Starting phenix.real_space_refine on Wed Sep 17 12:40:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjm_38401/09_2025/8xjm_38401.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjm_38401/09_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_38401/09_2025/8xjm_38401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjm_38401/09_2025/8xjm_38401.map" model { file = "/net/cci-nas-00/data/ceres_data/8xjm_38401/09_2025/8xjm_38401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjm_38401/09_2025/8xjm_38401.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 2, 'HIS: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: 2.30, per 1000 atoms: 0.26 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: 0.86 Conformation dependent library (CDL) restraints added in 347.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.29 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: 1.48 Time building geometry restraints manager: 1.11 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.040 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:6.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.002 0.000 ARG A 241 TYR 0.012 0.001 TYR E 190 PHE 0.009 0.001 PHE B 199 TRP 0.011 0.001 TRP A 133 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9027) covalent geometry : angle 0.41646 (12228) SS BOND : bond 0.00128 ( 3) SS BOND : angle 0.80147 ( 6) hydrogen bonds : bond 0.22910 ( 484) hydrogen bonds : angle 7.43729 ( 1398) *********************** 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 : 0.339 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: 0.8292 (ttp) REVERT: A 123 ASN cc_start: 0.8834 (m-40) cc_final: 0.8425 (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: 0.5953 time to fit residues: 146.3778 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 : 0.391 ------------------------------------------------------------------------------- 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 108 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 16 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.117930 restraints weight = 10229.384| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.79 r_work: 0.3021 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9030 Z= 0.252 Angle : 0.606 9.369 12234 Z= 0.328 Chirality : 0.045 0.151 1398 Planarity : 0.004 0.043 1548 Dihedral : 6.971 144.097 1272 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.43 % Allowed : 10.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.25), residues: 1122 helix: 2.56 (0.24), residues: 417 sheet: 0.79 (0.30), residues: 286 loop : 0.51 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 308 TYR 0.018 0.002 TYR E 190 PHE 0.014 0.002 PHE E 26 TRP 0.020 0.002 TRP B 169 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00591 ( 9027) covalent geometry : angle 0.60562 (12228) SS BOND : bond 0.00166 ( 3) SS BOND : angle 0.90277 ( 6) hydrogen bonds : bond 0.05231 ( 484) hydrogen bonds : angle 4.97761 ( 1398) *********************** 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 190 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.354 Fit side-chains REVERT: A 17 LYS cc_start: 0.8000 (mttt) cc_final: 0.7699 (mtpt) REVERT: A 70 PHE cc_start: 0.7776 (t80) cc_final: 0.7488 (t80) REVERT: A 83 MET cc_start: 0.8942 (ttp) cc_final: 0.8445 (ttp) REVERT: A 238 MET cc_start: 0.8628 (ttm) cc_final: 0.8377 (ttm) REVERT: B 59 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.7841 (m-80) REVERT: B 197 ARG cc_start: 0.7131 (mmm160) cc_final: 0.6836 (mmm-85) REVERT: B 219 ARG cc_start: 0.8068 (mtp85) cc_final: 0.7725 (mtp85) REVERT: B 259 GLN cc_start: 0.8200 (pt0) cc_final: 0.7882 (pt0) REVERT: B 266 HIS cc_start: 0.8245 (t-90) cc_final: 0.8036 (t70) REVERT: B 304 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7632 (ttm110) REVERT: B 314 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7502 (ttt180) REVERT: C 21 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8286 (tpp) REVERT: E 171 ASN cc_start: 0.9292 (m-40) cc_final: 0.8996 (m-40) REVERT: E 202 ARG cc_start: 0.7652 (ptp90) cc_final: 0.7280 (ptp90) REVERT: E 234 GLU cc_start: 0.8324 (pt0) cc_final: 0.8073 (pt0) REVERT: R 28 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7692 (pp) REVERT: R 101 PHE cc_start: 0.7386 (m-80) cc_final: 0.6383 (p90) REVERT: R 246 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8138 (tp30) outliers start: 42 outliers final: 19 residues processed: 175 average time/residue: 0.6303 time to fit residues: 117.0716 Evaluate side-chains 167 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 72 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 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 48 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 16 ASN B 156 GLN B 220 GLN B 268 ASN B 293 ASN E 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.153724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120907 restraints weight = 10200.096| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.79 r_work: 0.3014 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9030 Z= 0.127 Angle : 0.492 6.579 12234 Z= 0.266 Chirality : 0.041 0.141 1398 Planarity : 0.003 0.045 1548 Dihedral : 7.000 148.936 1270 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.11 % Allowed : 13.19 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.25), residues: 1122 helix: 2.90 (0.24), residues: 419 sheet: 0.94 (0.30), residues: 273 loop : 0.36 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 308 TYR 0.018 0.001 TYR E 190 PHE 0.011 0.001 PHE B 199 TRP 0.016 0.002 TRP B 169 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9027) covalent geometry : angle 0.49188 (12228) SS BOND : bond 0.00218 ( 3) SS BOND : angle 0.49573 ( 6) hydrogen bonds : bond 0.04131 ( 484) hydrogen bonds : angle 4.50847 ( 1398) *********************** 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 191 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.351 Fit side-chains REVERT: A 17 LYS cc_start: 0.7781 (mttt) cc_final: 0.7542 (mtpt) REVERT: A 70 PHE cc_start: 0.7642 (t80) cc_final: 0.7272 (t80) REVERT: A 73 LYS cc_start: 0.8554 (mttt) cc_final: 0.8036 (mtpm) REVERT: A 83 MET cc_start: 0.8782 (ttp) cc_final: 0.8233 (ttp) REVERT: A 222 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7610 (mm-30) REVERT: A 225 ARG cc_start: 0.8320 (ttm-80) cc_final: 0.8065 (tpp-160) REVERT: B 59 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.7739 (m-80) REVERT: B 197 ARG cc_start: 0.7146 (mmm160) cc_final: 0.6712 (mmm-85) REVERT: B 219 ARG cc_start: 0.8023 (mtp85) cc_final: 0.7596 (mtp85) REVERT: B 234 PHE cc_start: 0.9325 (OUTLIER) cc_final: 0.8874 (m-80) REVERT: B 259 GLN cc_start: 0.8162 (pt0) cc_final: 0.7812 (pt0) REVERT: B 266 HIS cc_start: 0.8237 (t-90) cc_final: 0.8032 (t70) REVERT: B 304 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7538 (ttm110) REVERT: B 314 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7422 (ttt180) REVERT: C 21 MET cc_start: 0.8485 (mmt) cc_final: 0.8215 (tpp) REVERT: E 17 ARG cc_start: 0.7487 (tpt170) cc_final: 0.7212 (tpt170) REVERT: E 171 ASN cc_start: 0.9241 (m-40) cc_final: 0.8847 (m-40) REVERT: E 202 ARG cc_start: 0.7509 (ptp90) cc_final: 0.7145 (ptp90) REVERT: E 234 GLU cc_start: 0.8294 (pt0) cc_final: 0.8047 (pt0) REVERT: R 28 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7473 (pp) REVERT: R 101 PHE cc_start: 0.7169 (m-80) cc_final: 0.6369 (OUTLIER) REVERT: R 246 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7987 (tp30) outliers start: 39 outliers final: 15 residues processed: 176 average time/residue: 0.6767 time to fit residues: 126.0223 Evaluate side-chains 165 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 136 THR 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 B residue 336 LEU 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 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 36 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 108 optimal weight: 0.0070 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 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 = 0.3816 r_free = 0.3816 target = 0.155831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123347 restraints weight = 10404.298| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.81 r_work: 0.3094 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9030 Z= 0.104 Angle : 0.466 6.977 12234 Z= 0.251 Chirality : 0.040 0.137 1398 Planarity : 0.003 0.044 1548 Dihedral : 6.852 151.418 1270 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.59 % Allowed : 14.77 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.25), residues: 1122 helix: 3.12 (0.24), residues: 420 sheet: 0.62 (0.30), residues: 268 loop : 0.40 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 308 TYR 0.017 0.001 TYR E 190 PHE 0.010 0.001 PHE B 199 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 9027) covalent geometry : angle 0.46577 (12228) SS BOND : bond 0.00147 ( 3) SS BOND : angle 0.50889 ( 6) hydrogen bonds : bond 0.03604 ( 484) hydrogen bonds : angle 4.27848 ( 1398) *********************** 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 184 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7770 (mttt) cc_final: 0.7519 (mtpt) REVERT: A 25 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: A 70 PHE cc_start: 0.7619 (t80) cc_final: 0.7301 (t80) REVERT: A 73 LYS cc_start: 0.8440 (mttt) cc_final: 0.8009 (mtpm) REVERT: A 83 MET cc_start: 0.8717 (ttp) cc_final: 0.8279 (ttp) REVERT: A 151 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: A 169 ARG cc_start: 0.7736 (mtm-85) cc_final: 0.7273 (mtm110) REVERT: B 35 ASN cc_start: 0.7961 (m110) cc_final: 0.7675 (m110) REVERT: B 57 LYS cc_start: 0.8260 (mtmm) cc_final: 0.8052 (mtmp) REVERT: B 59 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7663 (m-80) REVERT: B 197 ARG cc_start: 0.6995 (mmm160) cc_final: 0.6587 (mmm-85) REVERT: B 209 LYS cc_start: 0.8392 (mttm) cc_final: 0.8160 (mmtp) REVERT: B 219 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7678 (mtp85) REVERT: B 234 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8814 (m-80) REVERT: B 259 GLN cc_start: 0.7988 (pt0) cc_final: 0.7653 (pt0) REVERT: B 266 HIS cc_start: 0.8275 (t-90) cc_final: 0.7955 (t70) REVERT: B 270 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8161 (pp) REVERT: B 304 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7437 (ttm110) REVERT: B 314 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7410 (ttt180) REVERT: C 21 MET cc_start: 0.8554 (mmt) cc_final: 0.8345 (tpp) REVERT: C 46 LYS cc_start: 0.8847 (pptt) cc_final: 0.8496 (mmmt) REVERT: E 171 ASN cc_start: 0.9103 (m-40) cc_final: 0.8722 (m-40) REVERT: E 234 GLU cc_start: 0.8298 (pt0) cc_final: 0.8053 (pt0) REVERT: R 28 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7560 (pp) REVERT: R 101 PHE cc_start: 0.7155 (m-80) cc_final: 0.6448 (p90) REVERT: R 246 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7790 (tt0) outliers start: 34 outliers final: 12 residues processed: 174 average time/residue: 0.6533 time to fit residues: 120.5386 Evaluate side-chains 161 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 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 33 ILE 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 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 245 LEU 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 44 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 0.0470 chunk 102 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 268 ASN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.153677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120989 restraints weight = 10290.037| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.80 r_work: 0.3123 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9030 Z= 0.146 Angle : 0.504 7.909 12234 Z= 0.269 Chirality : 0.042 0.174 1398 Planarity : 0.003 0.044 1548 Dihedral : 6.886 153.299 1269 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.11 % Allowed : 14.77 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.25), residues: 1122 helix: 3.08 (0.24), residues: 419 sheet: 0.61 (0.31), residues: 261 loop : 0.32 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 308 TYR 0.015 0.001 TYR E 190 PHE 0.010 0.001 PHE B 199 TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9027) covalent geometry : angle 0.50422 (12228) SS BOND : bond 0.00173 ( 3) SS BOND : angle 0.59161 ( 6) hydrogen bonds : bond 0.03869 ( 484) hydrogen bonds : angle 4.35549 ( 1398) *********************** 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 185 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7856 (mttt) cc_final: 0.7619 (mtpt) REVERT: A 25 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7610 (mt-10) REVERT: A 70 PHE cc_start: 0.7652 (t80) cc_final: 0.7348 (t80) REVERT: A 73 LYS cc_start: 0.8479 (mttt) cc_final: 0.8039 (mtpm) REVERT: A 83 MET cc_start: 0.8783 (ttp) cc_final: 0.8340 (ttp) REVERT: A 148 LEU cc_start: 0.8490 (mt) cc_final: 0.8147 (mp) REVERT: A 222 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: B 35 ASN cc_start: 0.8011 (m110) cc_final: 0.7684 (m110) REVERT: B 59 TYR cc_start: 0.8237 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: B 197 ARG cc_start: 0.7208 (mmm160) cc_final: 0.6806 (mmm-85) REVERT: B 209 LYS cc_start: 0.8466 (mttm) cc_final: 0.8256 (mmtp) REVERT: B 219 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7665 (mtp85) REVERT: B 234 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.8812 (m-80) REVERT: B 259 GLN cc_start: 0.8121 (pt0) cc_final: 0.7774 (pt0) REVERT: B 304 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7475 (ttm110) REVERT: B 314 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7456 (ttt180) REVERT: C 21 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8316 (tpp) REVERT: E 45 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: E 171 ASN cc_start: 0.9105 (m-40) cc_final: 0.8780 (m-40) REVERT: E 234 GLU cc_start: 0.8299 (pt0) cc_final: 0.8057 (pt0) REVERT: R 28 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7574 (pp) REVERT: R 101 PHE cc_start: 0.7131 (m-80) cc_final: 0.6348 (p90) outliers start: 39 outliers final: 15 residues processed: 167 average time/residue: 0.6436 time to fit residues: 114.3052 Evaluate side-chains 165 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 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 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 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 E residue 204 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 30 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 0.0970 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 175 GLN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.155649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123297 restraints weight = 10286.674| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.78 r_work: 0.3168 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9030 Z= 0.107 Angle : 0.470 7.338 12234 Z= 0.251 Chirality : 0.040 0.162 1398 Planarity : 0.003 0.044 1548 Dihedral : 6.823 153.513 1269 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.11 % Allowed : 14.66 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.25), residues: 1122 helix: 3.24 (0.24), residues: 414 sheet: 0.61 (0.31), residues: 260 loop : 0.33 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 160 TYR 0.016 0.001 TYR E 190 PHE 0.010 0.001 PHE B 199 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9027) covalent geometry : angle 0.47037 (12228) SS BOND : bond 0.00190 ( 3) SS BOND : angle 0.53107 ( 6) hydrogen bonds : bond 0.03491 ( 484) hydrogen bonds : angle 4.22288 ( 1398) *********************** 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 188 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7760 (mttt) cc_final: 0.7532 (mtpt) REVERT: A 70 PHE cc_start: 0.7572 (t80) cc_final: 0.7283 (t80) REVERT: A 73 LYS cc_start: 0.8439 (mttt) cc_final: 0.8027 (mtpm) REVERT: A 83 MET cc_start: 0.8667 (ttp) cc_final: 0.8263 (ttp) REVERT: A 148 LEU cc_start: 0.8428 (mt) cc_final: 0.8081 (mp) REVERT: A 166 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8383 (mm-30) REVERT: A 222 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7635 (mm-30) REVERT: B 35 ASN cc_start: 0.7934 (m110) cc_final: 0.7633 (m110) REVERT: B 57 LYS cc_start: 0.8290 (mtmm) cc_final: 0.7992 (ptpp) REVERT: B 59 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: B 175 GLN cc_start: 0.8255 (pt0) cc_final: 0.8003 (pt0) REVERT: B 209 LYS cc_start: 0.8403 (mttm) cc_final: 0.8182 (mmtp) REVERT: B 219 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7653 (mtp85) REVERT: B 234 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8797 (m-80) REVERT: B 259 GLN cc_start: 0.7927 (pt0) cc_final: 0.7544 (pt0) REVERT: B 314 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7398 (ttt180) REVERT: C 21 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8332 (tpp) REVERT: C 46 LYS cc_start: 0.8269 (mmpt) cc_final: 0.8020 (mmmt) REVERT: E 171 ASN cc_start: 0.9025 (m-40) cc_final: 0.8679 (m-40) REVERT: E 234 GLU cc_start: 0.8294 (pt0) cc_final: 0.8044 (pt0) REVERT: R 28 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7648 (pp) REVERT: R 101 PHE cc_start: 0.7051 (m-80) cc_final: 0.6319 (p90) REVERT: R 246 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7963 (tt0) outliers start: 39 outliers final: 16 residues processed: 170 average time/residue: 0.6575 time to fit residues: 118.6331 Evaluate side-chains 170 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 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 221 THR 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 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 182 SER Chi-restraints excluded: chain R residue 246 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.152201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.119450 restraints weight = 10387.940| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.79 r_work: 0.2995 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9030 Z= 0.179 Angle : 0.535 7.899 12234 Z= 0.284 Chirality : 0.043 0.224 1398 Planarity : 0.003 0.044 1548 Dihedral : 6.821 151.616 1269 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.90 % Allowed : 15.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.25), residues: 1122 helix: 3.06 (0.24), residues: 414 sheet: 0.62 (0.31), residues: 260 loop : 0.29 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 160 TYR 0.014 0.001 TYR E 190 PHE 0.011 0.001 PHE B 151 TRP 0.013 0.002 TRP A 96 HIS 0.007 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9027) covalent geometry : angle 0.53521 (12228) SS BOND : bond 0.00132 ( 3) SS BOND : angle 0.73455 ( 6) hydrogen bonds : bond 0.04027 ( 484) hydrogen bonds : angle 4.44353 ( 1398) *********************** 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 180 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.348 Fit side-chains REVERT: A 17 LYS cc_start: 0.7819 (mttt) cc_final: 0.7557 (mtpt) REVERT: A 70 PHE cc_start: 0.7623 (t80) cc_final: 0.7284 (t80) REVERT: A 73 LYS cc_start: 0.8580 (mttt) cc_final: 0.8061 (mtpm) REVERT: A 83 MET cc_start: 0.8781 (ttp) cc_final: 0.8283 (ttp) REVERT: A 148 LEU cc_start: 0.8398 (mt) cc_final: 0.8066 (mp) REVERT: A 166 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.7831 (mm-30) REVERT: A 208 ARG cc_start: 0.7502 (mtp180) cc_final: 0.6492 (mmp-170) REVERT: A 222 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: B 35 ASN cc_start: 0.7974 (m110) cc_final: 0.7645 (m110) REVERT: B 59 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: B 209 LYS cc_start: 0.8470 (mttm) cc_final: 0.8246 (mmtp) REVERT: B 219 ARG cc_start: 0.8107 (mtp85) cc_final: 0.7692 (mtp85) REVERT: B 234 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.8859 (m-80) REVERT: B 259 GLN cc_start: 0.8154 (pt0) cc_final: 0.7777 (pt0) REVERT: B 314 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7409 (ttt180) REVERT: C 21 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8251 (tpp) REVERT: E 171 ASN cc_start: 0.9145 (m-40) cc_final: 0.8812 (m-40) REVERT: E 234 GLU cc_start: 0.8299 (pt0) cc_final: 0.8058 (pt0) REVERT: R 28 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7718 (pp) REVERT: R 101 PHE cc_start: 0.7268 (m-80) cc_final: 0.6170 (p90) outliers start: 37 outliers final: 16 residues processed: 166 average time/residue: 0.6559 time to fit residues: 115.4446 Evaluate side-chains 159 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 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 74 SER 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 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 52 MET Chi-restraints excluded: chain R residue 182 SER 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 9 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.154447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.121984 restraints weight = 10254.860| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.80 r_work: 0.3195 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2789 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= 0.122 Angle : 0.500 7.614 12234 Z= 0.265 Chirality : 0.041 0.209 1398 Planarity : 0.003 0.045 1548 Dihedral : 6.751 150.755 1269 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.16 % Allowed : 16.56 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.25), residues: 1122 helix: 3.15 (0.24), residues: 414 sheet: 0.61 (0.31), residues: 265 loop : 0.31 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 160 TYR 0.016 0.001 TYR E 190 PHE 0.021 0.001 PHE R 90 TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9027) covalent geometry : angle 0.49979 (12228) SS BOND : bond 0.00141 ( 3) SS BOND : angle 0.62710 ( 6) hydrogen bonds : bond 0.03609 ( 484) hydrogen bonds : angle 4.30099 ( 1398) *********************** 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 175 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7788 (mttt) cc_final: 0.7580 (mtpt) REVERT: A 70 PHE cc_start: 0.7628 (t80) cc_final: 0.7330 (t80) REVERT: A 73 LYS cc_start: 0.8499 (mttt) cc_final: 0.8052 (mtpm) REVERT: A 83 MET cc_start: 0.8714 (ttp) cc_final: 0.8302 (ttp) REVERT: A 148 LEU cc_start: 0.8491 (mt) cc_final: 0.8144 (mp) REVERT: A 208 ARG cc_start: 0.7427 (mtp180) cc_final: 0.6519 (mmp-170) REVERT: A 222 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7655 (mm-30) REVERT: B 35 ASN cc_start: 0.7960 (m110) cc_final: 0.7633 (m110) REVERT: B 44 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7558 (mm-40) REVERT: B 57 LYS cc_start: 0.8266 (mtmm) cc_final: 0.8044 (ptpp) REVERT: B 59 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: B 197 ARG cc_start: 0.7255 (mmm160) cc_final: 0.6756 (mmm-85) REVERT: B 209 LYS cc_start: 0.8435 (mttm) cc_final: 0.8224 (mmtp) REVERT: B 219 ARG cc_start: 0.8097 (mtp85) cc_final: 0.7679 (mtp85) REVERT: B 234 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8817 (m-80) REVERT: B 259 GLN cc_start: 0.8051 (pt0) cc_final: 0.7680 (pt0) REVERT: B 270 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8251 (pp) REVERT: B 314 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7442 (ttt180) REVERT: C 21 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8267 (tpp) REVERT: E 171 ASN cc_start: 0.9047 (m-40) cc_final: 0.8721 (m-40) REVERT: E 234 GLU cc_start: 0.8312 (pt0) cc_final: 0.8082 (pt0) REVERT: R 28 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7722 (pp) REVERT: R 101 PHE cc_start: 0.7257 (m-80) cc_final: 0.6198 (p90) outliers start: 30 outliers final: 15 residues processed: 161 average time/residue: 0.6268 time to fit residues: 107.2922 Evaluate side-chains 163 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 93 optimal weight: 0.0070 chunk 55 optimal weight: 3.9990 overall best weight: 1.7404 ------------------------------------------------------------------------------- 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 ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115221 restraints weight = 10461.713| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.86 r_work: 0.3120 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9030 Z= 0.182 Angle : 0.540 7.312 12234 Z= 0.287 Chirality : 0.043 0.224 1398 Planarity : 0.003 0.045 1548 Dihedral : 6.797 150.362 1269 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.69 % Allowed : 16.35 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.25), residues: 1122 helix: 2.99 (0.24), residues: 414 sheet: 0.56 (0.30), residues: 273 loop : 0.25 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 160 TYR 0.014 0.001 TYR E 190 PHE 0.018 0.002 PHE R 90 TRP 0.013 0.002 TRP A 96 HIS 0.006 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9027) covalent geometry : angle 0.53971 (12228) SS BOND : bond 0.00193 ( 3) SS BOND : angle 0.83533 ( 6) hydrogen bonds : bond 0.04046 ( 484) hydrogen bonds : angle 4.45552 ( 1398) *********************** 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 174 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.351 Fit side-chains REVERT: A 17 LYS cc_start: 0.7748 (mttt) cc_final: 0.7478 (mtpt) REVERT: A 25 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7620 (mt-10) REVERT: A 70 PHE cc_start: 0.7660 (t80) cc_final: 0.7360 (t80) REVERT: A 73 LYS cc_start: 0.8577 (mttt) cc_final: 0.8040 (mtpm) REVERT: A 83 MET cc_start: 0.8773 (ttp) cc_final: 0.8278 (ttp) REVERT: A 148 LEU cc_start: 0.8434 (mt) cc_final: 0.8094 (mp) REVERT: A 208 ARG cc_start: 0.7437 (mtp180) cc_final: 0.6501 (mmp-170) REVERT: A 222 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7757 (mm-30) REVERT: B 16 ASN cc_start: 0.8379 (m-40) cc_final: 0.8127 (m-40) REVERT: B 44 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7567 (mm-40) REVERT: B 59 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: B 209 LYS cc_start: 0.8463 (mttm) cc_final: 0.8243 (mmtp) REVERT: B 219 ARG cc_start: 0.8100 (mtp85) cc_final: 0.7588 (mtp85) REVERT: B 234 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.8809 (m-80) REVERT: B 259 GLN cc_start: 0.8161 (pt0) cc_final: 0.7771 (pt0) REVERT: B 270 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8205 (pp) REVERT: B 304 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7467 (ttm110) REVERT: B 314 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7409 (ttt180) REVERT: C 21 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8313 (tpp) REVERT: C 46 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8165 (mmpt) REVERT: E 171 ASN cc_start: 0.9141 (m-40) cc_final: 0.8806 (m-40) REVERT: E 234 GLU cc_start: 0.8298 (pt0) cc_final: 0.8061 (pt0) REVERT: R 28 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7697 (pp) REVERT: R 101 PHE cc_start: 0.7301 (m-80) cc_final: 0.6151 (p90) outliers start: 35 outliers final: 17 residues processed: 159 average time/residue: 0.6512 time to fit residues: 109.8365 Evaluate side-chains 164 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 270 ILE Chi-restraints excluded: chain B residue 304 ARG 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 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 52 MET Chi-restraints excluded: chain R residue 182 SER 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 22 optimal weight: 20.0000 chunk 28 optimal weight: 0.6980 chunk 69 optimal weight: 0.0030 chunk 108 optimal weight: 0.0040 chunk 44 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 93 optimal weight: 0.0030 chunk 19 optimal weight: 0.0570 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 overall best weight: 0.1530 ------------------------------------------------------------------------------- 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 91 HIS B 293 ASN E 167 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.157830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.125120 restraints weight = 10278.424| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.81 r_work: 0.3249 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9030 Z= 0.091 Angle : 0.465 7.384 12234 Z= 0.249 Chirality : 0.040 0.172 1398 Planarity : 0.003 0.047 1548 Dihedral : 6.715 151.913 1269 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.32 % Allowed : 17.93 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.26), residues: 1122 helix: 3.28 (0.24), residues: 414 sheet: 0.58 (0.31), residues: 265 loop : 0.29 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 160 TYR 0.018 0.001 TYR E 190 PHE 0.020 0.001 PHE R 90 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 9027) covalent geometry : angle 0.46503 (12228) SS BOND : bond 0.00143 ( 3) SS BOND : angle 0.63056 ( 6) hydrogen bonds : bond 0.03252 ( 484) hydrogen bonds : angle 4.14178 ( 1398) ********************** 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 177 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7749 (mttt) cc_final: 0.7529 (mtpt) REVERT: A 70 PHE cc_start: 0.7571 (t80) cc_final: 0.7242 (t80) REVERT: A 73 LYS cc_start: 0.8437 (mttt) cc_final: 0.8029 (mtpm) REVERT: A 83 MET cc_start: 0.8625 (ttp) cc_final: 0.8297 (ttp) REVERT: A 148 LEU cc_start: 0.8453 (mt) cc_final: 0.8098 (mp) REVERT: A 222 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: B 16 ASN cc_start: 0.8392 (m-40) cc_final: 0.8144 (m-40) REVERT: B 57 LYS cc_start: 0.8287 (mtmm) cc_final: 0.8059 (ptpp) REVERT: B 59 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7689 (m-80) REVERT: B 197 ARG cc_start: 0.7151 (mmm160) cc_final: 0.6626 (mmm-85) REVERT: B 219 ARG cc_start: 0.8055 (mtp85) cc_final: 0.7667 (mtp85) REVERT: B 234 PHE cc_start: 0.9270 (OUTLIER) cc_final: 0.8778 (m-80) REVERT: B 259 GLN cc_start: 0.7916 (pt0) cc_final: 0.7464 (pt0) REVERT: B 270 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8255 (pp) REVERT: C 21 MET cc_start: 0.8571 (mmt) cc_final: 0.8289 (tpp) REVERT: C 46 LYS cc_start: 0.8502 (mmmt) cc_final: 0.8198 (mmpt) REVERT: E 171 ASN cc_start: 0.8894 (m-40) cc_final: 0.8624 (m-40) REVERT: E 183 GLN cc_start: 0.8078 (mp10) cc_final: 0.7719 (mm-40) REVERT: E 234 GLU cc_start: 0.8326 (pt0) cc_final: 0.8121 (pt0) REVERT: R 28 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7646 (pp) REVERT: R 101 PHE cc_start: 0.7234 (m-80) cc_final: 0.6320 (p90) REVERT: R 292 MET cc_start: 0.7889 (ttm) cc_final: 0.7688 (ttm) outliers start: 22 outliers final: 13 residues processed: 169 average time/residue: 0.5745 time to fit residues: 103.3696 Evaluate side-chains 160 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 222 GLU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 44 GLN B 155 ASN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.153165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.120517 restraints weight = 10170.834| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.78 r_work: 0.3021 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9030 Z= 0.168 Angle : 0.532 7.169 12234 Z= 0.282 Chirality : 0.043 0.197 1398 Planarity : 0.004 0.045 1548 Dihedral : 6.757 150.603 1269 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.11 % Allowed : 18.78 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.26), residues: 1122 helix: 3.11 (0.24), residues: 414 sheet: 0.62 (0.31), residues: 264 loop : 0.26 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 132 TYR 0.016 0.001 TYR C 40 PHE 0.028 0.002 PHE E 67 TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9027) covalent geometry : angle 0.53106 (12228) SS BOND : bond 0.00249 ( 3) SS BOND : angle 1.33466 ( 6) hydrogen bonds : bond 0.03900 ( 484) hydrogen bonds : angle 4.36185 ( 1398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4113.78 seconds wall clock time: 70 minutes 55.54 seconds (4255.54 seconds total)