Starting phenix.real_space_refine on Tue Apr 29 13:57:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjm_38401/04_2025/8xjm_38401.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjm_38401/04_2025/8xjm_38401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xjm_38401/04_2025/8xjm_38401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjm_38401/04_2025/8xjm_38401.map" model { file = "/net/cci-nas-00/data/ceres_data/8xjm_38401/04_2025/8xjm_38401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjm_38401/04_2025/8xjm_38401.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 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 62 5.16 5 C 5627 2.51 5 N 1513 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8849 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1821 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2171 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'7WT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.17, per 1000 atoms: 0.58 Number of scatterers: 8849 At special positions: 0 Unit cell: (108.07, 118.77, 110.21, 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 62 16.00 O 1647 8.00 N 1513 7.00 C 5627 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 186 " 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: 2.21 Conformation dependent library (CDL) restraints added in 1.0 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 16 sheets defined 40.4% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.599A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 131 through 135 removed outlier: 4.075A pdb=" N ARG A 135 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.218A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 183 through 204 removed outlier: 3.516A pdb=" N PHE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 245 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 27 through 31 Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.545A pdb=" N THR E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 60 removed outlier: 4.006A pdb=" N SER R 33 " --> pdb=" O SER R 29 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN R 56 " --> pdb=" O MET R 52 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG R 57 " --> pdb=" O LYS R 53 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN R 60 " --> pdb=" O GLN R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 94 Processing helix chain 'R' and resid 97 through 102 Processing helix chain 'R' and resid 105 through 139 Proline residue: R 122 - end of helix Processing helix chain 'R' and resid 139 through 146 Processing helix chain 'R' and resid 148 through 173 Proline residue: R 170 - end of helix Processing helix chain 'R' and resid 195 through 232 removed outlier: 3.972A pdb=" N LEU R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 243 through 276 removed outlier: 3.529A pdb=" N TRP R 262 " --> pdb=" O SER R 258 " (cutoff:3.500A) Proline residue: R 264 - end of helix Processing helix chain 'R' and resid 277 through 279 No H-bonds generated for 'chain 'R' and resid 277 through 279' Processing helix chain 'R' and resid 282 through 305 removed outlier: 3.671A pdb=" N ASN R 296 " --> pdb=" O MET R 292 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN R 297 " --> pdb=" O ALA R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 321 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 76 removed outlier: 6.190A pdb=" N LEU A 34 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N PHE A 84 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 36 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL A 86 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU A 38 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N ALA A 105 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 76 removed outlier: 6.190A pdb=" N LEU A 34 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N PHE A 84 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 36 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL A 86 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU A 38 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N ALA A 105 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.755A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.786A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.940A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.294A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.837A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.297A 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: 6.499A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.899A 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: 3.663A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.828A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 11 removed outlier: 4.337A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.112A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.032A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 178 through 179 501 hydrogen bonds defined for protein. 1398 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: 2.61 Time building geometry restraints manager: 2.61 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: 2873 1.34 - 1.46: 2157 1.46 - 1.58: 3901 1.58 - 1.69: 6 1.69 - 1.81: 90 Bond restraints: 9027 Sorted by residual: bond pdb=" C12 7WT R 601 " pdb=" C13 7WT R 601 " ideal model delta sigma weight residual 1.503 1.580 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C10 7WT R 601 " pdb=" C11 7WT R 601 " ideal model delta sigma weight residual 1.524 1.585 -0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" C04 7WT R 601 " pdb=" C08 7WT R 601 " ideal model delta sigma weight residual 1.524 1.582 -0.058 2.00e-02 2.50e+03 8.51e+00 bond pdb=" C09 7WT R 601 " pdb=" C10 7WT R 601 " ideal model delta sigma weight residual 1.528 1.584 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" C02 7WT R 601 " pdb=" C03 7WT R 601 " ideal model delta sigma weight residual 1.527 1.578 -0.051 2.00e-02 2.50e+03 6.49e+00 ... (remaining 9022 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 12034 1.24 - 2.47: 138 2.47 - 3.71: 38 3.71 - 4.95: 12 4.95 - 6.19: 6 Bond angle restraints: 12228 Sorted by residual: angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 126.17 -4.63 1.91e+00 2.74e-01 5.88e+00 angle pdb=" O TYR R 92 " pdb=" C TYR R 92 " pdb=" N ALA R 93 " ideal model delta sigma weight residual 122.12 124.45 -2.33 1.06e+00 8.90e-01 4.82e+00 angle pdb=" C06 7WT R 601 " pdb=" C05 7WT R 601 " pdb=" O07 7WT R 601 " ideal model delta sigma weight residual 113.84 107.65 6.19 3.00e+00 1.11e-01 4.25e+00 angle pdb=" CA TYR R 92 " pdb=" C TYR R 92 " pdb=" O TYR R 92 " ideal model delta sigma weight residual 120.55 118.50 2.05 1.06e+00 8.90e-01 3.73e+00 angle pdb=" C11 7WT R 601 " pdb=" C12 7WT R 601 " pdb=" C13 7WT R 601 " ideal model delta sigma weight residual 111.45 117.23 -5.78 3.00e+00 1.11e-01 3.71e+00 ... (remaining 12223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.63: 5281 27.63 - 55.25: 80 55.25 - 82.88: 6 82.88 - 110.50: 1 110.50 - 138.13: 1 Dihedral angle restraints: 5369 sinusoidal: 2074 harmonic: 3295 Sorted by residual: dihedral pdb=" C21 7WT R 601 " pdb=" C22 7WT R 601 " pdb=" C23 7WT R 601 " pdb=" C24 7WT R 601 " ideal model delta sinusoidal sigma weight residual 116.31 -105.56 -138.13 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 158.76 21.24 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1112 0.046 - 0.091: 220 0.091 - 0.137: 64 0.137 - 0.183: 0 0.183 - 0.228: 2 Chirality restraints: 1398 Sorted by residual: chirality pdb=" C03 7WT R 601 " pdb=" C02 7WT R 601 " pdb=" C04 7WT R 601 " pdb=" C20 7WT R 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.75 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C04 7WT R 601 " pdb=" C03 7WT R 601 " pdb=" C05 7WT R 601 " pdb=" C08 7WT R 601 " both_signs ideal model delta sigma weight residual False 2.63 2.81 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" C10 7WT R 601 " pdb=" C09 7WT R 601 " pdb=" C11 7WT R 601 " pdb=" O19 7WT R 601 " both_signs ideal model delta sigma weight residual False 2.40 2.53 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 1395 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO B 236 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 263 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO R 264 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO R 264 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 264 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " 0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO B 194 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " 0.014 5.00e-02 4.00e+02 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1939 2.78 - 3.31: 8319 3.31 - 3.84: 14777 3.84 - 4.37: 18449 4.37 - 4.90: 31698 Nonbonded interactions: 75182 Sorted by model distance: nonbonded pdb=" O VAL R 303 " pdb=" NH2 ARG R 308 " model vdw 2.256 3.120 nonbonded pdb=" O LYS C 20 " pdb=" ND2 ASN C 24 " model vdw 2.283 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.291 3.040 nonbonded pdb=" NE2 GLN A 52 " pdb=" O ALA A 218 " model vdw 2.294 3.120 nonbonded pdb=" O GLY R 40 " pdb=" ND2 ASN R 44 " model vdw 2.313 3.120 ... (remaining 75177 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 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: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.790 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:10.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9030 Z= 0.132 Angle : 0.417 6.186 12234 Z= 0.214 Chirality : 0.039 0.228 1398 Planarity : 0.003 0.038 1548 Dihedral : 10.253 138.130 3232 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.05 % Allowed : 3.16 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.55 (0.25), residues: 1122 helix: 1.91 (0.24), residues: 411 sheet: 0.80 (0.29), residues: 288 loop : 0.45 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 133 HIS 0.002 0.001 HIS B 91 PHE 0.009 0.001 PHE B 199 TYR 0.012 0.001 TYR E 190 ARG 0.002 0.000 ARG A 241 Details of bonding type rmsd hydrogen bonds : bond 0.22910 ( 484) hydrogen bonds : angle 7.43729 ( 1398) SS BOND : bond 0.00128 ( 3) SS BOND : angle 0.80147 ( 6) covalent geometry : bond 0.00276 ( 9027) covalent geometry : angle 0.41646 (12228) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 225 time to evaluate : 0.946 Fit side-chains REVERT: A 17 LYS cc_start: 0.8198 (mttt) cc_final: 0.7863 (mtmt) REVERT: A 83 MET cc_start: 0.8839 (ttp) cc_final: 0.8291 (ttp) REVERT: A 123 ASN cc_start: 0.8834 (m-40) cc_final: 0.8426 (m110) REVERT: A 136 THR cc_start: 0.8838 (p) cc_final: 0.8628 (m) REVERT: A 238 MET cc_start: 0.8575 (ttm) cc_final: 0.8321 (ttm) REVERT: A 242 GLU cc_start: 0.8819 (tt0) cc_final: 0.8563 (tt0) REVERT: B 59 TYR cc_start: 0.7829 (m-80) cc_final: 0.7327 (m-80) REVERT: B 101 MET cc_start: 0.9073 (mtp) cc_final: 0.8865 (mtp) REVERT: B 209 LYS cc_start: 0.8691 (mttm) cc_final: 0.8466 (mmtp) REVERT: B 219 ARG cc_start: 0.7613 (mtp85) cc_final: 0.7259 (mtp85) REVERT: B 259 GLN cc_start: 0.7893 (pt0) cc_final: 0.7506 (pt0) REVERT: R 28 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7735 (pp) REVERT: R 57 ARG cc_start: 0.8165 (ttm170) cc_final: 0.7908 (ttp-110) outliers start: 10 outliers final: 3 residues processed: 231 average time/residue: 1.3377 time to fit residues: 329.4175 Evaluate side-chains 158 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 154 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain R residue 28 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 52 GLN A 209 HIS ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 266 HIS B 293 ASN E 112 GLN E 171 ASN E 179 GLN R 180 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.151903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118797 restraints weight = 10228.826| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.81 r_work: 0.3023 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9030 Z= 0.201 Angle : 0.564 7.892 12234 Z= 0.307 Chirality : 0.044 0.152 1398 Planarity : 0.004 0.042 1548 Dihedral : 6.886 144.704 1272 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.22 % Allowed : 10.55 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.25), residues: 1122 helix: 2.70 (0.24), residues: 417 sheet: 0.91 (0.30), residues: 282 loop : 0.51 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS B 91 PHE 0.013 0.001 PHE B 199 TYR 0.019 0.002 TYR E 190 ARG 0.006 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.05100 ( 484) hydrogen bonds : angle 4.89930 ( 1398) SS BOND : bond 0.00483 ( 3) SS BOND : angle 0.74191 ( 6) covalent geometry : bond 0.00466 ( 9027) covalent geometry : angle 0.56362 (12228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.907 Fit side-chains REVERT: A 17 LYS cc_start: 0.7927 (mttt) cc_final: 0.7680 (mtpt) REVERT: A 70 PHE cc_start: 0.7730 (t80) cc_final: 0.7418 (t80) REVERT: A 83 MET cc_start: 0.8897 (ttp) cc_final: 0.8308 (ttp) REVERT: A 238 MET cc_start: 0.8534 (ttm) cc_final: 0.8307 (ttm) REVERT: B 59 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: B 197 ARG cc_start: 0.7061 (mmm160) cc_final: 0.6734 (mmm-85) REVERT: B 219 ARG cc_start: 0.8055 (mtp85) cc_final: 0.7723 (mtt-85) REVERT: B 259 GLN cc_start: 0.8134 (pt0) cc_final: 0.7812 (pt0) REVERT: B 266 HIS cc_start: 0.8194 (t-90) cc_final: 0.7992 (t70) REVERT: B 304 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7642 (ttm110) REVERT: B 314 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7462 (ttt180) REVERT: C 21 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8282 (tpp) REVERT: E 171 ASN cc_start: 0.9278 (m-40) cc_final: 0.8929 (m-40) REVERT: E 202 ARG cc_start: 0.7539 (ptp90) cc_final: 0.7189 (ptp90) REVERT: E 234 GLU cc_start: 0.8320 (pt0) cc_final: 0.8074 (pt0) REVERT: R 28 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7593 (pp) REVERT: R 101 PHE cc_start: 0.7185 (m-80) cc_final: 0.6380 (p90) REVERT: R 246 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8129 (tp30) outliers start: 40 outliers final: 17 residues processed: 177 average time/residue: 1.1888 time to fit residues: 224.1524 Evaluate side-chains 172 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 246 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 0.0170 chunk 72 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 268 ASN B 293 ASN E 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.155559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.123016 restraints weight = 10260.245| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.80 r_work: 0.3149 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9030 Z= 0.113 Angle : 0.477 6.364 12234 Z= 0.258 Chirality : 0.041 0.140 1398 Planarity : 0.003 0.045 1548 Dihedral : 6.974 149.906 1270 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 4.01 % Allowed : 12.97 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.25), residues: 1122 helix: 3.02 (0.24), residues: 419 sheet: 0.76 (0.30), residues: 266 loop : 0.39 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.011 0.001 PHE B 199 TYR 0.018 0.001 TYR E 190 ARG 0.004 0.000 ARG R 308 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 484) hydrogen bonds : angle 4.41723 ( 1398) SS BOND : bond 0.00164 ( 3) SS BOND : angle 0.46912 ( 6) covalent geometry : bond 0.00245 ( 9027) covalent geometry : angle 0.47702 (12228) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7827 (mttt) cc_final: 0.7595 (mtpt) REVERT: A 70 PHE cc_start: 0.7654 (t80) cc_final: 0.7339 (t80) REVERT: A 73 LYS cc_start: 0.8457 (mttt) cc_final: 0.8017 (mtpm) REVERT: A 83 MET cc_start: 0.8732 (ttp) cc_final: 0.8278 (ttp) REVERT: A 222 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: B 57 LYS cc_start: 0.8280 (mtmm) cc_final: 0.8074 (mtmp) REVERT: B 59 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: B 197 ARG cc_start: 0.7135 (mmm160) cc_final: 0.6909 (mmm160) REVERT: B 219 ARG cc_start: 0.8031 (mtp85) cc_final: 0.7658 (mtp85) REVERT: B 234 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.8823 (m-80) REVERT: B 259 GLN cc_start: 0.8141 (pt0) cc_final: 0.7841 (pt0) REVERT: B 304 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7582 (ttm110) REVERT: B 314 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7457 (ttt180) REVERT: C 21 MET cc_start: 0.8499 (mmt) cc_final: 0.8224 (tpp) REVERT: C 46 LYS cc_start: 0.8810 (pptt) cc_final: 0.8434 (mmmt) REVERT: E 171 ASN cc_start: 0.9189 (m-40) cc_final: 0.8807 (m-40) REVERT: E 234 GLU cc_start: 0.8277 (pt0) cc_final: 0.8032 (pt0) REVERT: R 28 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7554 (pp) REVERT: R 101 PHE cc_start: 0.7235 (m-80) cc_final: 0.6374 (OUTLIER) REVERT: R 246 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7978 (tp30) outliers start: 38 outliers final: 12 residues processed: 178 average time/residue: 1.2623 time to fit residues: 239.0351 Evaluate side-chains 162 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 246 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 13 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 155 ASN B 220 GLN B 266 HIS B 268 ASN B 293 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.153865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.121055 restraints weight = 10269.185| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.81 r_work: 0.3065 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9030 Z= 0.136 Angle : 0.494 6.728 12234 Z= 0.266 Chirality : 0.041 0.141 1398 Planarity : 0.003 0.044 1548 Dihedral : 6.879 150.956 1269 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.32 % Allowed : 13.61 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.25), residues: 1122 helix: 3.02 (0.24), residues: 420 sheet: 0.65 (0.31), residues: 260 loop : 0.38 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.010 0.001 PHE B 199 TYR 0.016 0.001 TYR E 190 ARG 0.004 0.000 ARG R 308 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 484) hydrogen bonds : angle 4.39044 ( 1398) SS BOND : bond 0.00168 ( 3) SS BOND : angle 0.57967 ( 6) covalent geometry : bond 0.00310 ( 9027) covalent geometry : angle 0.49421 (12228) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7772 (mttt) cc_final: 0.7527 (mtpt) REVERT: A 25 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: A 70 PHE cc_start: 0.7616 (t80) cc_final: 0.7265 (t80) REVERT: A 73 LYS cc_start: 0.8458 (mttt) cc_final: 0.8012 (mtpm) REVERT: A 83 MET cc_start: 0.8827 (ttp) cc_final: 0.8357 (ttp) REVERT: A 166 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8087 (mm-30) REVERT: B 35 ASN cc_start: 0.7950 (m110) cc_final: 0.7685 (m110) REVERT: B 59 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: B 197 ARG cc_start: 0.7012 (mmm160) cc_final: 0.6787 (mmm-85) REVERT: B 209 LYS cc_start: 0.8439 (mttm) cc_final: 0.8217 (mmtp) REVERT: B 219 ARG cc_start: 0.8089 (mtp85) cc_final: 0.7676 (mtp85) REVERT: B 234 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.8805 (m-80) REVERT: B 259 GLN cc_start: 0.8086 (pt0) cc_final: 0.7709 (pt0) REVERT: B 304 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7497 (ttm110) REVERT: B 314 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7431 (ttt180) REVERT: C 21 MET cc_start: 0.8497 (mmt) cc_final: 0.8283 (tpp) REVERT: E 45 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7668 (tt0) REVERT: E 171 ASN cc_start: 0.9127 (m-40) cc_final: 0.8741 (m-40) REVERT: E 234 GLU cc_start: 0.8266 (pt0) cc_final: 0.8015 (pt0) REVERT: R 28 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7590 (pp) REVERT: R 101 PHE cc_start: 0.7197 (m-80) cc_final: 0.6347 (p90) REVERT: R 246 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8052 (tp30) outliers start: 41 outliers final: 13 residues processed: 172 average time/residue: 1.3120 time to fit residues: 240.1100 Evaluate side-chains 165 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 246 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 66 optimal weight: 0.0000 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 175 GLN B 293 ASN E 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.156682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124533 restraints weight = 10191.320| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.77 r_work: 0.3237 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9030 Z= 0.098 Angle : 0.467 7.482 12234 Z= 0.249 Chirality : 0.040 0.150 1398 Planarity : 0.003 0.044 1548 Dihedral : 6.828 152.559 1269 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.11 % Allowed : 14.35 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.25), residues: 1122 helix: 3.16 (0.24), residues: 420 sheet: 0.61 (0.31), residues: 260 loop : 0.40 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 PHE 0.009 0.001 PHE B 199 TYR 0.017 0.001 TYR E 190 ARG 0.004 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 484) hydrogen bonds : angle 4.21370 ( 1398) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.45499 ( 6) covalent geometry : bond 0.00212 ( 9027) covalent geometry : angle 0.46718 (12228) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7832 (mttt) cc_final: 0.7592 (mtpt) REVERT: A 25 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: A 70 PHE cc_start: 0.7573 (t80) cc_final: 0.7282 (t80) REVERT: A 73 LYS cc_start: 0.8453 (mttt) cc_final: 0.8056 (mtpm) REVERT: A 83 MET cc_start: 0.8663 (ttp) cc_final: 0.8257 (ttp) REVERT: A 166 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8199 (mm-30) REVERT: A 222 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7637 (mm-30) REVERT: B 35 ASN cc_start: 0.8016 (m110) cc_final: 0.7757 (m110) REVERT: B 57 LYS cc_start: 0.8258 (mtmm) cc_final: 0.8011 (ptpp) REVERT: B 59 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7604 (m-80) REVERT: B 197 ARG cc_start: 0.7112 (mmm160) cc_final: 0.6691 (mmm-85) REVERT: B 209 LYS cc_start: 0.8391 (mttm) cc_final: 0.8177 (mmtp) REVERT: B 219 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7639 (mtp85) REVERT: B 234 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8732 (m-80) REVERT: B 259 GLN cc_start: 0.7813 (pt0) cc_final: 0.7458 (pt0) REVERT: B 270 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8202 (pp) REVERT: B 304 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7448 (ttm110) REVERT: B 314 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7391 (ttt180) REVERT: C 21 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8325 (tpp) REVERT: C 46 LYS cc_start: 0.8201 (mmpt) cc_final: 0.7972 (mmmt) REVERT: E 171 ASN cc_start: 0.8960 (m-40) cc_final: 0.8643 (m-40) REVERT: E 234 GLU cc_start: 0.8281 (pt0) cc_final: 0.8047 (pt0) REVERT: R 28 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7634 (pp) REVERT: R 101 PHE cc_start: 0.7055 (m-80) cc_final: 0.6399 (OUTLIER) REVERT: R 246 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7840 (tt0) outliers start: 39 outliers final: 15 residues processed: 168 average time/residue: 1.2571 time to fit residues: 224.6643 Evaluate side-chains 170 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 246 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 91 HIS B 175 GLN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.150186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.117148 restraints weight = 10246.275| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.78 r_work: 0.3048 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9030 Z= 0.263 Angle : 0.600 8.416 12234 Z= 0.318 Chirality : 0.046 0.221 1398 Planarity : 0.004 0.044 1548 Dihedral : 6.965 149.923 1269 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.32 % Allowed : 14.87 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.91 (0.25), residues: 1122 helix: 2.84 (0.24), residues: 413 sheet: 0.55 (0.30), residues: 280 loop : 0.27 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 96 HIS 0.005 0.001 HIS E 34 PHE 0.014 0.002 PHE B 151 TYR 0.015 0.002 TYR C 40 ARG 0.006 0.001 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.04602 ( 484) hydrogen bonds : angle 4.65387 ( 1398) SS BOND : bond 0.00154 ( 3) SS BOND : angle 0.82265 ( 6) covalent geometry : bond 0.00626 ( 9027) covalent geometry : angle 0.59959 (12228) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8003 (mttt) cc_final: 0.7630 (mtmt) REVERT: A 25 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7617 (mt-10) REVERT: A 70 PHE cc_start: 0.7681 (t80) cc_final: 0.7349 (t80) REVERT: A 83 MET cc_start: 0.8881 (ttp) cc_final: 0.8440 (ttp) REVERT: A 148 LEU cc_start: 0.8479 (mt) cc_final: 0.8232 (mp) REVERT: A 222 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7654 (mm-30) REVERT: B 35 ASN cc_start: 0.8048 (m110) cc_final: 0.7776 (m110) REVERT: B 59 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: B 175 GLN cc_start: 0.8327 (pt0) cc_final: 0.8066 (pt0) REVERT: B 219 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7722 (mtp85) REVERT: B 234 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8883 (m-80) REVERT: B 259 GLN cc_start: 0.8127 (pt0) cc_final: 0.7767 (pt0) REVERT: B 304 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7553 (ttm110) REVERT: B 314 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7475 (ttt180) REVERT: C 21 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8261 (tpp) REVERT: E 234 GLU cc_start: 0.8298 (pt0) cc_final: 0.8087 (pt0) REVERT: R 31 PHE cc_start: 0.7849 (m-80) cc_final: 0.7645 (m-80) REVERT: R 101 PHE cc_start: 0.7278 (m-80) cc_final: 0.6186 (p90) outliers start: 41 outliers final: 19 residues processed: 158 average time/residue: 1.2969 time to fit residues: 218.1730 Evaluate side-chains 146 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 52 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 48 optimal weight: 0.0370 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.154696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.121953 restraints weight = 10283.559| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.84 r_work: 0.3058 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9030 Z= 0.114 Angle : 0.492 7.846 12234 Z= 0.262 Chirality : 0.041 0.176 1398 Planarity : 0.003 0.045 1548 Dihedral : 6.769 150.007 1269 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.69 % Allowed : 15.61 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.25), residues: 1122 helix: 3.13 (0.24), residues: 413 sheet: 0.55 (0.30), residues: 268 loop : 0.32 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 295 HIS 0.004 0.001 HIS B 266 PHE 0.011 0.001 PHE B 199 TYR 0.017 0.001 TYR E 190 ARG 0.006 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 484) hydrogen bonds : angle 4.31997 ( 1398) SS BOND : bond 0.00189 ( 3) SS BOND : angle 0.57452 ( 6) covalent geometry : bond 0.00258 ( 9027) covalent geometry : angle 0.49189 (12228) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7762 (mttt) cc_final: 0.7528 (mtpt) REVERT: A 25 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7595 (mt-10) REVERT: A 70 PHE cc_start: 0.7611 (t80) cc_final: 0.7253 (t80) REVERT: A 73 LYS cc_start: 0.8522 (mttt) cc_final: 0.8017 (mtpm) REVERT: A 83 MET cc_start: 0.8713 (ttp) cc_final: 0.8277 (ttp) REVERT: A 148 LEU cc_start: 0.8330 (mt) cc_final: 0.7977 (mp) REVERT: A 166 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8205 (mm-30) REVERT: A 222 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7642 (mm-30) REVERT: B 35 ASN cc_start: 0.7993 (m110) cc_final: 0.7703 (m110) REVERT: B 57 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7958 (ptpp) REVERT: B 59 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: B 219 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7670 (mtp85) REVERT: B 234 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8735 (m-80) REVERT: B 259 GLN cc_start: 0.7857 (pt0) cc_final: 0.7441 (pt0) REVERT: B 304 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7449 (ttm110) REVERT: B 314 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7389 (ttt180) REVERT: C 21 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8283 (tpp) REVERT: E 171 ASN cc_start: 0.9095 (m-40) cc_final: 0.8748 (m-40) REVERT: E 234 GLU cc_start: 0.8305 (pt0) cc_final: 0.8065 (pt0) REVERT: R 28 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7754 (pp) REVERT: R 101 PHE cc_start: 0.7227 (m-80) cc_final: 0.6288 (p90) REVERT: R 246 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7794 (tt0) outliers start: 35 outliers final: 14 residues processed: 163 average time/residue: 1.2894 time to fit residues: 223.5242 Evaluate side-chains 161 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 246 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.155832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123301 restraints weight = 10341.922| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.82 r_work: 0.3093 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9030 Z= 0.107 Angle : 0.476 7.148 12234 Z= 0.254 Chirality : 0.041 0.176 1398 Planarity : 0.003 0.044 1548 Dihedral : 6.716 152.557 1269 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.06 % Allowed : 16.14 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.25), residues: 1122 helix: 3.19 (0.24), residues: 414 sheet: 0.58 (0.31), residues: 265 loop : 0.36 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS B 266 PHE 0.012 0.001 PHE R 232 TYR 0.016 0.001 TYR E 190 ARG 0.004 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 484) hydrogen bonds : angle 4.22006 ( 1398) SS BOND : bond 0.00128 ( 3) SS BOND : angle 0.65503 ( 6) covalent geometry : bond 0.00240 ( 9027) covalent geometry : angle 0.47609 (12228) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7786 (mttt) cc_final: 0.7538 (mtpt) REVERT: A 25 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7723 (mt-10) REVERT: A 70 PHE cc_start: 0.7596 (t80) cc_final: 0.7278 (t80) REVERT: A 73 LYS cc_start: 0.8487 (mttt) cc_final: 0.8049 (mtpm) REVERT: A 83 MET cc_start: 0.8698 (ttp) cc_final: 0.8281 (ttp) REVERT: A 148 LEU cc_start: 0.8377 (mt) cc_final: 0.8025 (mp) REVERT: B 35 ASN cc_start: 0.8042 (m110) cc_final: 0.7740 (m110) REVERT: B 44 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7542 (mm-40) REVERT: B 59 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: B 197 ARG cc_start: 0.7100 (mmm160) cc_final: 0.6813 (mmm-85) REVERT: B 219 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7689 (mtp85) REVERT: B 234 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8660 (m-80) REVERT: B 259 GLN cc_start: 0.7859 (pt0) cc_final: 0.7467 (pt0) REVERT: B 304 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7379 (ttm110) REVERT: B 314 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7422 (ttt180) REVERT: C 21 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8316 (tpp) REVERT: E 171 ASN cc_start: 0.8984 (m-40) cc_final: 0.8666 (m-40) REVERT: E 183 GLN cc_start: 0.8047 (mp10) cc_final: 0.7659 (mm-40) REVERT: E 234 GLU cc_start: 0.8290 (pt0) cc_final: 0.8075 (pt0) REVERT: R 101 PHE cc_start: 0.7326 (m-80) cc_final: 0.6269 (p90) REVERT: R 246 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: R 290 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7746 (tp) outliers start: 29 outliers final: 14 residues processed: 159 average time/residue: 1.5712 time to fit residues: 266.5702 Evaluate side-chains 165 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.155673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.123191 restraints weight = 10356.032| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.81 r_work: 0.3185 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9030 Z= 0.118 Angle : 0.487 7.033 12234 Z= 0.259 Chirality : 0.041 0.201 1398 Planarity : 0.003 0.044 1548 Dihedral : 6.684 151.554 1269 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.27 % Allowed : 16.67 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.25), residues: 1122 helix: 3.21 (0.24), residues: 413 sheet: 0.58 (0.31), residues: 265 loop : 0.32 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 266 PHE 0.010 0.001 PHE B 151 TYR 0.015 0.001 TYR E 190 ARG 0.004 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 484) hydrogen bonds : angle 4.21383 ( 1398) SS BOND : bond 0.00104 ( 3) SS BOND : angle 0.73549 ( 6) covalent geometry : bond 0.00270 ( 9027) covalent geometry : angle 0.48731 (12228) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7808 (mttt) cc_final: 0.7565 (mtpt) REVERT: A 70 PHE cc_start: 0.7586 (t80) cc_final: 0.7272 (t80) REVERT: A 73 LYS cc_start: 0.8481 (mttt) cc_final: 0.8054 (mtpm) REVERT: A 83 MET cc_start: 0.8689 (ttp) cc_final: 0.8288 (ttp) REVERT: A 148 LEU cc_start: 0.8396 (mt) cc_final: 0.8056 (mp) REVERT: B 35 ASN cc_start: 0.8057 (m110) cc_final: 0.7739 (m110) REVERT: B 44 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7611 (mm-40) REVERT: B 59 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.7826 (m-80) REVERT: B 197 ARG cc_start: 0.7139 (mmm160) cc_final: 0.6790 (mmm-85) REVERT: B 219 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7706 (mtp85) REVERT: B 234 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8732 (m-80) REVERT: B 259 GLN cc_start: 0.7888 (pt0) cc_final: 0.7512 (pt0) REVERT: B 270 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8255 (pp) REVERT: B 314 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7450 (ttt180) REVERT: C 21 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8312 (tpp) REVERT: C 46 LYS cc_start: 0.8298 (mmpt) cc_final: 0.8085 (mmmt) REVERT: E 171 ASN cc_start: 0.8968 (m-40) cc_final: 0.8660 (m-40) REVERT: E 234 GLU cc_start: 0.8324 (pt0) cc_final: 0.8102 (pt0) REVERT: R 28 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7685 (pp) REVERT: R 101 PHE cc_start: 0.7169 (m-80) cc_final: 0.6171 (p90) REVERT: R 246 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: R 290 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7773 (tp) outliers start: 31 outliers final: 13 residues processed: 161 average time/residue: 1.2923 time to fit residues: 221.7136 Evaluate side-chains 156 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 290 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.151564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.118444 restraints weight = 10308.693| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.80 r_work: 0.2973 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9030 Z= 0.218 Angle : 0.577 7.282 12234 Z= 0.305 Chirality : 0.044 0.228 1398 Planarity : 0.004 0.043 1548 Dihedral : 6.820 151.119 1269 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.74 % Allowed : 17.62 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.94 (0.25), residues: 1122 helix: 2.94 (0.24), residues: 413 sheet: 0.55 (0.30), residues: 273 loop : 0.21 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 96 HIS 0.005 0.001 HIS E 34 PHE 0.014 0.002 PHE B 151 TYR 0.013 0.002 TYR E 58 ARG 0.006 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 484) hydrogen bonds : angle 4.51548 ( 1398) SS BOND : bond 0.00208 ( 3) SS BOND : angle 0.99727 ( 6) covalent geometry : bond 0.00518 ( 9027) covalent geometry : angle 0.57630 (12228) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7842 (mttt) cc_final: 0.7487 (mtmt) REVERT: A 70 PHE cc_start: 0.7631 (t80) cc_final: 0.7313 (t80) REVERT: A 83 MET cc_start: 0.8795 (ttp) cc_final: 0.8280 (ttp) REVERT: A 148 LEU cc_start: 0.8317 (mt) cc_final: 0.7976 (mp) REVERT: A 208 ARG cc_start: 0.7470 (mtp180) cc_final: 0.6473 (mmp-170) REVERT: B 35 ASN cc_start: 0.7986 (m110) cc_final: 0.7644 (m110) REVERT: B 59 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7951 (m-80) REVERT: B 197 ARG cc_start: 0.7212 (mmm160) cc_final: 0.6882 (mmm-85) REVERT: B 219 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7719 (mtp85) REVERT: B 234 PHE cc_start: 0.9318 (OUTLIER) cc_final: 0.8849 (m-80) REVERT: B 259 GLN cc_start: 0.8026 (pt0) cc_final: 0.7626 (pt0) REVERT: B 266 HIS cc_start: 0.8600 (t70) cc_final: 0.8365 (t70) REVERT: B 314 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7401 (ttt180) REVERT: C 46 LYS cc_start: 0.8328 (mmpt) cc_final: 0.8056 (mmmt) REVERT: R 28 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7749 (pp) REVERT: R 101 PHE cc_start: 0.7191 (m-80) cc_final: 0.6095 (p90) REVERT: R 246 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8100 (tp30) outliers start: 26 outliers final: 16 residues processed: 148 average time/residue: 1.6746 time to fit residues: 264.3301 Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 217 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 106 optimal weight: 0.0000 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.155083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.122589 restraints weight = 10308.315| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.79 r_work: 0.3127 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9030 Z= 0.114 Angle : 0.501 7.180 12234 Z= 0.265 Chirality : 0.041 0.197 1398 Planarity : 0.003 0.045 1548 Dihedral : 6.714 150.950 1269 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.53 % Allowed : 18.46 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.26), residues: 1122 helix: 3.11 (0.24), residues: 414 sheet: 0.49 (0.30), residues: 273 loop : 0.29 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS B 266 PHE 0.010 0.001 PHE B 151 TYR 0.016 0.001 TYR E 190 ARG 0.006 0.000 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 484) hydrogen bonds : angle 4.27490 ( 1398) SS BOND : bond 0.00129 ( 3) SS BOND : angle 0.83070 ( 6) covalent geometry : bond 0.00261 ( 9027) covalent geometry : angle 0.50037 (12228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8464.48 seconds wall clock time: 148 minutes 32.59 seconds (8912.59 seconds total)