Starting phenix.real_space_refine on Fri Oct 11 00:08:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjn_38402/10_2024/8xjn_38402.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjn_38402/10_2024/8xjn_38402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjn_38402/10_2024/8xjn_38402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjn_38402/10_2024/8xjn_38402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjn_38402/10_2024/8xjn_38402.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xjn_38402/10_2024/8xjn_38402.cif" } resolution = 3.06 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= -0.000 sd= 0.011 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 58 5.16 5 Cl 1 4.86 5 C 5672 2.51 5 N 1546 2.21 5 O 1671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 8948 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1825 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2257 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 295} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 94 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'A1D5A': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.36, per 1000 atoms: 0.60 Number of scatterers: 8948 At special positions: 0 Unit cell: (114.49, 125.19, 109.14, 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) Cl 1 17.00 S 58 16.00 O 1671 8.00 N 1546 7.00 C 5672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 102 " distance=2.03 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 183 " 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: 2.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 16 sheets defined 37.9% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.613A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.713A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.864A pdb=" N ARG A 135 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.242A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.527A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 244 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.509A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.529A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 56 removed outlier: 3.988A pdb=" N PHE R 34 " --> pdb=" O PHE R 30 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS R 35 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA R 52 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY R 56 " --> pdb=" O ALA R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 91 removed outlier: 3.536A pdb=" N THR R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY R 82 " --> pdb=" O LEU R 78 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA R 90 " --> pdb=" O VAL R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 136 Proline residue: R 119 - end of helix removed outlier: 3.568A pdb=" N SER R 128 " --> pdb=" O ALA R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 140 Processing helix chain 'R' and resid 146 through 165 removed outlier: 4.367A pdb=" N THR R 152 " --> pdb=" O ARG R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 170 Processing helix chain 'R' and resid 190 through 227 Processing helix chain 'R' and resid 228 through 235 removed outlier: 3.771A pdb=" N GLN R 233 " --> pdb=" O GLN R 229 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG R 235 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 270 removed outlier: 3.604A pdb=" N GLN R 246 " --> pdb=" O GLU R 242 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER R 255 " --> pdb=" O MET R 251 " (cutoff:3.500A) Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 283 through 299 removed outlier: 3.710A pdb=" N TRP R 299 " --> pdb=" O ARG R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 308 Proline residue: R 305 - end of helix Processing helix chain 'R' and resid 312 through 320 removed outlier: 4.590A pdb=" N ARG R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU R 319 " --> pdb=" O VAL R 315 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN R 320 " --> pdb=" O LEU R 316 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 76 removed outlier: 6.380A pdb=" N LEU A 34 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N PHE A 84 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU A 36 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N ALA A 105 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 76 removed outlier: 6.380A pdb=" N LEU A 34 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N PHE A 84 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU A 36 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N ALA A 105 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.652A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.608A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.981A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.254A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.809A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.583A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.748A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.867A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.357A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.572A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.153A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 174 through 176 469 hydrogen bonds defined for protein. 1299 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: 3.01 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2936 1.34 - 1.46: 2155 1.46 - 1.58: 3953 1.58 - 1.69: 3 1.69 - 1.81: 86 Bond restraints: 9133 Sorted by residual: bond pdb=" C10 A1D5A R 601 " pdb=" C11 A1D5A R 601 " ideal model delta sigma weight residual 1.543 1.311 0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C14 A1D5A R 601 " pdb=" C15 A1D5A R 601 " ideal model delta sigma weight residual 1.523 1.338 0.185 2.00e-02 2.50e+03 8.53e+01 bond pdb=" C10 A1D5A R 601 " pdb=" C15 A1D5A R 601 " ideal model delta sigma weight residual 1.535 1.694 -0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" C21 A1D5A R 601 " pdb=" O20 A1D5A R 601 " ideal model delta sigma weight residual 1.342 1.422 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C11 A1D5A R 601 " pdb=" C13 A1D5A R 601 " ideal model delta sigma weight residual 1.538 1.616 -0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 9128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 12340 2.59 - 5.18: 47 5.18 - 7.77: 4 7.77 - 10.36: 1 10.36 - 12.96: 1 Bond angle restraints: 12393 Sorted by residual: angle pdb=" C06 A1D5A R 601 " pdb=" C07 A1D5A R 601 " pdb=" C08 A1D5A R 601 " ideal model delta sigma weight residual 127.33 114.37 12.96 3.00e+00 1.11e-01 1.86e+01 angle pdb=" C07 A1D5A R 601 " pdb=" C08 A1D5A R 601 " pdb=" C09 A1D5A R 601 " ideal model delta sigma weight residual 127.18 118.41 8.77 3.00e+00 1.11e-01 8.54e+00 angle pdb=" N GLU R 242 " pdb=" CA GLU R 242 " pdb=" C GLU R 242 " ideal model delta sigma weight residual 111.82 109.18 2.64 1.16e+00 7.43e-01 5.18e+00 angle pdb=" O01 A1D5A R 601 " pdb=" C02 A1D5A R 601 " pdb=" O03 A1D5A R 601 " ideal model delta sigma weight residual 126.47 120.06 6.41 3.00e+00 1.11e-01 4.56e+00 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 125.30 -3.76 1.91e+00 2.74e-01 3.87e+00 ... (remaining 12388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 5179 17.04 - 34.08: 198 34.08 - 51.11: 39 51.11 - 68.15: 6 68.15 - 85.19: 8 Dihedral angle restraints: 5430 sinusoidal: 2082 harmonic: 3348 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ILE R 309 " pdb=" C ILE R 309 " pdb=" N LEU R 310 " pdb=" CA LEU R 310 " ideal model delta harmonic sigma weight residual -180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 5427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1043 0.037 - 0.073: 256 0.073 - 0.110: 88 0.110 - 0.146: 22 0.146 - 0.183: 3 Chirality restraints: 1412 Sorted by residual: chirality pdb=" C10 A1D5A R 601 " pdb=" C09 A1D5A R 601 " pdb=" C11 A1D5A R 601 " pdb=" C15 A1D5A R 601 " both_signs ideal model delta sigma weight residual False -2.56 -2.74 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" C15 A1D5A R 601 " pdb=" C10 A1D5A R 601 " pdb=" C14 A1D5A R 601 " pdb=" C16 A1D5A R 601 " both_signs ideal model delta sigma weight residual False 2.59 2.76 -0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" C11 A1D5A R 601 " pdb=" C10 A1D5A R 601 " pdb=" C13 A1D5A R 601 " pdb=" O12 A1D5A R 601 " both_signs ideal model delta sigma weight residual False 2.65 2.49 0.16 2.00e-01 2.50e+01 6.36e-01 ... (remaining 1409 not shown) Planarity restraints: 1582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO B 236 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 235 " -0.016 5.00e-02 4.00e+02 2.47e-02 9.77e-01 pdb=" N PRO R 236 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO R 236 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 236 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 54 " -0.016 5.00e-02 4.00e+02 2.38e-02 9.08e-01 pdb=" N PRO C 55 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " -0.013 5.00e-02 4.00e+02 ... (remaining 1579 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 815 2.75 - 3.28: 8705 3.28 - 3.82: 14877 3.82 - 4.36: 18327 4.36 - 4.90: 31948 Nonbonded interactions: 74672 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.207 3.040 nonbonded pdb=" O VAL R 307 " pdb=" NH1 ARG R 312 " model vdw 2.236 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.252 3.040 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.255 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.281 3.040 ... (remaining 74667 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 23.490 Find NCS groups from input model: 0.120 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 : 0.004 0.232 9133 Z= 0.261 Angle : 0.428 12.955 12393 Z= 0.211 Chirality : 0.039 0.183 1412 Planarity : 0.003 0.038 1582 Dihedral : 10.298 85.190 3262 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.85 % Allowed : 3.70 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.92 (0.24), residues: 1148 helix: 0.71 (0.26), residues: 407 sheet: 0.82 (0.30), residues: 281 loop : 0.60 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 95 HIS 0.004 0.001 HIS A 209 PHE 0.010 0.001 PHE A 108 TYR 0.010 0.001 TYR E 190 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 265 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8763 (tp40) cc_final: 0.8530 (tp-100) REVERT: A 75 GLN cc_start: 0.8040 (tt0) cc_final: 0.7835 (tt0) REVERT: A 123 ASN cc_start: 0.8669 (m-40) cc_final: 0.8442 (m110) REVERT: A 126 LYS cc_start: 0.8723 (ttmt) cc_final: 0.8072 (tttm) REVERT: A 129 TRP cc_start: 0.8375 (t-100) cc_final: 0.8065 (t-100) REVERT: A 185 ARG cc_start: 0.8572 (mtm180) cc_final: 0.8251 (mmm160) REVERT: A 222 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7426 (mp0) REVERT: B 20 ASP cc_start: 0.8588 (m-30) cc_final: 0.8168 (m-30) REVERT: B 59 TYR cc_start: 0.7835 (m-80) cc_final: 0.7372 (m-80) REVERT: B 137 ARG cc_start: 0.7826 (mmt-90) cc_final: 0.7611 (mmt180) REVERT: B 212 ASP cc_start: 0.8578 (t0) cc_final: 0.8298 (t0) REVERT: B 217 MET cc_start: 0.7883 (ppp) cc_final: 0.6749 (ppp) REVERT: B 335 PHE cc_start: 0.8754 (m-10) cc_final: 0.8541 (m-10) REVERT: C 38 MET cc_start: 0.8647 (ttp) cc_final: 0.8419 (ttm) REVERT: E 109 ASP cc_start: 0.8842 (p0) cc_final: 0.8617 (p0) REVERT: E 213 THR cc_start: 0.7800 (m) cc_final: 0.7559 (p) REVERT: R 79 LEU cc_start: 0.9006 (tp) cc_final: 0.8788 (tt) REVERT: R 237 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.5198 (ppt170) outliers start: 8 outliers final: 2 residues processed: 268 average time/residue: 0.2895 time to fit residues: 100.1279 Evaluate side-chains 191 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 188 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 237 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.8000 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9133 Z= 0.202 Angle : 0.526 6.414 12393 Z= 0.280 Chirality : 0.041 0.149 1412 Planarity : 0.004 0.042 1582 Dihedral : 6.623 74.972 1302 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.27 % Allowed : 10.25 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.60 (0.25), residues: 1148 helix: 1.88 (0.26), residues: 412 sheet: 0.79 (0.31), residues: 273 loop : 0.64 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 211 HIS 0.007 0.001 HIS A 209 PHE 0.009 0.001 PHE B 199 TYR 0.013 0.001 TYR E 190 ARG 0.007 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 208 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8304 (tp40) cc_final: 0.8081 (tp-100) REVERT: A 75 GLN cc_start: 0.7918 (tt0) cc_final: 0.7699 (tt0) REVERT: A 126 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7700 (tttm) REVERT: A 161 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7388 (mm-30) REVERT: A 195 LYS cc_start: 0.8767 (tptp) cc_final: 0.8446 (tptp) REVERT: B 59 TYR cc_start: 0.8159 (m-80) cc_final: 0.7401 (m-80) REVERT: B 137 ARG cc_start: 0.7557 (mmt-90) cc_final: 0.7261 (mmt180) REVERT: B 266 HIS cc_start: 0.8555 (t70) cc_final: 0.8098 (t70) REVERT: E 144 THR cc_start: 0.7858 (m) cc_final: 0.7541 (p) REVERT: E 160 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7808 (ttp80) REVERT: E 215 THR cc_start: 0.7968 (m) cc_final: 0.7372 (p) REVERT: R 163 LEU cc_start: 0.8136 (tp) cc_final: 0.7793 (tp) outliers start: 12 outliers final: 5 residues processed: 217 average time/residue: 0.2692 time to fit residues: 76.2302 Evaluate side-chains 190 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 185 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 237 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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: 0.8018 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9133 Z= 0.214 Angle : 0.500 6.415 12393 Z= 0.264 Chirality : 0.041 0.144 1412 Planarity : 0.004 0.042 1582 Dihedral : 6.178 76.232 1298 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.33 % Allowed : 12.26 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.74 (0.25), residues: 1148 helix: 2.31 (0.26), residues: 408 sheet: 0.51 (0.31), residues: 275 loop : 0.64 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.006 0.001 HIS A 209 PHE 0.009 0.001 PHE A 74 TYR 0.011 0.001 TYR R 226 ARG 0.005 0.001 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 194 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8449 (p) REVERT: A 126 LYS cc_start: 0.8307 (ttmt) cc_final: 0.7752 (tttm) REVERT: A 161 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7571 (mm-30) REVERT: B 137 ARG cc_start: 0.7562 (mmt-90) cc_final: 0.7247 (mmt180) REVERT: B 189 SER cc_start: 0.9450 (p) cc_final: 0.9017 (t) REVERT: B 266 HIS cc_start: 0.8511 (t70) cc_final: 0.8078 (t70) REVERT: C 20 LYS cc_start: 0.9068 (ttmm) cc_final: 0.8685 (mtmm) REVERT: E 160 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7868 (ttp80) REVERT: R 30 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7095 (t80) REVERT: R 108 MET cc_start: 0.6804 (tpt) cc_final: 0.6430 (tpt) REVERT: R 163 LEU cc_start: 0.8060 (tp) cc_final: 0.7673 (tp) REVERT: R 203 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7752 (tp) REVERT: R 271 ARG cc_start: 0.7553 (ttp80) cc_final: 0.7238 (ttp-170) outliers start: 22 outliers final: 13 residues processed: 206 average time/residue: 0.2521 time to fit residues: 68.6941 Evaluate side-chains 194 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 259 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8007 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9133 Z= 0.176 Angle : 0.471 6.413 12393 Z= 0.250 Chirality : 0.040 0.144 1412 Planarity : 0.003 0.044 1582 Dihedral : 5.762 74.703 1298 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.22 % Allowed : 13.85 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.85 (0.25), residues: 1148 helix: 2.58 (0.26), residues: 409 sheet: 0.47 (0.30), residues: 271 loop : 0.61 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS A 209 PHE 0.009 0.001 PHE B 151 TYR 0.011 0.001 TYR E 190 ARG 0.006 0.000 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8307 (ttmt) cc_final: 0.7744 (tttm) REVERT: A 161 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7490 (mm-30) REVERT: A 195 LYS cc_start: 0.8479 (tptp) cc_final: 0.7743 (tptp) REVERT: B 57 LYS cc_start: 0.8533 (mtmm) cc_final: 0.7803 (mtmm) REVERT: B 59 TYR cc_start: 0.8099 (m-80) cc_final: 0.7489 (m-80) REVERT: B 75 GLN cc_start: 0.8932 (mt0) cc_final: 0.8378 (mt0) REVERT: B 137 ARG cc_start: 0.7547 (mmt-90) cc_final: 0.7212 (mmt180) REVERT: B 215 GLU cc_start: 0.8471 (mp0) cc_final: 0.8127 (mp0) REVERT: C 20 LYS cc_start: 0.9061 (ttmm) cc_final: 0.8652 (mtmm) REVERT: E 160 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7870 (ttp80) REVERT: E 215 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7548 (p) REVERT: R 30 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.6987 (t80) REVERT: R 106 ARG cc_start: 0.8005 (mpp80) cc_final: 0.7600 (mpp80) REVERT: R 108 MET cc_start: 0.6835 (tpt) cc_final: 0.6485 (tpt) REVERT: R 163 LEU cc_start: 0.8108 (tp) cc_final: 0.7688 (tp) REVERT: R 203 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7711 (tp) REVERT: R 271 ARG cc_start: 0.7581 (ttp80) cc_final: 0.7208 (ttp-170) outliers start: 21 outliers final: 13 residues processed: 201 average time/residue: 0.2530 time to fit residues: 67.4733 Evaluate side-chains 194 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 259 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 0.3980 chunk 0 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8001 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9133 Z= 0.157 Angle : 0.457 6.744 12393 Z= 0.241 Chirality : 0.040 0.142 1412 Planarity : 0.003 0.044 1582 Dihedral : 5.684 73.966 1298 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.01 % Allowed : 15.33 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.92 (0.25), residues: 1148 helix: 2.70 (0.26), residues: 409 sheet: 0.42 (0.30), residues: 271 loop : 0.63 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.009 0.001 PHE B 151 TYR 0.011 0.001 TYR E 190 ARG 0.007 0.000 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 187 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7751 (tttm) REVERT: A 161 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7455 (mm-30) REVERT: A 233 ASP cc_start: 0.8725 (t0) cc_final: 0.8331 (t0) REVERT: B 57 LYS cc_start: 0.8591 (mtmm) cc_final: 0.7917 (mtmm) REVERT: B 59 TYR cc_start: 0.8100 (m-80) cc_final: 0.7652 (m-80) REVERT: B 75 GLN cc_start: 0.8862 (mt0) cc_final: 0.8317 (mt0) REVERT: B 130 GLU cc_start: 0.8787 (mp0) cc_final: 0.8586 (mp0) REVERT: B 215 GLU cc_start: 0.8417 (mp0) cc_final: 0.8055 (mp0) REVERT: B 266 HIS cc_start: 0.8587 (t70) cc_final: 0.8141 (t70) REVERT: C 17 GLU cc_start: 0.9098 (tp30) cc_final: 0.8727 (tp30) REVERT: C 20 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8652 (mtmm) REVERT: E 160 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7874 (ttp80) REVERT: E 215 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7565 (p) REVERT: R 30 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6991 (t80) REVERT: R 108 MET cc_start: 0.6744 (tpt) cc_final: 0.6403 (tpt) REVERT: R 163 LEU cc_start: 0.8100 (tp) cc_final: 0.7661 (tp) REVERT: R 203 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7701 (tp) REVERT: R 271 ARG cc_start: 0.7595 (ttp80) cc_final: 0.7342 (ttp80) outliers start: 19 outliers final: 11 residues processed: 197 average time/residue: 0.2543 time to fit residues: 66.4051 Evaluate side-chains 191 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 177 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 237 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 0.1980 chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 0.1980 chunk 92 optimal weight: 0.0000 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.4184 ------------------------------------------------------------------------------- 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: 0.7970 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9133 Z= 0.124 Angle : 0.446 7.247 12393 Z= 0.232 Chirality : 0.039 0.143 1412 Planarity : 0.003 0.042 1582 Dihedral : 5.579 71.058 1298 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.01 % Allowed : 15.12 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.04 (0.26), residues: 1148 helix: 2.81 (0.26), residues: 413 sheet: 0.39 (0.30), residues: 276 loop : 0.74 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.009 0.001 PHE B 151 TYR 0.012 0.001 TYR E 190 ARG 0.007 0.000 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 194 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8299 (ttmt) cc_final: 0.7753 (tttm) REVERT: A 161 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 233 ASP cc_start: 0.8675 (t0) cc_final: 0.8319 (t0) REVERT: B 57 LYS cc_start: 0.8588 (mtmm) cc_final: 0.8174 (mtmm) REVERT: B 134 ARG cc_start: 0.8114 (mtm110) cc_final: 0.7717 (ptt-90) REVERT: B 215 GLU cc_start: 0.8425 (mp0) cc_final: 0.8052 (mp0) REVERT: C 17 GLU cc_start: 0.9039 (tp30) cc_final: 0.8623 (tp30) REVERT: C 20 LYS cc_start: 0.9082 (ttmm) cc_final: 0.8664 (mtmm) REVERT: E 160 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7854 (ttp80) REVERT: E 215 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7540 (p) REVERT: R 30 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.6896 (t80) REVERT: R 108 MET cc_start: 0.6755 (tpt) cc_final: 0.6433 (tpt) REVERT: R 163 LEU cc_start: 0.8006 (tp) cc_final: 0.7567 (tp) REVERT: R 203 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7600 (tp) REVERT: R 271 ARG cc_start: 0.7545 (ttp80) cc_final: 0.7299 (ttp80) outliers start: 19 outliers final: 13 residues processed: 204 average time/residue: 0.2473 time to fit residues: 66.8146 Evaluate side-chains 198 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 182 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 237 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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: 0.8007 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9133 Z= 0.191 Angle : 0.476 7.622 12393 Z= 0.249 Chirality : 0.040 0.150 1412 Planarity : 0.003 0.044 1582 Dihedral : 5.567 71.314 1298 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.43 % Allowed : 16.17 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.96 (0.26), residues: 1148 helix: 2.78 (0.26), residues: 412 sheet: 0.22 (0.30), residues: 280 loop : 0.76 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS A 209 PHE 0.010 0.001 PHE R 184 TYR 0.020 0.001 TYR B 59 ARG 0.008 0.000 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 183 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7739 (tttm) REVERT: A 161 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7433 (mm-30) REVERT: B 57 LYS cc_start: 0.8471 (mtmm) cc_final: 0.8052 (pttm) REVERT: B 59 TYR cc_start: 0.7613 (m-80) cc_final: 0.6879 (m-80) REVERT: B 215 GLU cc_start: 0.8365 (mp0) cc_final: 0.7991 (mp0) REVERT: C 20 LYS cc_start: 0.9077 (ttmm) cc_final: 0.8651 (mtmm) REVERT: E 160 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7828 (ttp80) REVERT: E 218 ARG cc_start: 0.7214 (ttp-110) cc_final: 0.6807 (tmm-80) REVERT: R 30 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.6914 (t80) REVERT: R 106 ARG cc_start: 0.7625 (mpp80) cc_final: 0.7418 (mpp80) REVERT: R 108 MET cc_start: 0.6797 (tpt) cc_final: 0.6465 (tpt) REVERT: R 163 LEU cc_start: 0.8045 (tp) cc_final: 0.7596 (tp) REVERT: R 203 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7607 (tp) outliers start: 23 outliers final: 17 residues processed: 194 average time/residue: 0.2601 time to fit residues: 67.9473 Evaluate side-chains 199 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 180 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 255 SER Chi-restraints excluded: chain R residue 270 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 0.2980 chunk 96 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8002 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9133 Z= 0.174 Angle : 0.472 7.666 12393 Z= 0.246 Chirality : 0.040 0.149 1412 Planarity : 0.003 0.045 1582 Dihedral : 5.572 70.648 1298 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.22 % Allowed : 16.38 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.97 (0.26), residues: 1148 helix: 2.84 (0.26), residues: 406 sheet: 0.17 (0.29), residues: 285 loop : 0.80 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.021 0.001 PHE R 184 TYR 0.011 0.001 TYR E 190 ARG 0.006 0.000 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 185 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8295 (ttmt) cc_final: 0.7742 (tttm) REVERT: A 161 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7421 (mm-30) REVERT: A 196 GLU cc_start: 0.7838 (tp30) cc_final: 0.7599 (tp30) REVERT: A 233 ASP cc_start: 0.8719 (t0) cc_final: 0.8339 (t0) REVERT: B 57 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8019 (pttm) REVERT: B 59 TYR cc_start: 0.7571 (m-80) cc_final: 0.7067 (m-80) REVERT: B 130 GLU cc_start: 0.8785 (mp0) cc_final: 0.8536 (mp0) REVERT: B 197 ARG cc_start: 0.7682 (mtp85) cc_final: 0.7462 (mmm160) REVERT: B 215 GLU cc_start: 0.8385 (mp0) cc_final: 0.7982 (mp0) REVERT: C 17 GLU cc_start: 0.9041 (tp30) cc_final: 0.8768 (tp30) REVERT: C 20 LYS cc_start: 0.9072 (ttmm) cc_final: 0.8692 (mtmm) REVERT: E 218 ARG cc_start: 0.7180 (ttp-110) cc_final: 0.6775 (tmm-80) REVERT: R 30 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6900 (t80) REVERT: R 108 MET cc_start: 0.6778 (tpt) cc_final: 0.6428 (tpt) REVERT: R 163 LEU cc_start: 0.8016 (tp) cc_final: 0.7645 (tp) REVERT: R 203 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7603 (tp) outliers start: 21 outliers final: 17 residues processed: 195 average time/residue: 0.2412 time to fit residues: 62.8406 Evaluate side-chains 198 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 179 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 255 SER Chi-restraints excluded: chain R residue 270 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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: 0.8058 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9133 Z= 0.332 Angle : 0.555 10.822 12393 Z= 0.286 Chirality : 0.043 0.149 1412 Planarity : 0.004 0.046 1582 Dihedral : 5.819 76.494 1298 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.54 % Allowed : 16.91 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.72 (0.25), residues: 1148 helix: 2.53 (0.27), residues: 409 sheet: 0.12 (0.30), residues: 273 loop : 0.66 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 339 HIS 0.006 0.001 HIS A 209 PHE 0.022 0.002 PHE R 184 TYR 0.012 0.001 TYR R 226 ARG 0.007 0.001 ARG E 218 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8361 (ttmt) cc_final: 0.7790 (tttm) REVERT: A 161 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7437 (mm-30) REVERT: A 195 LYS cc_start: 0.8402 (tptp) cc_final: 0.8123 (tptp) REVERT: B 57 LYS cc_start: 0.8545 (mtmm) cc_final: 0.8136 (mtmm) REVERT: B 59 TYR cc_start: 0.7866 (m-80) cc_final: 0.7171 (m-80) REVERT: B 130 GLU cc_start: 0.8812 (mp0) cc_final: 0.8594 (mp0) REVERT: B 197 ARG cc_start: 0.7735 (mtp85) cc_final: 0.7487 (mmm160) REVERT: B 215 GLU cc_start: 0.8334 (mp0) cc_final: 0.7926 (mp0) REVERT: B 260 GLU cc_start: 0.8662 (tt0) cc_final: 0.8443 (tt0) REVERT: C 17 GLU cc_start: 0.9038 (tp30) cc_final: 0.8753 (tp30) REVERT: C 20 LYS cc_start: 0.9083 (ttmm) cc_final: 0.8696 (mtmm) REVERT: R 30 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.7138 (t80) REVERT: R 108 MET cc_start: 0.6787 (tpt) cc_final: 0.6432 (tpt) REVERT: R 163 LEU cc_start: 0.8106 (tp) cc_final: 0.7693 (tp) REVERT: R 203 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7651 (tp) REVERT: R 312 ARG cc_start: 0.7955 (mmp80) cc_final: 0.6545 (mmp80) outliers start: 24 outliers final: 17 residues processed: 197 average time/residue: 0.2518 time to fit residues: 66.5718 Evaluate side-chains 201 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 255 SER Chi-restraints excluded: chain R residue 270 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8013 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9133 Z= 0.176 Angle : 0.499 10.769 12393 Z= 0.259 Chirality : 0.040 0.147 1412 Planarity : 0.004 0.045 1582 Dihedral : 5.935 78.219 1298 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.80 % Allowed : 18.82 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.85 (0.26), residues: 1148 helix: 2.79 (0.27), residues: 404 sheet: 0.12 (0.29), residues: 283 loop : 0.66 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.020 0.001 PHE R 184 TYR 0.012 0.001 TYR E 190 ARG 0.010 0.000 ARG E 218 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 184 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8317 (ttmt) cc_final: 0.7790 (tttm) REVERT: A 161 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7424 (mm-30) REVERT: A 233 ASP cc_start: 0.8692 (t0) cc_final: 0.8329 (t0) REVERT: B 33 ILE cc_start: 0.8841 (mm) cc_final: 0.8604 (mt) REVERT: B 57 LYS cc_start: 0.8492 (mtmm) cc_final: 0.8186 (mtmm) REVERT: B 59 TYR cc_start: 0.7635 (m-80) cc_final: 0.7283 (m-80) REVERT: B 99 TRP cc_start: 0.8393 (m100) cc_final: 0.8067 (m100) REVERT: B 130 GLU cc_start: 0.8773 (mp0) cc_final: 0.8570 (mp0) REVERT: B 197 ARG cc_start: 0.7675 (mtp85) cc_final: 0.7462 (mmm160) REVERT: B 215 GLU cc_start: 0.8331 (mp0) cc_final: 0.7946 (mp0) REVERT: B 266 HIS cc_start: 0.8492 (t70) cc_final: 0.8103 (t70) REVERT: C 20 LYS cc_start: 0.9071 (ttmm) cc_final: 0.8660 (mtmm) REVERT: E 218 ARG cc_start: 0.7108 (ttp-110) cc_final: 0.6602 (tmm-80) REVERT: E 220 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7706 (mt-10) REVERT: R 30 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.7038 (t80) REVERT: R 108 MET cc_start: 0.6849 (tpt) cc_final: 0.6527 (tpt) REVERT: R 163 LEU cc_start: 0.8081 (tp) cc_final: 0.7618 (tp) REVERT: R 203 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7585 (tp) REVERT: R 312 ARG cc_start: 0.7794 (mmp80) cc_final: 0.6452 (mmp80) outliers start: 17 outliers final: 13 residues processed: 192 average time/residue: 0.2344 time to fit residues: 60.2195 Evaluate side-chains 195 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 180 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 270 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 5.9990 chunk 84 optimal weight: 30.0000 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 91 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.152932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.112652 restraints weight = 10948.830| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.51 r_work: 0.3062 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9133 Z= 0.397 Angle : 0.600 10.769 12393 Z= 0.311 Chirality : 0.044 0.149 1412 Planarity : 0.004 0.044 1582 Dihedral : 6.031 81.738 1298 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.43 % Allowed : 18.29 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.46 (0.25), residues: 1148 helix: 2.35 (0.26), residues: 405 sheet: -0.07 (0.28), residues: 298 loop : 0.56 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.007 0.001 HIS A 209 PHE 0.020 0.002 PHE R 184 TYR 0.014 0.002 TYR B 59 ARG 0.010 0.001 ARG E 218 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2484.57 seconds wall clock time: 45 minutes 16.01 seconds (2716.01 seconds total)