 2.66 - 3.22: 8395 3.22 - 3.78: 13445 3.78 - 4.34: 18910 4.34 - 4.90: 31516 Nonbonded interactions: 72393 Sorted by model distance: nonbonded pdb=" O ASP B 180 " pdb=" OG1 THR B 181 " model vdw 2.097 3.040 nonbonded pdb=" OG1 THR B 291 " pdb=" O VAL B 332 " model vdw 2.121 3.040 nonbonded pdb=" O ASP B 350 " pdb=" OG SER B 351 " model vdw 2.158 3.040 nonbonded pdb=" OE2 GLU A 71 " pdb=" NH1 ARG A 82 " model vdw 2.160 3.120 nonbonded pdb=" O THR B 103 " pdb=" OG1 THR B 104 " model vdw 2.198 3.040 ... (remaining 72388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.100 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 0.003 0.074 8826 Z= 0.172 Angle : 0.527 13.297 11973 Z= 0.310 Chirality : 0.039 0.164 1384 Planarity : 0.002 0.026 1500 Dihedral : 12.193 87.715 3048 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.22 % Allowed : 0.44 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.26), residues: 1106 helix: 1.86 (0.28), residues: 384 sheet: -0.92 (0.28), residues: 291 loop : -0.33 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 125 TYR 0.008 0.001 TYR B 76 PHE 0.011 0.001 PHE B 216 TRP 0.009 0.001 TRP B 99 HIS 0.002 0.001 HIS R 94 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8824) covalent geometry : angle 0.52695 (11969) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.26171 ( 4) hydrogen bonds : bond 0.14998 ( 466) hydrogen bonds : angle 6.52461 ( 1320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 0.357 Fit side-chains REVERT: R 63 PHE cc_start: 0.7390 (t80) cc_final: 0.7186 (t80) REVERT: R 78 THR cc_start: 0.5616 (m) cc_final: 0.5307 (p) REVERT: R 83 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6913 (ttm170) REVERT: R 87 ASN cc_start: 0.8717 (m110) cc_final: 0.8192 (m-40) REVERT: R 284 ASN cc_start: 0.7823 (t0) cc_final: 0.7503 (t0) REVERT: A 73 GLN cc_start: 0.8547 (mt0) cc_final: 0.8281 (mt0) REVERT: A 120 GLU cc_start: 0.7035 (mp0) cc_final: 0.6792 (tt0) REVERT: A 123 HIS cc_start: 0.6358 (t-90) cc_final: 0.6084 (t-90) REVERT: A 135 SER cc_start: 0.8278 (t) cc_final: 0.7940 (p) REVERT: A 181 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7825 (tp40) REVERT: A 220 LYS cc_start: 0.6409 (ttpt) cc_final: 0.5948 (mptt) REVERT: B 53 ASN cc_start: 0.7093 (m-40) cc_final: 0.6770 (p0) REVERT: B 59 ARG cc_start: 0.7169 (mmm160) cc_final: 0.6893 (mmp-170) REVERT: B 63 ARG cc_start: 0.7723 (ttt180) cc_final: 0.7000 (mmm160) REVERT: B 141 TYR cc_start: 0.8370 (m-80) cc_final: 0.7916 (m-80) REVERT: G 47 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7624 (mp0) REVERT: S 65 LYS cc_start: 0.7686 (tptt) cc_final: 0.7452 (tptt) outliers start: 2 outliers final: 1 residues processed: 224 average time/residue: 0.0968 time to fit residues: 30.1608 Evaluate side-chains 167 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 179 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0040 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.0270 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 0.1980 overall best weight: 0.2650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 284 ASN A 130 ASN A 197 HIS S 171 GLN S 182 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.169400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133215 restraints weight = 11055.522| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.56 r_work: 0.3428 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8826 Z= 0.118 Angle : 0.489 7.113 11973 Z= 0.268 Chirality : 0.041 0.164 1384 Planarity : 0.003 0.022 1500 Dihedral : 5.870 86.729 1209 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.66 % Allowed : 9.93 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.26), residues: 1106 helix: 2.47 (0.27), residues: 389 sheet: -0.64 (0.29), residues: 275 loop : -0.42 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 236 TYR 0.012 0.001 TYR S 178 PHE 0.014 0.001 PHE R 106 TRP 0.013 0.001 TRP B 356 HIS 0.004 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8824) covalent geometry : angle 0.48916 (11969) SS BOND : bond 0.00267 ( 2) SS BOND : angle 0.80362 ( 4) hydrogen bonds : bond 0.03900 ( 466) hydrogen bonds : angle 4.66227 ( 1320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.338 Fit side-chains REVERT: R 120 LEU cc_start: 0.8209 (mp) cc_final: 0.7970 (mm) REVERT: R 197 MET cc_start: 0.8324 (mtt) cc_final: 0.8118 (mtm) REVERT: R 243 PHE cc_start: 0.7219 (m-80) cc_final: 0.6913 (m-80) REVERT: A 35 LYS cc_start: 0.8344 (mttt) cc_final: 0.8002 (mtmm) REVERT: A 73 GLN cc_start: 0.8665 (mt0) cc_final: 0.8433 (mt0) REVERT: A 120 GLU cc_start: 0.7544 (mp0) cc_final: 0.7181 (tt0) REVERT: A 123 HIS cc_start: 0.6823 (t-90) cc_final: 0.6477 (t-90) REVERT: A 181 GLN cc_start: 0.8380 (mm-40) cc_final: 0.7991 (tp40) REVERT: A 220 LYS cc_start: 0.6811 (ttpt) cc_final: 0.6430 (mptt) REVERT: B 53 ASN cc_start: 0.7288 (m-40) cc_final: 0.6987 (p0) REVERT: B 59 ARG cc_start: 0.7262 (mmm160) cc_final: 0.7007 (mmp-170) REVERT: B 63 ARG cc_start: 0.8394 (ttt180) cc_final: 0.7561 (mmm160) REVERT: G 47 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7669 (mp0) REVERT: S 65 LYS cc_start: 0.7685 (tptt) cc_final: 0.7340 (tptt) REVERT: S 146 SER cc_start: 0.9051 (m) cc_final: 0.8698 (t) outliers start: 15 outliers final: 7 residues processed: 166 average time/residue: 0.0937 time to fit residues: 21.8083 Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 137 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain S residue 142 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 0.5980 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 90 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 151 HIS S 39 GLN S 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.161266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126491 restraints weight = 11073.411| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.43 r_work: 0.3346 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8826 Z= 0.164 Angle : 0.526 6.661 11973 Z= 0.290 Chirality : 0.042 0.139 1384 Planarity : 0.004 0.081 1500 Dihedral : 5.896 77.980 1205 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.10 % Allowed : 13.36 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.25), residues: 1106 helix: 2.15 (0.26), residues: 391 sheet: -0.66 (0.29), residues: 271 loop : -0.63 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 29 TYR 0.019 0.002 TYR R 240 PHE 0.030 0.002 PHE R 63 TRP 0.028 0.002 TRP R 124 HIS 0.005 0.001 HIS R 208 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8824) covalent geometry : angle 0.52571 (11969) SS BOND : bond 0.00263 ( 2) SS BOND : angle 0.77119 ( 4) hydrogen bonds : bond 0.04089 ( 466) hydrogen bonds : angle 4.71426 ( 1320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.349 Fit side-chains REVERT: R 120 LEU cc_start: 0.8451 (mp) cc_final: 0.8164 (mm) REVERT: R 140 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7078 (t80) REVERT: A 10 LYS cc_start: 0.7907 (mttt) cc_final: 0.7641 (mtpt) REVERT: A 35 LYS cc_start: 0.8420 (mttt) cc_final: 0.8090 (mttp) REVERT: A 120 GLU cc_start: 0.7664 (mp0) cc_final: 0.7255 (tt0) REVERT: A 135 SER cc_start: 0.8238 (t) cc_final: 0.7946 (p) REVERT: A 176 ASN cc_start: 0.7178 (m-40) cc_final: 0.6906 (t0) REVERT: A 181 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8046 (tp40) REVERT: B 63 ARG cc_start: 0.8377 (ttt180) cc_final: 0.7500 (ttm-80) REVERT: B 147 GLU cc_start: 0.7934 (mp0) cc_final: 0.7186 (mp0) REVERT: B 254 ASN cc_start: 0.8031 (t0) cc_final: 0.7791 (t0) REVERT: G 47 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7801 (mp0) REVERT: S 146 SER cc_start: 0.9091 (m) cc_final: 0.8726 (t) REVERT: S 174 GLN cc_start: 0.7771 (mt0) cc_final: 0.7232 (pt0) outliers start: 19 outliers final: 9 residues processed: 156 average time/residue: 0.0926 time to fit residues: 20.3517 Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain S residue 142 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN S 39 GLN S 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.157865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123924 restraints weight = 11416.552| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.33 r_work: 0.3318 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8826 Z= 0.172 Angle : 0.521 6.327 11973 Z= 0.290 Chirality : 0.042 0.154 1384 Planarity : 0.004 0.039 1500 Dihedral : 5.829 75.496 1205 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.31 % Allowed : 15.78 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.25), residues: 1106 helix: 1.91 (0.26), residues: 394 sheet: -0.71 (0.29), residues: 271 loop : -0.72 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 236 TYR 0.017 0.002 TYR B 76 PHE 0.020 0.002 PHE A 211 TRP 0.014 0.002 TRP R 124 HIS 0.004 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 8824) covalent geometry : angle 0.52131 (11969) SS BOND : bond 0.00187 ( 2) SS BOND : angle 0.67495 ( 4) hydrogen bonds : bond 0.04025 ( 466) hydrogen bonds : angle 4.85475 ( 1320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.351 Fit side-chains REVERT: R 119 PHE cc_start: 0.6925 (t80) cc_final: 0.6129 (t80) REVERT: R 120 LEU cc_start: 0.8430 (mp) cc_final: 0.7960 (mm) REVERT: R 140 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7028 (t80) REVERT: A 5 VAL cc_start: 0.8352 (t) cc_final: 0.7986 (p) REVERT: A 10 LYS cc_start: 0.8055 (mttt) cc_final: 0.7826 (mtpt) REVERT: A 35 LYS cc_start: 0.8456 (mttt) cc_final: 0.8172 (mttp) REVERT: A 102 ASP cc_start: 0.7862 (m-30) cc_final: 0.7513 (p0) REVERT: A 120 GLU cc_start: 0.7684 (mp0) cc_final: 0.7280 (tt0) REVERT: A 124 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8131 (tp) REVERT: B 59 ARG cc_start: 0.7495 (mmm160) cc_final: 0.7119 (mmp-170) REVERT: B 63 ARG cc_start: 0.8435 (ttt180) cc_final: 0.7610 (mtp85) REVERT: B 147 GLU cc_start: 0.7990 (mp0) cc_final: 0.7268 (mp0) REVERT: G 42 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7955 (tm-30) REVERT: G 47 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7889 (mp0) REVERT: G 58 GLU cc_start: 0.6200 (mm-30) cc_final: 0.4922 (mt-10) REVERT: S 146 SER cc_start: 0.9059 (m) cc_final: 0.8719 (t) REVERT: S 174 GLN cc_start: 0.7772 (mt0) cc_final: 0.7261 (pt0) outliers start: 30 outliers final: 17 residues processed: 166 average time/residue: 0.0943 time to fit residues: 21.9314 Evaluate side-chains 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 53 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 17 optimal weight: 0.0270 chunk 107 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 ASN B 254 ASN B 256 ASN S 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.156411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122429 restraints weight = 11403.587| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.30 r_work: 0.3301 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8826 Z= 0.179 Angle : 0.530 8.732 11973 Z= 0.291 Chirality : 0.042 0.142 1384 Planarity : 0.003 0.037 1500 Dihedral : 5.778 73.994 1205 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.42 % Allowed : 17.22 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.25), residues: 1106 helix: 1.83 (0.25), residues: 394 sheet: -0.77 (0.29), residues: 271 loop : -0.76 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.016 0.002 TYR B 76 PHE 0.018 0.002 PHE A 211 TRP 0.012 0.002 TRP R 124 HIS 0.004 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8824) covalent geometry : angle 0.52977 (11969) SS BOND : bond 0.00206 ( 2) SS BOND : angle 0.65063 ( 4) hydrogen bonds : bond 0.04116 ( 466) hydrogen bonds : angle 4.90095 ( 1320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.360 Fit side-chains REVERT: R 119 PHE cc_start: 0.6862 (t80) cc_final: 0.6080 (t80) REVERT: R 140 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7141 (t80) REVERT: R 243 PHE cc_start: 0.7464 (m-80) cc_final: 0.6983 (m-80) REVERT: A 5 VAL cc_start: 0.8431 (t) cc_final: 0.8082 (p) REVERT: A 10 LYS cc_start: 0.8315 (mttt) cc_final: 0.8112 (mtpt) REVERT: A 35 LYS cc_start: 0.8592 (mttt) cc_final: 0.8333 (mttp) REVERT: A 102 ASP cc_start: 0.7845 (m-30) cc_final: 0.7617 (p0) REVERT: A 120 GLU cc_start: 0.7713 (mp0) cc_final: 0.7367 (tt0) REVERT: A 124 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8347 (tp) REVERT: A 135 SER cc_start: 0.8254 (t) cc_final: 0.7990 (p) REVERT: B 59 ARG cc_start: 0.7593 (mmm160) cc_final: 0.7239 (mmp-170) REVERT: B 63 ARG cc_start: 0.8591 (ttt180) cc_final: 0.7836 (mtp85) REVERT: G 17 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6989 (mm-30) REVERT: G 42 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8129 (tm-30) REVERT: G 47 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8045 (mp0) REVERT: G 58 GLU cc_start: 0.6189 (mm-30) cc_final: 0.5437 (mt-10) REVERT: S 146 SER cc_start: 0.9063 (m) cc_final: 0.8745 (t) REVERT: S 174 GLN cc_start: 0.7823 (mt0) cc_final: 0.7448 (pt0) outliers start: 31 outliers final: 17 residues processed: 164 average time/residue: 0.0899 time to fit residues: 20.9314 Evaluate side-chains 159 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 181 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.159685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125354 restraints weight = 11332.190| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.31 r_work: 0.3321 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8826 Z= 0.142 Angle : 0.519 11.458 11973 Z= 0.281 Chirality : 0.041 0.145 1384 Planarity : 0.003 0.030 1500 Dihedral : 5.646 74.075 1205 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.76 % Allowed : 18.43 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.25), residues: 1106 helix: 1.98 (0.26), residues: 394 sheet: -0.73 (0.29), residues: 271 loop : -0.76 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 236 TYR 0.014 0.001 TYR S 178 PHE 0.011 0.001 PHE A 211 TRP 0.013 0.001 TRP B 186 HIS 0.003 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8824) covalent geometry : angle 0.51924 (11969) SS BOND : bond 0.00240 ( 2) SS BOND : angle 0.64532 ( 4) hydrogen bonds : bond 0.03813 ( 466) hydrogen bonds : angle 4.74602 ( 1320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.338 Fit side-chains REVERT: R 119 PHE cc_start: 0.6888 (t80) cc_final: 0.6098 (t80) REVERT: R 140 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7163 (t80) REVERT: R 243 PHE cc_start: 0.7420 (m-80) cc_final: 0.6999 (m-80) REVERT: A 5 VAL cc_start: 0.8401 (t) cc_final: 0.8027 (p) REVERT: A 35 LYS cc_start: 0.8596 (mttt) cc_final: 0.8338 (mttp) REVERT: A 102 ASP cc_start: 0.7844 (m-30) cc_final: 0.7612 (p0) REVERT: A 120 GLU cc_start: 0.7701 (mp0) cc_final: 0.7370 (tt0) REVERT: A 124 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8319 (tp) REVERT: B 59 ARG cc_start: 0.7564 (mmm160) cc_final: 0.7222 (mmp-170) REVERT: B 63 ARG cc_start: 0.8587 (ttt180) cc_final: 0.7839 (mtp85) REVERT: B 254 ASN cc_start: 0.8031 (t0) cc_final: 0.7772 (t0) REVERT: B 278 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8500 (mp) REVERT: G 17 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6935 (mm-30) REVERT: G 47 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8024 (mp0) REVERT: G 58 GLU cc_start: 0.6129 (mm-30) cc_final: 0.5341 (mt-10) REVERT: S 146 SER cc_start: 0.9015 (m) cc_final: 0.8717 (t) REVERT: S 174 GLN cc_start: 0.7869 (mt0) cc_final: 0.7461 (pt0) outliers start: 25 outliers final: 17 residues processed: 154 average time/residue: 0.0934 time to fit residues: 20.1791 Evaluate side-chains 151 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.155579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121709 restraints weight = 11516.131| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.26 r_work: 0.3291 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8826 Z= 0.195 Angle : 0.566 11.288 11973 Z= 0.303 Chirality : 0.043 0.235 1384 Planarity : 0.004 0.045 1500 Dihedral : 5.764 73.489 1205 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.53 % Allowed : 17.88 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.25), residues: 1106 helix: 1.81 (0.25), residues: 394 sheet: -0.74 (0.29), residues: 271 loop : -0.85 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 32 TYR 0.015 0.002 TYR B 76 PHE 0.017 0.002 PHE A 211 TRP 0.013 0.002 TRP S 47 HIS 0.004 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 8824) covalent geometry : angle 0.56574 (11969) SS BOND : bond 0.00188 ( 2) SS BOND : angle 0.71957 ( 4) hydrogen bonds : bond 0.04100 ( 466) hydrogen bonds : angle 4.91852 ( 1320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.365 Fit side-chains REVERT: R 119 PHE cc_start: 0.6894 (t80) cc_final: 0.6078 (t80) REVERT: R 140 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7157 (t80) REVERT: R 243 PHE cc_start: 0.7347 (m-80) cc_final: 0.6973 (m-80) REVERT: A 5 VAL cc_start: 0.8417 (t) cc_final: 0.8061 (p) REVERT: A 35 LYS cc_start: 0.8633 (mttt) cc_final: 0.8366 (mttp) REVERT: A 120 GLU cc_start: 0.7702 (mp0) cc_final: 0.7376 (tt0) REVERT: A 124 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8350 (tp) REVERT: A 135 SER cc_start: 0.8327 (t) cc_final: 0.8046 (p) REVERT: A 225 ASP cc_start: 0.8366 (t0) cc_final: 0.7970 (t0) REVERT: B 59 ARG cc_start: 0.7575 (mmm160) cc_final: 0.7285 (mmp-170) REVERT: B 63 ARG cc_start: 0.8597 (ttt180) cc_final: 0.7866 (mtp85) REVERT: B 254 ASN cc_start: 0.8154 (t0) cc_final: 0.7916 (t0) REVERT: B 278 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8485 (mp) REVERT: G 17 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6938 (mm-30) REVERT: G 42 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8118 (tm-30) REVERT: G 47 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8060 (mp0) REVERT: G 58 GLU cc_start: 0.6167 (mm-30) cc_final: 0.5351 (mt-10) REVERT: S 146 SER cc_start: 0.9044 (m) cc_final: 0.8721 (t) REVERT: S 174 GLN cc_start: 0.7837 (mt0) cc_final: 0.7431 (pt0) outliers start: 32 outliers final: 22 residues processed: 164 average time/residue: 0.0826 time to fit residues: 19.5185 Evaluate side-chains 158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 208 HIS Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.158916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124946 restraints weight = 11194.825| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.25 r_work: 0.3313 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8826 Z= 0.152 Angle : 0.542 11.503 11973 Z= 0.289 Chirality : 0.042 0.249 1384 Planarity : 0.003 0.038 1500 Dihedral : 5.635 73.781 1205 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.65 % Allowed : 19.32 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.25), residues: 1106 helix: 1.96 (0.25), residues: 394 sheet: -0.73 (0.29), residues: 275 loop : -0.78 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 32 TYR 0.014 0.001 TYR S 178 PHE 0.011 0.001 PHE R 72 TRP 0.013 0.001 TRP B 186 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8824) covalent geometry : angle 0.54144 (11969) SS BOND : bond 0.00223 ( 2) SS BOND : angle 0.78402 ( 4) hydrogen bonds : bond 0.03849 ( 466) hydrogen bonds : angle 4.79771 ( 1320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.353 Fit side-chains REVERT: R 87 ASN cc_start: 0.9141 (m-40) cc_final: 0.8936 (m110) REVERT: R 119 PHE cc_start: 0.6866 (t80) cc_final: 0.5953 (t80) REVERT: R 140 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7170 (t80) REVERT: A 5 VAL cc_start: 0.8342 (t) cc_final: 0.7963 (p) REVERT: A 35 LYS cc_start: 0.8667 (mttt) cc_final: 0.8394 (mttp) REVERT: A 120 GLU cc_start: 0.7704 (mp0) cc_final: 0.7364 (tt0) REVERT: A 124 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8328 (tp) REVERT: A 135 SER cc_start: 0.8279 (t) cc_final: 0.8010 (p) REVERT: A 225 ASP cc_start: 0.8306 (t0) cc_final: 0.7918 (t0) REVERT: B 59 ARG cc_start: 0.7520 (mmm160) cc_final: 0.7240 (mmp-170) REVERT: B 63 ARG cc_start: 0.8595 (ttt180) cc_final: 0.7854 (mtp85) REVERT: B 254 ASN cc_start: 0.8131 (t0) cc_final: 0.7890 (t0) REVERT: B 278 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8487 (mp) REVERT: G 17 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6990 (mm-30) REVERT: G 47 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8001 (mp0) REVERT: G 58 GLU cc_start: 0.6084 (mm-30) cc_final: 0.5236 (mt-10) REVERT: S 146 SER cc_start: 0.9029 (m) cc_final: 0.8716 (t) REVERT: S 174 GLN cc_start: 0.7842 (mt0) cc_final: 0.7469 (pt0) outliers start: 24 outliers final: 20 residues processed: 149 average time/residue: 0.0874 time to fit residues: 18.7453 Evaluate side-chains 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 181 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.0170 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.158309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124465 restraints weight = 11295.962| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.25 r_work: 0.3308 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8826 Z= 0.158 Angle : 0.548 12.604 11973 Z= 0.292 Chirality : 0.042 0.255 1384 Planarity : 0.003 0.036 1500 Dihedral : 5.628 74.318 1205 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.87 % Allowed : 19.21 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.25), residues: 1106 helix: 2.00 (0.25), residues: 393 sheet: -0.71 (0.29), residues: 282 loop : -0.77 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.014 0.001 TYR S 178 PHE 0.011 0.001 PHE A 211 TRP 0.013 0.001 TRP B 99 HIS 0.004 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8824) covalent geometry : angle 0.54771 (11969) SS BOND : bond 0.00184 ( 2) SS BOND : angle 0.65398 ( 4) hydrogen bonds : bond 0.03887 ( 466) hydrogen bonds : angle 4.80847 ( 1320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.355 Fit side-chains REVERT: R 119 PHE cc_start: 0.6918 (t80) cc_final: 0.6023 (t80) REVERT: R 140 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7186 (t80) REVERT: R 243 PHE cc_start: 0.7425 (m-80) cc_final: 0.7002 (m-80) REVERT: A 5 VAL cc_start: 0.8366 (t) cc_final: 0.7988 (p) REVERT: A 35 LYS cc_start: 0.8696 (mttt) cc_final: 0.8430 (mttp) REVERT: A 120 GLU cc_start: 0.7702 (mp0) cc_final: 0.7402 (tt0) REVERT: A 135 SER cc_start: 0.8276 (t) cc_final: 0.8013 (p) REVERT: A 225 ASP cc_start: 0.8335 (t0) cc_final: 0.7947 (t0) REVERT: B 59 ARG cc_start: 0.7531 (mmm160) cc_final: 0.7252 (mmp-170) REVERT: B 63 ARG cc_start: 0.8600 (ttt180) cc_final: 0.7868 (mtp85) REVERT: B 254 ASN cc_start: 0.8147 (t0) cc_final: 0.7898 (t0) REVERT: B 278 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8489 (mp) REVERT: G 17 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6998 (mm-30) REVERT: G 47 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8013 (mp0) REVERT: G 58 GLU cc_start: 0.6040 (mm-30) cc_final: 0.5164 (mt-10) REVERT: S 146 SER cc_start: 0.9036 (m) cc_final: 0.8718 (t) REVERT: S 174 GLN cc_start: 0.7841 (mt0) cc_final: 0.7440 (pt0) outliers start: 26 outliers final: 22 residues processed: 144 average time/residue: 0.0825 time to fit residues: 17.3136 Evaluate side-chains 151 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 181 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125361 restraints weight = 11254.555| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.24 r_work: 0.3318 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8826 Z= 0.145 Angle : 0.538 12.485 11973 Z= 0.287 Chirality : 0.042 0.260 1384 Planarity : 0.003 0.033 1500 Dihedral : 5.556 74.942 1205 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.87 % Allowed : 19.76 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.25), residues: 1106 helix: 2.08 (0.25), residues: 393 sheet: -0.74 (0.29), residues: 277 loop : -0.78 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 236 TYR 0.014 0.001 TYR S 178 PHE 0.011 0.001 PHE B 216 TRP 0.013 0.001 TRP B 99 HIS 0.003 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8824) covalent geometry : angle 0.53811 (11969) SS BOND : bond 0.00212 ( 2) SS BOND : angle 0.74957 ( 4) hydrogen bonds : bond 0.03742 ( 466) hydrogen bonds : angle 4.73545 ( 1320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2212 Ramachandran restraints generated. 1106 Oldfield, 0 Emsley, 1106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.288 Fit side-chains REVERT: R 85 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7459 (tp) REVERT: R 140 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7277 (t80) REVERT: R 243 PHE cc_start: 0.7420 (m-80) cc_final: 0.6978 (m-80) REVERT: A 5 VAL cc_start: 0.8350 (t) cc_final: 0.7965 (p) REVERT: A 35 LYS cc_start: 0.8659 (mttt) cc_final: 0.8394 (mttp) REVERT: A 120 GLU cc_start: 0.7687 (mp0) cc_final: 0.7407 (tt0) REVERT: A 135 SER cc_start: 0.8171 (t) cc_final: 0.7955 (p) REVERT: A 225 ASP cc_start: 0.8324 (t0) cc_final: 0.7958 (t0) REVERT: B 59 ARG cc_start: 0.7493 (mmm160) cc_final: 0.7222 (mmp-170) REVERT: B 63 ARG cc_start: 0.8596 (ttt180) cc_final: 0.7868 (mtp85) REVERT: B 254 ASN cc_start: 0.8136 (t0) cc_final: 0.7886 (t0) REVERT: B 278 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8462 (mp) REVERT: G 17 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6957 (mm-30) REVERT: G 47 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8016 (mp0) REVERT: G 58 GLU cc_start: 0.6018 (mm-30) cc_final: 0.5151 (mt-10) REVERT: G 62 ARG cc_start: 0.7357 (ptt-90) cc_final: 0.7124 (ptt-90) REVERT: S 146 SER cc_start: 0.9038 (m) cc_final: 0.8719 (t) REVERT: S 174 GLN cc_start: 0.7837 (mt0) cc_final: 0.7443 (pt0) outliers start: 26 outliers final: 23 residues processed: 149 average time/residue: 0.0799 time to fit residues: 17.1185 Evaluate side-chains 157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 135 LEU Chi-restraints excluded: chain R residue 140 PHE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 142 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 181 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.160442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.126486 restraints weight = 11265.761| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.27 r_work: 0.3333 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8826 Z= 0.126 Angle : 0.525 12.621 11973 Z= 0.280 Chirality : 0.041 0.259 1384 Planarity : 0.003 0.030 1500 Dihedral : 5.451 76.234 1205 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.09 % Allowed : 19.54 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.26), residues: 1106 helix: 2.23 (0.26), residues: 393 sheet: -0.67 (0.29), residues: 277 loop : -0.72 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 236 TYR 0.013 0.001 TYR S 178 PHE 0.011 0.001 PHE R 72 TRP 0.014 0.001 TRP B 99 HIS 0.003 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8824) covalent geometry : angle 0.52444 (11969) SS BOND : bond 0.00236 ( 2) SS BOND : angle 0.76886 ( 4) hydrogen bonds : bond 0.03545 ( 466) hydrogen bonds : angle 4.60125 ( 1320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2893.37 seconds wall clock time: 50 minutes 15.11 seconds (3015.11 seconds total)