Starting phenix.real_space_refine on Thu Feb 13 00:29:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wj5_32543/02_2025/7wj5_32543.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wj5_32543/02_2025/7wj5_32543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wj5_32543/02_2025/7wj5_32543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wj5_32543/02_2025/7wj5_32543.map" model { file = "/net/cci-nas-00/data/ceres_data/7wj5_32543/02_2025/7wj5_32543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wj5_32543/02_2025/7wj5_32543.cif" } resolution = 3.72 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= 1.033 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: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 5551 2.51 5 N 1476 2.21 5 O 1568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8660 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1653 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2226 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 11, 'TRANS': 270} Chain: "S" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Time building chain proxies: 5.12, per 1000 atoms: 0.59 Number of scatterers: 8660 At special positions: 0 Unit cell: (106.112, 124.35, 117.718, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 1568 8.00 N 1476 7.00 C 5551 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 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 193 " distance=2.03 Simple disulfide: pdb=" SG CYS S 3 " - pdb=" SG CYS S 14 " 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: 2.30 Conformation dependent library (CDL) restraints added in 1.0 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 16 sheets defined 35.3% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.895A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.209A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.735A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.560A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 24 removed outlier: 3.776A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.902A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'R' and resid 42 through 71 Processing helix chain 'R' and resid 72 through 75 removed outlier: 3.822A pdb=" N LYS R 75 " --> pdb=" O ALA R 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 72 through 75' Processing helix chain 'R' and resid 76 through 95 Processing helix chain 'R' and resid 95 through 106 removed outlier: 4.283A pdb=" N LEU R 99 " --> pdb=" O GLY R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 146 Processing helix chain 'R' and resid 148 through 153 removed outlier: 4.055A pdb=" N LYS R 152 " --> pdb=" O LYS R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 173 Processing helix chain 'R' and resid 174 through 180 Processing helix chain 'R' and resid 202 through 217 removed outlier: 3.658A pdb=" N THR R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 237 Processing helix chain 'R' and resid 251 through 282 Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 287 through 315 removed outlier: 3.891A pdb=" N TYR R 302 " --> pdb=" O VAL R 298 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER R 305 " --> pdb=" O THR R 301 " (cutoff:3.500A) Proline residue: R 309 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190 removed outlier: 9.613A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 9.613A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.652A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.649A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.090A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.033A 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: 3.569A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.291A 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: 3.572A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.772A 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: 6.791A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.345A 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: 3.685A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (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 10 through 12 removed outlier: 6.067A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.067A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.270A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 143 through 147 Processing sheet with id=AB6, first strand: chain 'R' and resid 181 through 185 Processing sheet with id=AB7, first strand: chain 'S' and resid 6 through 7 removed outlier: 3.544A pdb=" N PHE S 7 " --> pdb=" O THR S 10 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1242 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: 2.70 Time building geometry restraints manager: 2.65 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: 2743 1.34 - 1.46: 2191 1.46 - 1.58: 3818 1.58 - 1.70: 0 1.70 - 1.81: 94 Bond restraints: 8846 Sorted by residual: bond pdb=" CA SER B 189 " pdb=" CB SER B 189 " ideal model delta sigma weight residual 1.535 1.516 0.019 1.90e-02 2.77e+03 1.02e+00 bond pdb=" CB PRO E 224 " pdb=" CG PRO E 224 " ideal model delta sigma weight residual 1.506 1.471 0.035 3.90e-02 6.57e+02 8.06e-01 bond pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 1.498 1.472 0.026 3.10e-02 1.04e+03 7.01e-01 bond pdb=" CG1 ILE R 209 " pdb=" CD1 ILE R 209 " ideal model delta sigma weight residual 1.513 1.481 0.032 3.90e-02 6.57e+02 6.79e-01 bond pdb=" C ILE A 264 " pdb=" N ILE A 265 " ideal model delta sigma weight residual 1.327 1.304 0.023 2.97e-02 1.13e+03 5.99e-01 ... (remaining 8841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 11837 1.79 - 3.58: 133 3.58 - 5.37: 15 5.37 - 7.17: 6 7.17 - 8.96: 3 Bond angle restraints: 11994 Sorted by residual: angle pdb=" N LEU R 96 " pdb=" CA LEU R 96 " pdb=" C LEU R 96 " ideal model delta sigma weight residual 109.81 115.83 -6.02 2.21e+00 2.05e-01 7.42e+00 angle pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " pdb=" CG LEU B 79 " ideal model delta sigma weight residual 116.30 125.26 -8.96 3.50e+00 8.16e-02 6.55e+00 angle pdb=" C ARG R 241 " pdb=" N VAL R 242 " pdb=" CA VAL R 242 " ideal model delta sigma weight residual 121.97 126.42 -4.45 1.80e+00 3.09e-01 6.10e+00 angle pdb=" CA LEU B 336 " pdb=" CB LEU B 336 " pdb=" CG LEU B 336 " ideal model delta sigma weight residual 116.30 124.90 -8.60 3.50e+00 8.16e-02 6.03e+00 angle pdb=" N MET E 180 " pdb=" CA MET E 180 " pdb=" CB MET E 180 " ideal model delta sigma weight residual 113.65 110.08 3.57 1.47e+00 4.63e-01 5.91e+00 ... (remaining 11989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 4868 16.60 - 33.19: 297 33.19 - 49.79: 47 49.79 - 66.38: 7 66.38 - 82.98: 1 Dihedral angle restraints: 5220 sinusoidal: 1953 harmonic: 3267 Sorted by residual: dihedral pdb=" CA TYR A 320 " pdb=" C TYR A 320 " pdb=" N THR A 321 " pdb=" CA THR A 321 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 161.26 18.74 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 844 0.032 - 0.064: 374 0.064 - 0.096: 112 0.096 - 0.127: 46 0.127 - 0.159: 6 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CA ILE A 319 " pdb=" N ILE A 319 " pdb=" C ILE A 319 " pdb=" CB ILE A 319 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1379 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO B 236 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 287 " 0.019 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO R 288 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO R 288 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 288 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP R 108 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO R 109 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO R 109 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 109 " 0.016 5.00e-02 4.00e+02 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 344 2.72 - 3.26: 8665 3.26 - 3.81: 14372 3.81 - 4.35: 17028 4.35 - 4.90: 30051 Nonbonded interactions: 70460 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.173 3.040 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.186 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" O SER R 244 " model vdw 2.199 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.206 3.040 nonbonded pdb=" O LYS A 349 " pdb=" ND2 ASN R 318 " model vdw 2.244 3.120 ... (remaining 70455 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 group one per residue 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: 0.850 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.720 Find NCS groups from input model: 0.080 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 0.035 8846 Z= 0.237 Angle : 0.546 8.958 11994 Z= 0.288 Chirality : 0.041 0.159 1382 Planarity : 0.003 0.031 1495 Dihedral : 10.788 82.979 3102 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.05 % Allowed : 7.63 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.05 (0.26), residues: 1111 helix: 2.25 (0.28), residues: 349 sheet: 0.33 (0.30), residues: 283 loop : -0.19 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS R 107 PHE 0.012 0.001 PHE E 27 TYR 0.010 0.001 TYR R 211 ARG 0.002 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.6043 (mmt) cc_final: 0.5559 (mpp) REVERT: B 57 LYS cc_start: 0.8052 (mtpt) cc_final: 0.7614 (mtpt) REVERT: B 59 TYR cc_start: 0.8299 (m-80) cc_final: 0.8076 (m-80) REVERT: B 75 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: B 76 ASP cc_start: 0.8563 (p0) cc_final: 0.8320 (p0) REVERT: B 234 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: B 267 ASP cc_start: 0.7322 (m-30) cc_final: 0.6784 (m-30) REVERT: R 51 PHE cc_start: 0.7190 (m-10) cc_final: 0.6873 (m-10) REVERT: R 180 TYR cc_start: 0.7496 (m-10) cc_final: 0.7110 (m-10) outliers start: 28 outliers final: 12 residues processed: 221 average time/residue: 0.2259 time to fit residues: 67.4702 Evaluate side-chains 189 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 240 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 220 GLN B 259 GLN C 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.167903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.127542 restraints weight = 11214.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.128599 restraints weight = 9248.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130152 restraints weight = 7731.048| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8846 Z= 0.208 Angle : 0.564 8.422 11994 Z= 0.294 Chirality : 0.042 0.153 1382 Planarity : 0.004 0.031 1495 Dihedral : 5.705 59.956 1238 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.79 % Favored : 97.12 % Rotamer: Outliers : 3.05 % Allowed : 10.78 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.04 (0.26), residues: 1111 helix: 2.19 (0.28), residues: 350 sheet: 0.43 (0.30), residues: 280 loop : -0.21 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.011 0.001 PHE A 250 TYR 0.015 0.001 TYR A 320 ARG 0.003 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.6017 (mmt) cc_final: 0.5804 (tpp) REVERT: B 57 LYS cc_start: 0.8044 (mtpt) cc_final: 0.7636 (mtpt) REVERT: B 59 TYR cc_start: 0.8339 (m-80) cc_final: 0.8104 (m-80) REVERT: B 234 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8213 (m-80) REVERT: R 51 PHE cc_start: 0.7116 (m-10) cc_final: 0.6858 (m-10) REVERT: R 180 TYR cc_start: 0.7319 (m-10) cc_final: 0.6950 (m-10) REVERT: R 251 GLU cc_start: 0.6045 (OUTLIER) cc_final: 0.5432 (mp0) outliers start: 28 outliers final: 18 residues processed: 202 average time/residue: 0.2222 time to fit residues: 61.0587 Evaluate side-chains 185 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 10 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 220 GLN E 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.168516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128468 restraints weight = 11382.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.130890 restraints weight = 9179.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131924 restraints weight = 7186.592| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8846 Z= 0.178 Angle : 0.537 7.890 11994 Z= 0.283 Chirality : 0.041 0.147 1382 Planarity : 0.004 0.031 1495 Dihedral : 5.030 58.412 1231 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.33 % Favored : 96.58 % Rotamer: Outliers : 4.47 % Allowed : 10.78 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.99 (0.26), residues: 1111 helix: 2.19 (0.28), residues: 348 sheet: 0.39 (0.30), residues: 268 loop : -0.25 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 197 HIS 0.003 0.001 HIS B 225 PHE 0.010 0.001 PHE E 27 TYR 0.012 0.001 TYR E 178 ARG 0.003 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7375 (mtm-85) cc_final: 0.6577 (ptp90) REVERT: A 243 MET cc_start: 0.6098 (mmt) cc_final: 0.5369 (mmm) REVERT: B 57 LYS cc_start: 0.8075 (mtpt) cc_final: 0.7693 (mtpt) REVERT: B 76 ASP cc_start: 0.8420 (p0) cc_final: 0.8172 (p0) REVERT: B 172 GLU cc_start: 0.7399 (pm20) cc_final: 0.7037 (pm20) REVERT: B 234 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8290 (m-80) REVERT: B 267 ASP cc_start: 0.7091 (m-30) cc_final: 0.6556 (m-30) REVERT: R 51 PHE cc_start: 0.7132 (m-10) cc_final: 0.6870 (m-10) REVERT: R 251 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5267 (mp0) outliers start: 41 outliers final: 27 residues processed: 200 average time/residue: 0.2280 time to fit residues: 61.7469 Evaluate side-chains 194 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 115 CYS Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 GLU Chi-restraints excluded: chain R residue 308 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 72 optimal weight: 0.0060 chunk 57 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.168136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127790 restraints weight = 11360.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128917 restraints weight = 9440.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.130438 restraints weight = 7774.823| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8846 Z= 0.199 Angle : 0.544 8.136 11994 Z= 0.286 Chirality : 0.041 0.149 1382 Planarity : 0.003 0.031 1495 Dihedral : 5.001 59.550 1231 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.15 % Favored : 96.76 % Rotamer: Outliers : 4.03 % Allowed : 13.83 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.97 (0.26), residues: 1111 helix: 2.23 (0.28), residues: 342 sheet: 0.25 (0.29), residues: 279 loop : -0.20 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 211 HIS 0.003 0.001 HIS B 142 PHE 0.010 0.001 PHE E 27 TYR 0.011 0.001 TYR E 178 ARG 0.006 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7407 (mtm-85) cc_final: 0.6656 (ptp90) REVERT: A 243 MET cc_start: 0.6123 (mmt) cc_final: 0.5380 (mmm) REVERT: B 57 LYS cc_start: 0.8031 (mtpt) cc_final: 0.7655 (mtpt) REVERT: B 76 ASP cc_start: 0.8345 (p0) cc_final: 0.8094 (p0) REVERT: B 172 GLU cc_start: 0.7395 (pm20) cc_final: 0.7121 (pm20) REVERT: B 234 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8354 (m-80) REVERT: B 267 ASP cc_start: 0.7199 (m-30) cc_final: 0.6645 (m-30) REVERT: E 206 ARG cc_start: 0.7615 (mtm110) cc_final: 0.7260 (ptp90) REVERT: R 51 PHE cc_start: 0.7119 (m-10) cc_final: 0.6870 (m-10) REVERT: R 153 TRP cc_start: 0.5904 (OUTLIER) cc_final: 0.5406 (m-10) REVERT: R 251 GLU cc_start: 0.5919 (OUTLIER) cc_final: 0.5245 (mp0) outliers start: 37 outliers final: 28 residues processed: 199 average time/residue: 0.2285 time to fit residues: 62.5701 Evaluate side-chains 195 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 GLU Chi-restraints excluded: chain R residue 308 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 75 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 chunk 77 optimal weight: 0.0060 chunk 84 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.171878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.132044 restraints weight = 11288.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.134038 restraints weight = 9256.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134871 restraints weight = 7144.163| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8846 Z= 0.137 Angle : 0.505 7.729 11994 Z= 0.267 Chirality : 0.041 0.157 1382 Planarity : 0.003 0.031 1495 Dihedral : 4.675 59.160 1230 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.61 % Favored : 97.30 % Rotamer: Outliers : 3.38 % Allowed : 15.03 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.02 (0.26), residues: 1111 helix: 2.11 (0.29), residues: 354 sheet: 0.48 (0.30), residues: 264 loop : -0.21 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 211 HIS 0.002 0.000 HIS R 107 PHE 0.010 0.001 PHE A 189 TYR 0.012 0.001 TYR E 178 ARG 0.003 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 208 ARG cc_start: 0.7394 (mtm-85) cc_final: 0.6369 (mmp80) REVERT: A 223 PHE cc_start: 0.7814 (t80) cc_final: 0.7597 (t80) REVERT: A 243 MET cc_start: 0.6241 (mmt) cc_final: 0.6029 (tpp) REVERT: B 57 LYS cc_start: 0.7884 (mtpt) cc_final: 0.7439 (mtpt) REVERT: B 59 TYR cc_start: 0.8391 (m-80) cc_final: 0.8097 (m-80) REVERT: B 76 ASP cc_start: 0.8142 (p0) cc_final: 0.7924 (p0) REVERT: B 234 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8318 (m-80) REVERT: B 267 ASP cc_start: 0.7260 (m-30) cc_final: 0.6686 (m-30) REVERT: E 206 ARG cc_start: 0.7504 (mtm110) cc_final: 0.7234 (ptp90) REVERT: R 51 PHE cc_start: 0.7080 (m-10) cc_final: 0.6746 (m-10) REVERT: R 153 TRP cc_start: 0.5878 (OUTLIER) cc_final: 0.5376 (m-10) REVERT: R 194 THR cc_start: 0.7756 (t) cc_final: 0.7504 (t) REVERT: R 251 GLU cc_start: 0.5896 (OUTLIER) cc_final: 0.5334 (mp0) outliers start: 31 outliers final: 20 residues processed: 197 average time/residue: 0.2184 time to fit residues: 58.7752 Evaluate side-chains 196 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 251 GLU Chi-restraints excluded: chain R residue 308 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 36 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 15 optimal weight: 0.0270 chunk 38 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.164956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.124539 restraints weight = 11314.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.126053 restraints weight = 9268.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127348 restraints weight = 7277.386| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8846 Z= 0.325 Angle : 0.616 9.420 11994 Z= 0.322 Chirality : 0.044 0.155 1382 Planarity : 0.004 0.032 1495 Dihedral : 5.110 58.380 1227 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.95 % Rotamer: Outliers : 4.03 % Allowed : 16.34 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.83 (0.26), residues: 1111 helix: 2.04 (0.28), residues: 342 sheet: 0.15 (0.30), residues: 277 loop : -0.21 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 197 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.002 PHE E 27 TYR 0.010 0.002 TYR R 71 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 1.050 Fit side-chains REVERT: A 208 ARG cc_start: 0.7282 (mtm-85) cc_final: 0.6513 (ptp90) REVERT: A 243 MET cc_start: 0.6204 (mmt) cc_final: 0.5524 (mmm) REVERT: B 57 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7776 (mtpt) REVERT: B 75 GLN cc_start: 0.8090 (mt0) cc_final: 0.7533 (mt0) REVERT: B 76 ASP cc_start: 0.8297 (p0) cc_final: 0.8081 (p0) REVERT: B 234 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: R 51 PHE cc_start: 0.7137 (m-10) cc_final: 0.6863 (m-10) REVERT: R 68 ILE cc_start: 0.8208 (mt) cc_final: 0.7933 (mt) REVERT: R 74 MET cc_start: 0.4761 (mmp) cc_final: 0.3992 (ppp) REVERT: R 153 TRP cc_start: 0.5873 (OUTLIER) cc_final: 0.5320 (m-10) REVERT: R 194 THR cc_start: 0.7844 (t) cc_final: 0.7562 (t) outliers start: 37 outliers final: 21 residues processed: 196 average time/residue: 0.2193 time to fit residues: 58.3180 Evaluate side-chains 190 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 240 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.169421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.130108 restraints weight = 11399.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.132264 restraints weight = 8925.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133513 restraints weight = 7353.679| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8846 Z= 0.169 Angle : 0.542 8.229 11994 Z= 0.286 Chirality : 0.041 0.199 1382 Planarity : 0.003 0.032 1495 Dihedral : 4.852 57.898 1227 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.79 % Favored : 97.12 % Rotamer: Outliers : 3.27 % Allowed : 17.54 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.81 (0.26), residues: 1111 helix: 2.02 (0.28), residues: 349 sheet: 0.11 (0.30), residues: 270 loop : -0.22 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 197 HIS 0.003 0.001 HIS B 225 PHE 0.010 0.001 PHE A 334 TYR 0.011 0.001 TYR E 178 ARG 0.007 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.990 Fit side-chains REVERT: A 208 ARG cc_start: 0.7250 (mtm-85) cc_final: 0.6523 (ptp90) REVERT: A 223 PHE cc_start: 0.7956 (t80) cc_final: 0.7699 (t80) REVERT: A 243 MET cc_start: 0.6231 (mmt) cc_final: 0.5902 (mmm) REVERT: B 57 LYS cc_start: 0.7985 (mtpt) cc_final: 0.7658 (mtpt) REVERT: B 101 MET cc_start: 0.8607 (mmt) cc_final: 0.7846 (mmt) REVERT: B 165 THR cc_start: 0.8021 (p) cc_final: 0.7674 (t) REVERT: B 188 MET cc_start: 0.7483 (ptp) cc_final: 0.7255 (ptp) REVERT: B 234 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8292 (m-80) REVERT: E 206 ARG cc_start: 0.7579 (mtm110) cc_final: 0.7183 (ptp90) REVERT: R 51 PHE cc_start: 0.7117 (m-10) cc_final: 0.6765 (m-10) REVERT: R 68 ILE cc_start: 0.8199 (mt) cc_final: 0.7995 (mt) REVERT: R 74 MET cc_start: 0.4538 (mmp) cc_final: 0.4132 (ppp) REVERT: R 153 TRP cc_start: 0.5919 (OUTLIER) cc_final: 0.5406 (m-10) REVERT: R 248 LYS cc_start: 0.7260 (mtmm) cc_final: 0.7024 (mptt) outliers start: 30 outliers final: 23 residues processed: 192 average time/residue: 0.2198 time to fit residues: 57.1603 Evaluate side-chains 196 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 240 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 8 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.167659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.128079 restraints weight = 11542.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.129211 restraints weight = 9020.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.131063 restraints weight = 7417.404| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8846 Z= 0.220 Angle : 0.576 11.765 11994 Z= 0.301 Chirality : 0.043 0.277 1382 Planarity : 0.004 0.032 1495 Dihedral : 4.899 57.838 1227 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.60 % Favored : 96.31 % Rotamer: Outliers : 3.59 % Allowed : 17.97 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.76 (0.26), residues: 1111 helix: 1.96 (0.28), residues: 348 sheet: 0.03 (0.30), residues: 281 loop : -0.21 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 197 HIS 0.002 0.001 HIS B 225 PHE 0.011 0.001 PHE E 27 TYR 0.010 0.001 TYR E 178 ARG 0.005 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 1.031 Fit side-chains REVERT: A 208 ARG cc_start: 0.7232 (mtm-85) cc_final: 0.6528 (ptp90) REVERT: A 223 PHE cc_start: 0.7927 (t80) cc_final: 0.7677 (t80) REVERT: A 243 MET cc_start: 0.6190 (mmt) cc_final: 0.5498 (mmm) REVERT: B 57 LYS cc_start: 0.8004 (mtpt) cc_final: 0.7667 (mtpt) REVERT: B 59 TYR cc_start: 0.8350 (m-80) cc_final: 0.8032 (m-80) REVERT: B 75 GLN cc_start: 0.7862 (mt0) cc_final: 0.7528 (mt0) REVERT: B 234 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8322 (m-80) REVERT: E 206 ARG cc_start: 0.7558 (mtm110) cc_final: 0.7198 (ptp90) REVERT: R 153 TRP cc_start: 0.5890 (OUTLIER) cc_final: 0.5345 (m-10) REVERT: R 194 THR cc_start: 0.7601 (t) cc_final: 0.7387 (t) REVERT: R 248 LYS cc_start: 0.7263 (mtmm) cc_final: 0.6778 (mptt) outliers start: 33 outliers final: 28 residues processed: 195 average time/residue: 0.2227 time to fit residues: 58.6442 Evaluate side-chains 202 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 240 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 82 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.169365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.129864 restraints weight = 11536.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130627 restraints weight = 9046.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131594 restraints weight = 8939.715| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8846 Z= 0.178 Angle : 0.567 12.097 11994 Z= 0.298 Chirality : 0.042 0.279 1382 Planarity : 0.003 0.031 1495 Dihedral : 4.819 57.092 1227 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.85 % Rotamer: Outliers : 3.38 % Allowed : 18.52 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.81 (0.26), residues: 1111 helix: 1.92 (0.28), residues: 349 sheet: 0.18 (0.31), residues: 268 loop : -0.20 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 197 HIS 0.002 0.001 HIS R 107 PHE 0.011 0.001 PHE R 127 TYR 0.011 0.001 TYR E 178 ARG 0.005 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.926 Fit side-chains REVERT: A 208 ARG cc_start: 0.7230 (mtm-85) cc_final: 0.6554 (ptp90) REVERT: A 223 PHE cc_start: 0.7885 (t80) cc_final: 0.7664 (t80) REVERT: A 243 MET cc_start: 0.6271 (mmt) cc_final: 0.5573 (mmm) REVERT: B 57 LYS cc_start: 0.7973 (mtpt) cc_final: 0.7608 (mtpt) REVERT: B 75 GLN cc_start: 0.7922 (mt0) cc_final: 0.7466 (mt0) REVERT: B 101 MET cc_start: 0.8606 (mmt) cc_final: 0.8339 (mmt) REVERT: B 165 THR cc_start: 0.7962 (p) cc_final: 0.7641 (t) REVERT: B 234 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8341 (m-80) REVERT: C 40 TYR cc_start: 0.8088 (t80) cc_final: 0.7862 (t80) REVERT: E 206 ARG cc_start: 0.7580 (mtm110) cc_final: 0.7237 (ptp90) REVERT: R 153 TRP cc_start: 0.5939 (OUTLIER) cc_final: 0.5424 (m-10) REVERT: R 248 LYS cc_start: 0.7163 (mtmm) cc_final: 0.6895 (mptt) REVERT: R 305 SER cc_start: 0.8047 (OUTLIER) cc_final: 0.7785 (t) outliers start: 31 outliers final: 26 residues processed: 196 average time/residue: 0.2201 time to fit residues: 58.5836 Evaluate side-chains 202 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.170550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130619 restraints weight = 11416.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.132283 restraints weight = 9374.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.133195 restraints weight = 7394.822| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8846 Z= 0.169 Angle : 0.557 12.123 11994 Z= 0.292 Chirality : 0.042 0.274 1382 Planarity : 0.003 0.031 1495 Dihedral : 4.702 56.230 1227 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.49 % Allowed : 18.52 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.82 (0.26), residues: 1111 helix: 1.94 (0.28), residues: 351 sheet: 0.26 (0.31), residues: 264 loop : -0.24 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP R 197 HIS 0.002 0.001 HIS B 225 PHE 0.011 0.001 PHE R 127 TYR 0.011 0.001 TYR E 178 ARG 0.005 0.000 ARG E 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 1.049 Fit side-chains REVERT: A 208 ARG cc_start: 0.7169 (mtm-85) cc_final: 0.6510 (ptp90) REVERT: A 223 PHE cc_start: 0.7888 (t80) cc_final: 0.7673 (t80) REVERT: A 243 MET cc_start: 0.6294 (mmt) cc_final: 0.5595 (mmm) REVERT: B 57 LYS cc_start: 0.7948 (mtpt) cc_final: 0.7598 (mtpt) REVERT: B 59 TYR cc_start: 0.8345 (m-80) cc_final: 0.7778 (m-80) REVERT: B 101 MET cc_start: 0.8612 (mmt) cc_final: 0.8290 (mmt) REVERT: B 234 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8314 (m-80) REVERT: E 206 ARG cc_start: 0.7538 (mtm110) cc_final: 0.7233 (ptp90) REVERT: R 153 TRP cc_start: 0.5920 (OUTLIER) cc_final: 0.5403 (m-10) REVERT: R 248 LYS cc_start: 0.7172 (mtmm) cc_final: 0.6929 (mptt) REVERT: R 305 SER cc_start: 0.7917 (OUTLIER) cc_final: 0.7630 (t) outliers start: 32 outliers final: 27 residues processed: 194 average time/residue: 0.2249 time to fit residues: 59.6112 Evaluate side-chains 199 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 153 TRP Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 240 ILE Chi-restraints excluded: chain R residue 305 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 0.0050 chunk 108 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN R 84 ASN R 318 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.170694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131408 restraints weight = 11469.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132191 restraints weight = 9219.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.133131 restraints weight = 8661.955| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8846 Z= 0.179 Angle : 0.563 11.942 11994 Z= 0.295 Chirality : 0.042 0.275 1382 Planarity : 0.004 0.031 1495 Dihedral : 4.677 55.637 1227 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.38 % Allowed : 18.85 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.84 (0.26), residues: 1111 helix: 1.97 (0.28), residues: 350 sheet: 0.26 (0.30), residues: 264 loop : -0.23 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP R 197 HIS 0.002 0.001 HIS R 107 PHE 0.011 0.001 PHE R 127 TYR 0.012 0.001 TYR B 59 ARG 0.006 0.000 ARG B 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2733.03 seconds wall clock time: 49 minutes 53.86 seconds (2993.86 seconds total)