Starting phenix.real_space_refine on Sat Aug 23 00:25:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bhw_44555/08_2025/9bhw_44555.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bhw_44555/08_2025/9bhw_44555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bhw_44555/08_2025/9bhw_44555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bhw_44555/08_2025/9bhw_44555.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bhw_44555/08_2025/9bhw_44555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bhw_44555/08_2025/9bhw_44555.map" } resolution = 2.72 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 40 5.16 5 C 5499 2.51 5 N 1556 2.21 5 O 1656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8759 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1929 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 232} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2429 Classifications: {'peptide': 299} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 287} Chain: "C" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2411 Classifications: {'peptide': 297} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 285} Chain: "D" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1878 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 225} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.70, per 1000 atoms: 0.19 Number of scatterers: 8759 At special positions: 0 Unit cell: (59.778, 79.461, 180.063, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 8 15.00 O 1656 8.00 N 1556 7.00 C 5499 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.59 Conformation dependent library (CDL) restraints added in 293.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 8 sheets defined 45.8% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 115 through 134 removed outlier: 3.831A pdb=" N SER A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 171 Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 188 through 206 Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.539A pdb=" N SER A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 269 through 279 Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.693A pdb=" N LEU A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'B' and resid 10 through 12 No H-bonds generated for 'chain 'B' and resid 10 through 12' Processing helix chain 'B' and resid 13 through 26 removed outlier: 3.806A pdb=" N ARG B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 104 through 124 Processing helix chain 'B' and resid 151 through 162 Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 178 through 196 Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 212 through 225 Processing helix chain 'B' and resid 262 through 272 removed outlier: 3.624A pdb=" N LEU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 285 through 296 Processing helix chain 'C' and resid 10 through 12 No H-bonds generated for 'chain 'C' and resid 10 through 12' Processing helix chain 'C' and resid 13 through 24 removed outlier: 4.142A pdb=" N ARG C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 50 Processing helix chain 'C' and resid 104 through 124 Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 178 through 196 Processing helix chain 'C' and resid 203 through 207 removed outlier: 3.513A pdb=" N LEU C 207 " --> pdb=" O LEU C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 225 removed outlier: 4.049A pdb=" N ARG C 217 " --> pdb=" O THR C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 272 Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 285 through 298 Processing helix chain 'D' and resid 50 through 59 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.745A pdb=" N GLY D 92 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 133 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'D' and resid 188 through 206 Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 269 through 278 Processing helix chain 'D' and resid 282 through 292 Processing helix chain 'D' and resid 292 through 302 Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 89 removed outlier: 6.216A pdb=" N PHE A 37 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR A 98 " --> pdb=" O PHE A 37 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE A 39 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ASP A 100 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 41 " --> pdb=" O ASP A 100 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N CYS A 148 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR A 40 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU A 150 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N MET A 42 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N PHE A 152 " --> pdb=" O MET A 42 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL A 44 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N CYS A 149 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU A 180 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR A 151 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 242 through 245 Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 79 Processing sheet with id=AA4, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 79 removed outlier: 6.541A pdb=" N CYS C 139 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL C 170 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR C 141 " --> pdb=" O VAL C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AA7, first strand: chain 'D' and resid 82 through 88 removed outlier: 6.309A pdb=" N PHE D 37 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N THR D 98 " --> pdb=" O PHE D 37 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE D 39 " --> pdb=" O THR D 98 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASP D 100 " --> pdb=" O PHE D 39 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU D 41 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR D 151 " --> pdb=" O ILE D 178 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 242 through 245 428 hydrogen bonds defined for protein. 1173 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: 0.84 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1571 1.32 - 1.44: 2148 1.44 - 1.56: 5127 1.56 - 1.69: 12 1.69 - 1.81: 60 Bond restraints: 8918 Sorted by residual: bond pdb=" C ASP B 175 " pdb=" O ASP B 175 " ideal model delta sigma weight residual 1.236 1.199 0.036 1.29e-02 6.01e+03 7.95e+00 bond pdb=" C5 GDP B 401 " pdb=" C4 GDP B 401 " ideal model delta sigma weight residual 1.490 1.442 0.048 2.00e-02 2.50e+03 5.68e+00 bond pdb=" N ASP A 185 " pdb=" CA ASP A 185 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.32e-02 5.74e+03 5.45e+00 bond pdb=" C5 GDP A 501 " pdb=" C4 GDP A 501 " ideal model delta sigma weight residual 1.490 1.448 0.042 2.00e-02 2.50e+03 4.33e+00 bond pdb=" C5 GDP D 501 " pdb=" C4 GDP D 501 " ideal model delta sigma weight residual 1.490 1.450 0.040 2.00e-02 2.50e+03 4.07e+00 ... (remaining 8913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 11827 2.13 - 4.26: 186 4.26 - 6.39: 35 6.39 - 8.52: 10 8.52 - 10.65: 7 Bond angle restraints: 12065 Sorted by residual: angle pdb=" CA ASP B 175 " pdb=" CB ASP B 175 " pdb=" CG ASP B 175 " ideal model delta sigma weight residual 112.60 121.45 -8.85 1.00e+00 1.00e+00 7.84e+01 angle pdb=" N THR B 297 " pdb=" CA THR B 297 " pdb=" C THR B 297 " ideal model delta sigma weight residual 113.88 108.78 5.10 1.23e+00 6.61e-01 1.72e+01 angle pdb=" O1A GDP B 401 " pdb=" PA GDP B 401 " pdb=" O2A GDP B 401 " ideal model delta sigma weight residual 109.50 120.15 -10.65 3.00e+00 1.11e-01 1.26e+01 angle pdb=" N ARG A 96 " pdb=" CA ARG A 96 " pdb=" C ARG A 96 " ideal model delta sigma weight residual 107.99 101.84 6.15 1.76e+00 3.23e-01 1.22e+01 angle pdb=" C LYS A 51 " pdb=" CA LYS A 51 " pdb=" CB LYS A 51 " ideal model delta sigma weight residual 110.90 116.04 -5.14 1.58e+00 4.01e-01 1.06e+01 ... (remaining 12060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.63: 5190 26.63 - 53.26: 197 53.26 - 79.89: 27 79.89 - 106.52: 2 106.52 - 133.15: 3 Dihedral angle restraints: 5419 sinusoidal: 2303 harmonic: 3116 Sorted by residual: dihedral pdb=" C5' GDP D 501 " pdb=" O5' GDP D 501 " pdb=" PA GDP D 501 " pdb=" O3A GDP D 501 " ideal model delta sinusoidal sigma weight residual 179.98 -46.87 -133.15 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" O5' GDP A 501 " pdb=" O3A GDP A 501 " pdb=" PA GDP A 501 " pdb=" PB GDP A 501 " ideal model delta sinusoidal sigma weight residual -179.98 -64.94 -115.04 1 2.00e+01 2.50e-03 3.42e+01 dihedral pdb=" C5' GDP B 401 " pdb=" O5' GDP B 401 " pdb=" PA GDP B 401 " pdb=" O3A GDP B 401 " ideal model delta sinusoidal sigma weight residual 179.98 -71.55 -108.47 1 2.00e+01 2.50e-03 3.16e+01 ... (remaining 5416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1006 0.048 - 0.095: 284 0.095 - 0.143: 76 0.143 - 0.191: 4 0.191 - 0.238: 4 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CB VAL A 79 " pdb=" CA VAL A 79 " pdb=" CG1 VAL A 79 " pdb=" CG2 VAL A 79 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA VAL A 79 " pdb=" N VAL A 79 " pdb=" C VAL A 79 " pdb=" CB VAL A 79 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ARG A 96 " pdb=" N ARG A 96 " pdb=" C ARG A 96 " pdb=" CB ARG A 96 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1371 not shown) Planarity restraints: 1529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 175 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" CG ASP B 175 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASP B 175 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 175 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 246 " 0.164 9.50e-02 1.11e+02 7.37e-02 4.07e+00 pdb=" NE ARG C 246 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C 246 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 246 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 246 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 267 " 0.152 9.50e-02 1.11e+02 6.87e-02 3.58e+00 pdb=" NE ARG B 267 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 267 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 267 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 267 " 0.001 2.00e-02 2.50e+03 ... (remaining 1526 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 212 2.71 - 3.25: 8470 3.25 - 3.80: 13701 3.80 - 4.35: 17826 4.35 - 4.90: 30470 Nonbonded interactions: 70679 Sorted by model distance: nonbonded pdb=" NH1 ARG A 253 " pdb=" OH TYR A 255 " model vdw 2.158 3.120 nonbonded pdb=" OE2 GLU C 116 " pdb=" OH TYR C 290 " model vdw 2.165 3.040 nonbonded pdb=" OH TYR A 151 " pdb=" OD1 ASP A 164 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR D 151 " pdb=" OD1 ASP D 164 " model vdw 2.204 3.040 nonbonded pdb=" OE1 GLU C 69 " pdb=" NZ LYS C 71 " model vdw 2.226 3.120 ... (remaining 70674 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 36 through 62 or resid 78 through 133 or resid 142 through \ 216 or resid 227 through 302 or resid 501)) selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 2 through 298 or resid 401)) selection = chain 'C' } 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: 6.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.090 Find NCS groups from input model: 0.160 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: 0.000 Load rotamer database and sin/cos tables:5.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.005 0.050 8918 Z= 0.238 Angle : 0.715 10.645 12065 Z= 0.361 Chirality : 0.048 0.238 1374 Planarity : 0.005 0.074 1529 Dihedral : 14.136 133.149 3393 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.31 % Allowed : 0.00 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 0.77 (0.25), residues: 1051 helix: 1.37 (0.26), residues: 420 sheet: 0.73 (0.36), residues: 177 loop : -0.32 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 246 TYR 0.016 0.002 TYR B 141 PHE 0.019 0.002 PHE B 29 TRP 0.017 0.002 TRP B 250 HIS 0.007 0.001 HIS D 147 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 8918) covalent geometry : angle 0.71545 (12065) hydrogen bonds : bond 0.16321 ( 428) hydrogen bonds : angle 6.18855 ( 1173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 209 GLN cc_start: 0.8197 (mp10) cc_final: 0.7920 (mp10) REVERT: D 124 LYS cc_start: 0.8726 (tppt) cc_final: 0.8505 (tppp) REVERT: D 128 ASP cc_start: 0.7729 (m-30) cc_final: 0.7194 (m-30) outliers start: 3 outliers final: 0 residues processed: 196 average time/residue: 0.7094 time to fit residues: 145.2289 Evaluate side-chains 80 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.0040 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 275 ASN B 284 GLN C 110 HIS C 114 GLN C 284 GLN D 121 HIS ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.091245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.068572 restraints weight = 15323.003| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.00 r_work: 0.2899 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8918 Z= 0.194 Angle : 0.628 9.489 12065 Z= 0.313 Chirality : 0.046 0.156 1374 Planarity : 0.005 0.050 1529 Dihedral : 8.429 100.837 1202 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.25 % Allowed : 10.14 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.28 (0.26), residues: 1051 helix: 2.02 (0.25), residues: 425 sheet: 0.61 (0.35), residues: 185 loop : -0.16 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 24 TYR 0.018 0.002 TYR D 211 PHE 0.013 0.001 PHE C 49 TRP 0.006 0.001 TRP D 115 HIS 0.006 0.001 HIS D 147 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 8918) covalent geometry : angle 0.62843 (12065) hydrogen bonds : bond 0.04751 ( 428) hydrogen bonds : angle 4.65298 ( 1173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 209 GLN cc_start: 0.8979 (mp10) cc_final: 0.8641 (mp10) REVERT: D 89 LYS cc_start: 0.8692 (tppp) cc_final: 0.8424 (tppt) REVERT: D 124 LYS cc_start: 0.8917 (tppt) cc_final: 0.8371 (tppp) REVERT: D 127 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7879 (pp20) REVERT: D 128 ASP cc_start: 0.8855 (m-30) cc_final: 0.8126 (m-30) REVERT: D 231 ARG cc_start: 0.7085 (mtt-85) cc_final: 0.6829 (mtt-85) outliers start: 22 outliers final: 6 residues processed: 106 average time/residue: 0.7257 time to fit residues: 80.7262 Evaluate side-chains 76 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 230 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 91 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN D 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.091209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.068423 restraints weight = 15295.696| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.03 r_work: 0.2854 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8918 Z= 0.157 Angle : 0.575 8.231 12065 Z= 0.282 Chirality : 0.044 0.147 1374 Planarity : 0.004 0.054 1529 Dihedral : 7.894 83.359 1202 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.15 % Allowed : 11.17 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.56 (0.26), residues: 1051 helix: 2.39 (0.25), residues: 422 sheet: 0.64 (0.35), residues: 185 loop : -0.08 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 24 TYR 0.014 0.001 TYR A 255 PHE 0.010 0.001 PHE C 49 TRP 0.015 0.001 TRP D 115 HIS 0.004 0.001 HIS D 147 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8918) covalent geometry : angle 0.57501 (12065) hydrogen bonds : bond 0.04186 ( 428) hydrogen bonds : angle 4.42987 ( 1173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 209 GLN cc_start: 0.8952 (mp10) cc_final: 0.8567 (mp10) REVERT: B 156 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7333 (mp0) REVERT: C 180 GLU cc_start: 0.8084 (mp0) cc_final: 0.7850 (tp30) REVERT: D 124 LYS cc_start: 0.8901 (tppt) cc_final: 0.8309 (tppp) REVERT: D 127 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7856 (pp20) REVERT: D 128 ASP cc_start: 0.8872 (m-30) cc_final: 0.8044 (m-30) outliers start: 21 outliers final: 6 residues processed: 94 average time/residue: 0.5876 time to fit residues: 58.3066 Evaluate side-chains 84 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 216 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN D 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.091088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.068238 restraints weight = 15574.708| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.06 r_work: 0.2846 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8918 Z= 0.147 Angle : 0.557 7.996 12065 Z= 0.273 Chirality : 0.044 0.144 1374 Planarity : 0.004 0.053 1529 Dihedral : 7.644 81.571 1202 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.84 % Allowed : 12.91 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.69 (0.26), residues: 1051 helix: 2.52 (0.25), residues: 422 sheet: 0.67 (0.36), residues: 186 loop : -0.02 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 24 TYR 0.012 0.001 TYR A 255 PHE 0.010 0.001 PHE C 49 TRP 0.008 0.001 TRP D 115 HIS 0.003 0.000 HIS D 147 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8918) covalent geometry : angle 0.55683 (12065) hydrogen bonds : bond 0.03946 ( 428) hydrogen bonds : angle 4.33546 ( 1173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 209 GLN cc_start: 0.8944 (mp10) cc_final: 0.8546 (mp10) REVERT: B 113 GLU cc_start: 0.8287 (tp30) cc_final: 0.7846 (tp30) REVERT: B 156 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7342 (mp0) REVERT: D 124 LYS cc_start: 0.8918 (tppt) cc_final: 0.8341 (tppp) REVERT: D 127 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7915 (pp20) REVERT: D 128 ASP cc_start: 0.8881 (m-30) cc_final: 0.8011 (m-30) outliers start: 18 outliers final: 9 residues processed: 98 average time/residue: 0.6712 time to fit residues: 69.0592 Evaluate side-chains 83 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 230 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 25 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 GLN D 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.091243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.068115 restraints weight = 15599.377| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.10 r_work: 0.2832 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8918 Z= 0.167 Angle : 0.569 7.791 12065 Z= 0.278 Chirality : 0.044 0.141 1374 Planarity : 0.004 0.059 1529 Dihedral : 7.612 78.870 1202 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.84 % Allowed : 13.93 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.74 (0.26), residues: 1051 helix: 2.52 (0.25), residues: 424 sheet: 0.93 (0.37), residues: 176 loop : -0.05 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 24 TYR 0.012 0.001 TYR A 129 PHE 0.010 0.001 PHE C 49 TRP 0.006 0.001 TRP D 115 HIS 0.010 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8918) covalent geometry : angle 0.56854 (12065) hydrogen bonds : bond 0.04047 ( 428) hydrogen bonds : angle 4.33585 ( 1173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 209 GLN cc_start: 0.8975 (mp10) cc_final: 0.8630 (mp10) REVERT: A 300 LYS cc_start: 0.9303 (mmmm) cc_final: 0.9053 (mmpt) REVERT: B 113 GLU cc_start: 0.8276 (tp30) cc_final: 0.7851 (tp30) REVERT: B 156 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7372 (mp0) REVERT: B 280 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7630 (tt0) REVERT: D 89 LYS cc_start: 0.9286 (tptt) cc_final: 0.8792 (tppt) REVERT: D 124 LYS cc_start: 0.8909 (tppt) cc_final: 0.8314 (tppp) REVERT: D 127 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7983 (pp20) REVERT: D 128 ASP cc_start: 0.8905 (m-30) cc_final: 0.8059 (m-30) outliers start: 18 outliers final: 11 residues processed: 93 average time/residue: 0.6361 time to fit residues: 62.3622 Evaluate side-chains 93 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 277 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 66 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 15 optimal weight: 0.0670 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.091256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.068118 restraints weight = 15512.523| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.05 r_work: 0.2859 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8918 Z= 0.139 Angle : 0.553 7.145 12065 Z= 0.271 Chirality : 0.043 0.140 1374 Planarity : 0.004 0.055 1529 Dihedral : 7.460 78.887 1202 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.74 % Allowed : 14.75 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.81 (0.26), residues: 1051 helix: 2.57 (0.25), residues: 428 sheet: 1.05 (0.37), residues: 175 loop : -0.06 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 24 TYR 0.012 0.001 TYR D 151 PHE 0.010 0.001 PHE C 49 TRP 0.005 0.001 TRP D 115 HIS 0.010 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8918) covalent geometry : angle 0.55297 (12065) hydrogen bonds : bond 0.03796 ( 428) hydrogen bonds : angle 4.25839 ( 1173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 209 GLN cc_start: 0.8992 (mp10) cc_final: 0.8645 (mp10) REVERT: A 300 LYS cc_start: 0.9317 (mmmm) cc_final: 0.9075 (mmpt) REVERT: B 113 GLU cc_start: 0.8287 (tp30) cc_final: 0.7869 (tp30) REVERT: B 156 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7346 (mp0) REVERT: B 280 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7651 (tt0) REVERT: D 89 LYS cc_start: 0.9268 (tptt) cc_final: 0.8765 (tppt) REVERT: D 124 LYS cc_start: 0.8916 (tppt) cc_final: 0.8316 (tppp) REVERT: D 127 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7979 (pp20) REVERT: D 128 ASP cc_start: 0.8895 (m-30) cc_final: 0.8039 (m-30) REVERT: D 231 ARG cc_start: 0.7445 (mtt90) cc_final: 0.6834 (mtt-85) outliers start: 17 outliers final: 10 residues processed: 95 average time/residue: 0.6654 time to fit residues: 66.4781 Evaluate side-chains 89 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 277 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 39 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 75 optimal weight: 0.0970 chunk 80 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.067687 restraints weight = 15561.006| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.04 r_work: 0.2842 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8918 Z= 0.154 Angle : 0.569 7.802 12065 Z= 0.279 Chirality : 0.044 0.158 1374 Planarity : 0.004 0.052 1529 Dihedral : 7.449 76.883 1202 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.05 % Allowed : 15.06 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.86 (0.26), residues: 1051 helix: 2.63 (0.25), residues: 425 sheet: 1.08 (0.37), residues: 175 loop : -0.05 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 24 TYR 0.010 0.001 TYR A 129 PHE 0.010 0.001 PHE C 49 TRP 0.005 0.001 TRP B 104 HIS 0.008 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8918) covalent geometry : angle 0.56915 (12065) hydrogen bonds : bond 0.03894 ( 428) hydrogen bonds : angle 4.28505 ( 1173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 209 GLN cc_start: 0.9000 (mp10) cc_final: 0.8648 (mp10) REVERT: A 300 LYS cc_start: 0.9287 (mmmm) cc_final: 0.9078 (mmpt) REVERT: B 16 GLU cc_start: 0.7538 (mp0) cc_final: 0.7237 (tm-30) REVERT: B 113 GLU cc_start: 0.8281 (tp30) cc_final: 0.7895 (tp30) REVERT: B 156 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7328 (mp0) REVERT: B 280 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7674 (tt0) REVERT: D 89 LYS cc_start: 0.9238 (tptt) cc_final: 0.8719 (tppt) REVERT: D 124 LYS cc_start: 0.8919 (tppt) cc_final: 0.8326 (tppp) REVERT: D 127 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8019 (pp20) REVERT: D 128 ASP cc_start: 0.8905 (m-30) cc_final: 0.8056 (m-30) outliers start: 20 outliers final: 12 residues processed: 90 average time/residue: 0.6077 time to fit residues: 57.6775 Evaluate side-chains 96 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 248 ARG Chi-restraints excluded: chain D residue 277 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 78 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 88 optimal weight: 0.0870 chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.091420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.068662 restraints weight = 15468.706| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.04 r_work: 0.2853 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8918 Z= 0.130 Angle : 0.570 7.854 12065 Z= 0.281 Chirality : 0.043 0.137 1374 Planarity : 0.004 0.050 1529 Dihedral : 7.333 77.139 1202 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.23 % Allowed : 16.09 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.98 (0.26), residues: 1051 helix: 2.75 (0.25), residues: 423 sheet: 1.13 (0.37), residues: 175 loop : 0.01 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 248 TYR 0.009 0.001 TYR A 255 PHE 0.009 0.001 PHE C 49 TRP 0.005 0.001 TRP D 115 HIS 0.008 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8918) covalent geometry : angle 0.56988 (12065) hydrogen bonds : bond 0.03718 ( 428) hydrogen bonds : angle 4.22380 ( 1173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 209 GLN cc_start: 0.9000 (mp10) cc_final: 0.8650 (mp10) REVERT: B 16 GLU cc_start: 0.7527 (mp0) cc_final: 0.7212 (tm-30) REVERT: B 113 GLU cc_start: 0.8263 (tp30) cc_final: 0.7879 (tp30) REVERT: B 156 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7323 (mp0) REVERT: B 280 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7665 (tt0) REVERT: C 191 GLN cc_start: 0.8446 (tp40) cc_final: 0.8177 (tp40) REVERT: D 89 LYS cc_start: 0.9234 (tptt) cc_final: 0.8699 (tppt) REVERT: D 96 ARG cc_start: 0.7253 (mtt90) cc_final: 0.6937 (mtt90) REVERT: D 124 LYS cc_start: 0.8923 (tppt) cc_final: 0.8330 (tppp) REVERT: D 127 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8020 (pp20) REVERT: D 128 ASP cc_start: 0.8908 (m-30) cc_final: 0.8066 (m-30) REVERT: D 231 ARG cc_start: 0.7451 (mtt90) cc_final: 0.7243 (mtt90) outliers start: 12 outliers final: 8 residues processed: 99 average time/residue: 0.5960 time to fit residues: 62.1672 Evaluate side-chains 89 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 230 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 21 optimal weight: 0.6980 chunk 100 optimal weight: 0.0040 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 102 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.091311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.068638 restraints weight = 15526.430| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 3.03 r_work: 0.2859 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8918 Z= 0.132 Angle : 0.572 7.996 12065 Z= 0.279 Chirality : 0.043 0.134 1374 Planarity : 0.004 0.052 1529 Dihedral : 7.244 76.223 1202 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.23 % Allowed : 16.39 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 2.01 (0.26), residues: 1051 helix: 2.79 (0.25), residues: 423 sheet: 1.17 (0.37), residues: 175 loop : 0.01 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 130 TYR 0.022 0.001 TYR A 297 PHE 0.010 0.001 PHE C 49 TRP 0.004 0.001 TRP B 104 HIS 0.008 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8918) covalent geometry : angle 0.57169 (12065) hydrogen bonds : bond 0.03677 ( 428) hydrogen bonds : angle 4.19289 ( 1173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 209 GLN cc_start: 0.9005 (mp10) cc_final: 0.8654 (mp10) REVERT: B 16 GLU cc_start: 0.7520 (mp0) cc_final: 0.7239 (tm-30) REVERT: B 113 GLU cc_start: 0.8266 (tp30) cc_final: 0.7885 (tp30) REVERT: B 156 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7316 (mp0) REVERT: B 280 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7657 (tt0) REVERT: C 191 GLN cc_start: 0.8475 (tp40) cc_final: 0.8205 (tp40) REVERT: D 89 LYS cc_start: 0.9209 (tptt) cc_final: 0.8665 (tppt) REVERT: D 124 LYS cc_start: 0.8919 (tppt) cc_final: 0.8330 (tppp) REVERT: D 127 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8030 (pp20) REVERT: D 128 ASP cc_start: 0.8905 (m-30) cc_final: 0.8068 (m-30) REVERT: D 231 ARG cc_start: 0.7443 (mtt90) cc_final: 0.7228 (mtt90) outliers start: 12 outliers final: 9 residues processed: 88 average time/residue: 0.8166 time to fit residues: 75.4956 Evaluate side-chains 85 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 230 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 13 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.066878 restraints weight = 15634.299| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.02 r_work: 0.2824 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8918 Z= 0.194 Angle : 0.605 7.789 12065 Z= 0.295 Chirality : 0.045 0.141 1374 Planarity : 0.004 0.056 1529 Dihedral : 7.480 77.196 1202 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.13 % Allowed : 16.60 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.88 (0.26), residues: 1051 helix: 2.63 (0.24), residues: 425 sheet: 1.11 (0.37), residues: 175 loop : -0.02 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 130 TYR 0.022 0.001 TYR A 297 PHE 0.011 0.001 PHE C 49 TRP 0.006 0.001 TRP B 104 HIS 0.008 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 8918) covalent geometry : angle 0.60476 (12065) hydrogen bonds : bond 0.04111 ( 428) hydrogen bonds : angle 4.31777 ( 1173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2102 Ramachandran restraints generated. 1051 Oldfield, 0 Emsley, 1051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 209 GLN cc_start: 0.9018 (mp10) cc_final: 0.8616 (mp10) REVERT: B 16 GLU cc_start: 0.7515 (mp0) cc_final: 0.7280 (tm-30) REVERT: B 113 GLU cc_start: 0.8293 (tp30) cc_final: 0.7911 (tp30) REVERT: B 156 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7221 (mt-10) REVERT: B 280 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7688 (tt0) REVERT: C 191 GLN cc_start: 0.8479 (tp40) cc_final: 0.8214 (tp40) REVERT: D 89 LYS cc_start: 0.9141 (tptt) cc_final: 0.8594 (tppt) REVERT: D 124 LYS cc_start: 0.8913 (tppt) cc_final: 0.8308 (tppp) REVERT: D 127 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8035 (pp20) REVERT: D 128 ASP cc_start: 0.8920 (m-30) cc_final: 0.8076 (m-30) REVERT: D 248 ARG cc_start: 0.8711 (ttp80) cc_final: 0.8093 (ptt90) outliers start: 11 outliers final: 9 residues processed: 84 average time/residue: 0.7278 time to fit residues: 64.5545 Evaluate side-chains 83 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 230 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 77 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN ** D 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.090029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.067312 restraints weight = 15525.006| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.01 r_work: 0.2830 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8918 Z= 0.172 Angle : 0.590 7.751 12065 Z= 0.287 Chirality : 0.044 0.141 1374 Planarity : 0.004 0.056 1529 Dihedral : 7.471 76.980 1202 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.43 % Allowed : 16.39 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.87 (0.26), residues: 1051 helix: 2.62 (0.25), residues: 425 sheet: 1.10 (0.37), residues: 175 loop : -0.02 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 130 TYR 0.021 0.001 TYR A 297 PHE 0.011 0.001 PHE C 49 TRP 0.005 0.001 TRP B 104 HIS 0.008 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8918) covalent geometry : angle 0.59045 (12065) hydrogen bonds : bond 0.04002 ( 428) hydrogen bonds : angle 4.30493 ( 1173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2507.65 seconds wall clock time: 43 minutes 35.79 seconds (2615.79 seconds total)