Starting phenix.real_space_refine on Sat Dec 28 14:50:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rql_19445/12_2024/8rql_19445.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rql_19445/12_2024/8rql_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_19445/12_2024/8rql_19445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rql_19445/12_2024/8rql_19445.map" model { file = "/net/cci-nas-00/data/ceres_data/8rql_19445/12_2024/8rql_19445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rql_19445/12_2024/8rql_19445.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG: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, 'ARG:plan': 2, 'ASP: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: 5.91, per 1000 atoms: 0.68 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.98 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: 2.85 Time building geometry restraints manager: 2.54 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: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.040 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.820 ------------------------------------------------------------------------------- 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 8824 Z= 0.196 Angle : 0.527 13.297 11969 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 : 5.46 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.009 0.001 TRP B 99 HIS 0.002 0.001 HIS R 94 PHE 0.011 0.001 PHE B 216 TYR 0.008 0.001 TYR B 76 ARG 0.006 0.000 ARG R 125 *********************** 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 : 0.768 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: 0.2122 time to fit residues: 66.0045 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 : 0.912 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 ASN R 87 ASN R 284 ASN A 130 ASN S 171 GLN S 182 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8824 Z= 0.247 Angle : 0.547 7.316 11969 Z= 0.300 Chirality : 0.043 0.183 1384 Planarity : 0.004 0.046 1500 Dihedral : 6.075 83.226 1209 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.66 % Allowed : 11.04 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1106 helix: 2.10 (0.26), residues: 390 sheet: -0.71 (0.28), residues: 271 loop : -0.54 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 124 HIS 0.005 0.001 HIS A 80 PHE 0.024 0.002 PHE A 211 TYR 0.017 0.002 TYR A 195 ARG 0.005 0.001 ARG B 236 *********************** 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 169 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.904 Fit side-chains REVERT: R 243 PHE cc_start: 0.6862 (m-80) cc_final: 0.6595 (m-80) REVERT: R 286 LYS cc_start: 0.8788 (tttm) cc_final: 0.8504 (tttm) REVERT: A 26 ASP cc_start: 0.6906 (m-30) cc_final: 0.6397 (m-30) REVERT: A 35 LYS cc_start: 0.8142 (mttt) cc_final: 0.7728 (mttp) REVERT: A 73 GLN cc_start: 0.8408 (mt0) cc_final: 0.8004 (mt0) REVERT: A 120 GLU cc_start: 0.7254 (mp0) cc_final: 0.6972 (tt0) REVERT: A 181 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7733 (tp40) REVERT: B 59 ARG cc_start: 0.7081 (mmm160) cc_final: 0.6747 (mmp-170) REVERT: B 63 ARG cc_start: 0.7723 (ttt180) cc_final: 0.6960 (mmm160) REVERT: B 118 MET cc_start: 0.8985 (mtp) cc_final: 0.8715 (mtp) REVERT: B 147 GLU cc_start: 0.7673 (mp0) cc_final: 0.6906 (mp0) REVERT: B 245 ASP cc_start: 0.8099 (m-30) cc_final: 0.7851 (m-30) REVERT: S 128 MET cc_start: 0.8376 (mmm) cc_final: 0.7865 (mmt) REVERT: S 146 SER cc_start: 0.8965 (m) cc_final: 0.8564 (t) outliers start: 15 outliers final: 6 residues processed: 163 average time/residue: 0.1877 time to fit residues: 43.6906 Evaluate side-chains 137 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 192 GLN Chi-restraints excluded: chain S residue 88 SER 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 55 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 87 ASN ** R 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 151 HIS A 197 HIS B 254 ASN B 256 ASN S 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8824 Z= 0.317 Angle : 0.563 7.156 11969 Z= 0.312 Chirality : 0.043 0.182 1384 Planarity : 0.004 0.038 1500 Dihedral : 6.053 76.089 1205 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.65 % Allowed : 14.24 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1106 helix: 1.77 (0.26), residues: 392 sheet: -0.74 (0.29), residues: 271 loop : -0.73 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 124 HIS 0.004 0.001 HIS A 98 PHE 0.025 0.002 PHE G 66 TYR 0.022 0.002 TYR R 240 ARG 0.006 0.001 ARG B 236 *********************** 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 167 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.018 Fit side-chains REVERT: R 140 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.6888 (t80) REVERT: A 5 VAL cc_start: 0.7418 (t) cc_final: 0.7119 (p) REVERT: A 35 LYS cc_start: 0.8217 (mttt) cc_final: 0.7781 (mttp) REVERT: A 73 GLN cc_start: 0.8420 (mt0) cc_final: 0.8069 (mt0) REVERT: A 118 MET cc_start: 0.8033 (tpp) cc_final: 0.7661 (tpp) REVERT: A 120 GLU cc_start: 0.7303 (mp0) cc_final: 0.6970 (tt0) REVERT: A 135 SER cc_start: 0.8187 (t) cc_final: 0.7810 (p) REVERT: A 181 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7788 (tp40) REVERT: B 59 ARG cc_start: 0.7159 (mmm160) cc_final: 0.6877 (mmp-170) REVERT: B 63 ARG cc_start: 0.7721 (ttt180) cc_final: 0.6871 (ttm-80) REVERT: S 109 ASP cc_start: 0.8449 (p0) cc_final: 0.8240 (p0) REVERT: S 146 SER cc_start: 0.8978 (m) cc_final: 0.8557 (t) REVERT: S 174 GLN cc_start: 0.7441 (mt0) cc_final: 0.6943 (pt0) outliers start: 24 outliers final: 12 residues processed: 156 average time/residue: 0.1928 time to fit residues: 42.4279 Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 THR 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 204 SER Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 353 LEU 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 98 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 31 ASN B 256 ASN S 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8824 Z= 0.233 Angle : 0.516 7.518 11969 Z= 0.284 Chirality : 0.041 0.143 1384 Planarity : 0.003 0.037 1500 Dihedral : 5.821 74.954 1205 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.42 % Allowed : 16.11 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1106 helix: 1.87 (0.26), residues: 393 sheet: -0.76 (0.29), residues: 271 loop : -0.79 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 356 HIS 0.004 0.001 HIS A 98 PHE 0.012 0.001 PHE A 211 TYR 0.016 0.002 TYR S 103 ARG 0.006 0.000 ARG B 236 *********************** 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 168 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.887 Fit side-chains REVERT: R 140 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.6924 (t80) REVERT: R 243 PHE cc_start: 0.6810 (m-80) cc_final: 0.6566 (m-80) REVERT: A 5 VAL cc_start: 0.7428 (t) cc_final: 0.7130 (p) REVERT: A 35 LYS cc_start: 0.8198 (mttt) cc_final: 0.7749 (mttp) REVERT: A 118 MET cc_start: 0.8062 (tpp) cc_final: 0.7587 (tpp) REVERT: A 120 GLU cc_start: 0.7230 (mp0) cc_final: 0.6971 (tt0) REVERT: A 181 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7700 (tp40) REVERT: B 59 ARG cc_start: 0.7087 (mmm160) cc_final: 0.6860 (mmp-170) REVERT: B 63 ARG cc_start: 0.7696 (ttt180) cc_final: 0.6919 (mtp85) REVERT: B 147 GLU cc_start: 0.7857 (mp0) cc_final: 0.6999 (mp0) REVERT: B 245 ASP cc_start: 0.8317 (m-30) cc_final: 0.8053 (m-30) REVERT: B 254 ASN cc_start: 0.7952 (t0) cc_final: 0.7689 (t0) REVERT: S 146 SER cc_start: 0.8975 (m) cc_final: 0.8576 (t) REVERT: S 174 GLN cc_start: 0.7422 (mt0) cc_final: 0.6936 (pt0) outliers start: 31 outliers final: 18 residues processed: 156 average time/residue: 0.2194 time to fit residues: 47.9982 Evaluate side-chains 148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 185 VAL Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 292 LEU Chi-restraints excluded: chain A residue 138 SER 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 348 SER 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 Chi-restraints excluded: chain S residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 0.0470 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8824 Z= 0.197 Angle : 0.508 11.616 11969 Z= 0.276 Chirality : 0.041 0.165 1384 Planarity : 0.003 0.032 1500 Dihedral : 5.651 74.785 1205 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.20 % Allowed : 16.45 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1106 helix: 2.02 (0.26), residues: 393 sheet: -0.83 (0.29), residues: 271 loop : -0.81 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 186 HIS 0.003 0.001 HIS A 98 PHE 0.011 0.001 PHE B 216 TYR 0.014 0.001 TYR S 178 ARG 0.006 0.000 ARG A 32 *********************** 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 161 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.895 Fit side-chains REVERT: R 10 THR cc_start: 0.7902 (OUTLIER) cc_final: 0.7564 (t) REVERT: R 78 THR cc_start: 0.6023 (m) cc_final: 0.5822 (p) REVERT: R 140 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.6929 (t80) REVERT: A 5 VAL cc_start: 0.7398 (t) cc_final: 0.7096 (p) REVERT: A 35 LYS cc_start: 0.8237 (mttt) cc_final: 0.7795 (mttp) REVERT: A 118 MET cc_start: 0.8059 (tpp) cc_final: 0.7615 (tpp) REVERT: A 120 GLU cc_start: 0.7319 (mp0) cc_final: 0.7033 (tt0) REVERT: B 59 ARG cc_start: 0.7051 (mmm160) cc_final: 0.6838 (mmp-170) REVERT: B 63 ARG cc_start: 0.7701 (ttt180) cc_final: 0.6920 (mtp85) REVERT: B 254 ASN cc_start: 0.7965 (t0) cc_final: 0.7727 (t0) REVERT: G 17 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7050 (mm-30) REVERT: S 146 SER cc_start: 0.8959 (m) cc_final: 0.8580 (t) outliers start: 29 outliers final: 17 residues processed: 148 average time/residue: 0.1925 time to fit residues: 40.4308 Evaluate side-chains 148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 10 THR 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 185 VAL Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 138 SER 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 348 SER 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 Chi-restraints excluded: chain S residue 181 SER Chi-restraints excluded: chain S residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8824 Z= 0.248 Angle : 0.530 7.937 11969 Z= 0.289 Chirality : 0.042 0.211 1384 Planarity : 0.003 0.036 1500 Dihedral : 5.698 74.107 1205 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.42 % Allowed : 17.33 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1106 helix: 1.94 (0.25), residues: 394 sheet: -0.86 (0.29), residues: 271 loop : -0.86 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.011 0.001 HIS R 208 PHE 0.012 0.001 PHE A 211 TYR 0.013 0.002 TYR S 178 ARG 0.007 0.000 ARG A 29 *********************** 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 166 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.956 Fit side-chains REVERT: R 78 THR cc_start: 0.6056 (m) cc_final: 0.5848 (p) REVERT: R 140 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.6991 (t80) REVERT: R 243 PHE cc_start: 0.6988 (m-80) cc_final: 0.6749 (m-80) REVERT: A 5 VAL cc_start: 0.7357 (t) cc_final: 0.7066 (p) REVERT: A 35 LYS cc_start: 0.8277 (mttt) cc_final: 0.7923 (mttp) REVERT: A 102 ASP cc_start: 0.7843 (m-30) cc_final: 0.7300 (p0) REVERT: A 118 MET cc_start: 0.8105 (tpp) cc_final: 0.7628 (tpp) REVERT: A 120 GLU cc_start: 0.7324 (mp0) cc_final: 0.7051 (tt0) REVERT: B 59 ARG cc_start: 0.7108 (mmm160) cc_final: 0.6840 (mmp-170) REVERT: B 254 ASN cc_start: 0.8030 (t0) cc_final: 0.7802 (t0) REVERT: B 278 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8117 (mp) REVERT: G 17 GLU cc_start: 0.7288 (mm-30) cc_final: 0.7034 (mm-30) REVERT: G 58 GLU cc_start: 0.4989 (OUTLIER) cc_final: 0.3263 (mp0) REVERT: S 146 SER cc_start: 0.8970 (m) cc_final: 0.8584 (t) REVERT: S 174 GLN cc_start: 0.7405 (mt0) cc_final: 0.6923 (pt0) outliers start: 31 outliers final: 22 residues processed: 155 average time/residue: 0.1970 time to fit residues: 43.6461 Evaluate side-chains 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 72 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 117 VAL 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 348 SER Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain G residue 58 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8824 Z= 0.235 Angle : 0.535 11.286 11969 Z= 0.291 Chirality : 0.042 0.228 1384 Planarity : 0.003 0.048 1500 Dihedral : 5.672 74.431 1205 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.87 % Allowed : 18.21 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1106 helix: 1.95 (0.25), residues: 392 sheet: -0.81 (0.29), residues: 275 loop : -0.80 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.010 0.001 HIS R 208 PHE 0.012 0.001 PHE R 63 TYR 0.014 0.001 TYR S 178 ARG 0.006 0.000 ARG B 236 *********************** 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 159 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.965 Fit side-chains REVERT: R 87 ASN cc_start: 0.9057 (m-40) cc_final: 0.8853 (m110) REVERT: R 140 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7002 (t80) REVERT: A 5 VAL cc_start: 0.7338 (t) cc_final: 0.7028 (p) REVERT: A 35 LYS cc_start: 0.8301 (mttt) cc_final: 0.7960 (mttp) REVERT: A 102 ASP cc_start: 0.7849 (m-30) cc_final: 0.7318 (p0) REVERT: A 118 MET cc_start: 0.8111 (tpp) cc_final: 0.7631 (tpp) REVERT: A 120 GLU cc_start: 0.7342 (mp0) cc_final: 0.7074 (tt0) REVERT: A 135 SER cc_start: 0.8082 (t) cc_final: 0.7712 (p) REVERT: B 59 ARG cc_start: 0.7068 (mmm160) cc_final: 0.6806 (mmp-170) REVERT: B 254 ASN cc_start: 0.8023 (t0) cc_final: 0.7804 (t0) REVERT: B 278 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8090 (mp) REVERT: G 58 GLU cc_start: 0.4800 (OUTLIER) cc_final: 0.3276 (mp0) REVERT: S 146 SER cc_start: 0.8998 (m) cc_final: 0.8605 (t) REVERT: S 174 GLN cc_start: 0.7421 (mt0) cc_final: 0.6972 (pt0) outliers start: 26 outliers final: 20 residues processed: 151 average time/residue: 0.2086 time to fit residues: 45.0446 Evaluate side-chains 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 185 VAL Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 117 VAL 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 348 SER Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain G residue 58 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 chunk 20 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 0.0050 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8824 Z= 0.182 Angle : 0.515 10.823 11969 Z= 0.279 Chirality : 0.041 0.245 1384 Planarity : 0.003 0.042 1500 Dihedral : 5.554 75.500 1205 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.76 % Allowed : 17.99 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1106 helix: 2.17 (0.25), residues: 393 sheet: -0.81 (0.29), residues: 273 loop : -0.78 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 186 HIS 0.009 0.001 HIS R 208 PHE 0.012 0.001 PHE R 63 TYR 0.014 0.001 TYR S 178 ARG 0.007 0.000 ARG B 236 *********************** 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 154 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.895 Fit side-chains REVERT: R 140 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7050 (t80) REVERT: R 243 PHE cc_start: 0.6911 (m-80) cc_final: 0.6614 (m-80) REVERT: A 35 LYS cc_start: 0.8259 (mttt) cc_final: 0.7916 (mttp) REVERT: A 102 ASP cc_start: 0.7856 (m-30) cc_final: 0.7347 (p0) REVERT: A 118 MET cc_start: 0.8087 (tpp) cc_final: 0.7638 (tpp) REVERT: A 120 GLU cc_start: 0.7339 (mp0) cc_final: 0.7081 (tt0) REVERT: B 59 ARG cc_start: 0.7015 (mmm160) cc_final: 0.6764 (mmp-170) REVERT: B 254 ASN cc_start: 0.8015 (t0) cc_final: 0.7762 (t0) REVERT: B 278 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8099 (mp) REVERT: S 146 SER cc_start: 0.8984 (m) cc_final: 0.8609 (t) REVERT: S 174 GLN cc_start: 0.7413 (mt0) cc_final: 0.6940 (pt0) outliers start: 25 outliers final: 19 residues processed: 145 average time/residue: 0.1984 time to fit residues: 41.0639 Evaluate side-chains 146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 113 ASN 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 261 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 131 CYS 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 348 SER 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 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 98 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 113 ASN S 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8824 Z= 0.250 Angle : 0.541 10.390 11969 Z= 0.293 Chirality : 0.042 0.251 1384 Planarity : 0.003 0.044 1500 Dihedral : 5.636 75.454 1205 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.54 % Allowed : 18.54 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1106 helix: 2.11 (0.25), residues: 393 sheet: -0.74 (0.29), residues: 272 loop : -0.79 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.009 0.001 HIS R 208 PHE 0.020 0.001 PHE A 229 TYR 0.013 0.001 TYR S 178 ARG 0.008 0.000 ARG A 29 *********************** 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 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.999 Fit side-chains REVERT: R 140 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7018 (t80) REVERT: R 243 PHE cc_start: 0.6930 (m-80) cc_final: 0.6654 (m-80) REVERT: A 5 VAL cc_start: 0.7381 (t) cc_final: 0.7078 (p) REVERT: A 29 ARG cc_start: 0.6716 (mtm110) cc_final: 0.6515 (mtm110) REVERT: A 35 LYS cc_start: 0.8305 (mttt) cc_final: 0.7966 (mttp) REVERT: A 102 ASP cc_start: 0.7838 (m-30) cc_final: 0.7353 (p0) REVERT: A 118 MET cc_start: 0.8109 (tpp) cc_final: 0.7641 (tpp) REVERT: A 120 GLU cc_start: 0.7341 (mp0) cc_final: 0.7084 (tt0) REVERT: A 135 SER cc_start: 0.8081 (t) cc_final: 0.7712 (p) REVERT: B 59 ARG cc_start: 0.7034 (mmm160) cc_final: 0.6783 (mmp-170) REVERT: B 254 ASN cc_start: 0.8043 (t0) cc_final: 0.7815 (t0) REVERT: B 278 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8097 (mp) REVERT: G 17 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6838 (mm-30) REVERT: S 146 SER cc_start: 0.8995 (m) cc_final: 0.8608 (t) REVERT: S 174 GLN cc_start: 0.7444 (mt0) cc_final: 0.6987 (pt0) outliers start: 23 outliers final: 19 residues processed: 147 average time/residue: 0.2235 time to fit residues: 45.9037 Evaluate side-chains 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 22 LEU 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 261 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 131 CYS 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 348 SER 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 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 49 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 100 optimal weight: 0.0670 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8824 Z= 0.200 Angle : 0.525 9.984 11969 Z= 0.284 Chirality : 0.042 0.266 1384 Planarity : 0.003 0.039 1500 Dihedral : 5.540 75.917 1205 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.87 % Allowed : 18.43 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1106 helix: 2.27 (0.25), residues: 393 sheet: -0.79 (0.29), residues: 278 loop : -0.75 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.009 0.001 HIS R 208 PHE 0.020 0.001 PHE A 229 TYR 0.014 0.001 TYR S 178 ARG 0.008 0.000 ARG A 29 ********************** 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 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.972 Fit side-chains REVERT: R 140 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7043 (t80) REVERT: R 243 PHE cc_start: 0.6932 (m-80) cc_final: 0.6672 (m-80) REVERT: A 29 ARG cc_start: 0.6496 (mtm110) cc_final: 0.6274 (mtm110) REVERT: A 35 LYS cc_start: 0.8262 (mttt) cc_final: 0.7923 (mttp) REVERT: A 102 ASP cc_start: 0.7835 (m-30) cc_final: 0.7409 (p0) REVERT: A 118 MET cc_start: 0.8097 (tpp) cc_final: 0.7636 (tpp) REVERT: A 120 GLU cc_start: 0.7337 (mp0) cc_final: 0.7082 (tt0) REVERT: A 135 SER cc_start: 0.7965 (t) cc_final: 0.7655 (p) REVERT: B 59 ARG cc_start: 0.6978 (mmm160) cc_final: 0.6731 (mmp-170) REVERT: B 254 ASN cc_start: 0.8028 (t0) cc_final: 0.7794 (t0) REVERT: B 278 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8068 (mp) REVERT: G 47 GLU cc_start: 0.8501 (mp0) cc_final: 0.7923 (mt-10) REVERT: S 146 SER cc_start: 0.9012 (m) cc_final: 0.8626 (t) REVERT: S 174 GLN cc_start: 0.7448 (mt0) cc_final: 0.6965 (pt0) outliers start: 26 outliers final: 22 residues processed: 146 average time/residue: 0.1987 time to fit residues: 40.8039 Evaluate side-chains 153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 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 138 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain B residue 131 CYS 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 348 SER 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 80 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.159064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125547 restraints weight = 11222.433| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.23 r_work: 0.3324 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8824 Z= 0.205 Angle : 0.522 9.765 11969 Z= 0.283 Chirality : 0.042 0.260 1384 Planarity : 0.003 0.036 1500 Dihedral : 5.502 76.653 1205 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.54 % Allowed : 18.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1106 helix: 2.28 (0.25), residues: 393 sheet: -0.83 (0.28), residues: 277 loop : -0.71 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.009 0.001 HIS R 208 PHE 0.020 0.001 PHE A 229 TYR 0.013 0.001 TYR S 178 ARG 0.007 0.000 ARG A 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2312.24 seconds wall clock time: 43 minutes 22.12 seconds (2602.12 seconds total)