Starting phenix.real_space_refine on Fri Sep 11 06:34:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24vr_69849/09_2026/24vr_69849.cif Found real_map, /net/cci-nas-00/data/ceres_data/24vr_69849/09_2026/24vr_69849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/24vr_69849/09_2026/24vr_69849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24vr_69849/09_2026/24vr_69849.map" model { file = "/net/cci-nas-00/data/ceres_data/24vr_69849/09_2026/24vr_69849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24vr_69849/09_2026/24vr_69849.cif" } resolution = 3.3 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= 0.008 sd= 0.120 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 2 5.49 5 S 38 5.16 5 C 5361 2.51 5 N 1296 2.21 5 O 1359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8056 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1913 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain breaks: 1 Chain: "B" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1982 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 4, 'TRANS': 238} Chain breaks: 1 Chain: "C" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1913 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain breaks: 1 Chain: "D" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2006 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 4, 'TRANS': 242} Chain breaks: 1 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'9PE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 81 Unusual residues: {'YJ0': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'9PE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 81 Unusual residues: {'YJ0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.05, per 1000 atoms: 0.25 Number of scatterers: 8056 At special positions: 0 Unit cell: (117.426, 126.044, 82.9521, 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 38 16.00 P 2 15.00 O 1359 8.00 N 1296 7.00 C 5361 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 396.3 milliseconds 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1780 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 79.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 110 through 116 Processing helix chain 'A' and resid 124 through 144 removed outlier: 3.950A pdb=" N THR A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 178 removed outlier: 3.793A pdb=" N TRP A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 removed outlier: 3.761A pdb=" N ARG A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 208 removed outlier: 3.528A pdb=" N ALA A 208 " --> pdb=" O PHE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 238 removed outlier: 3.850A pdb=" N GLN A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 257 removed outlier: 4.073A pdb=" N LEU A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 283 Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 326 through 345 removed outlier: 3.614A pdb=" N LEU A 331 " --> pdb=" O TRP A 327 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 366 removed outlier: 3.519A pdb=" N GLY A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 91 through 114 removed outlier: 3.923A pdb=" N HIS B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 147 Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.840A pdb=" N ILE B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 Processing helix chain 'B' and resid 227 through 253 removed outlier: 3.690A pdb=" N THR B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 286 through 305 removed outlier: 3.723A pdb=" N ALA B 305 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 326 removed outlier: 3.555A pdb=" N GLY B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 116 Processing helix chain 'C' and resid 123 through 144 removed outlier: 3.835A pdb=" N THR C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 178 removed outlier: 3.838A pdb=" N TRP C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 195 Processing helix chain 'C' and resid 196 through 208 removed outlier: 3.616A pdb=" N ALA C 208 " --> pdb=" O PHE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 238 removed outlier: 3.976A pdb=" N GLN C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE C 234 " --> pdb=" O ARG C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 257 removed outlier: 3.940A pdb=" N LEU C 250 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS C 257 " --> pdb=" O ALA C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 283 Processing helix chain 'C' and resid 302 through 315 Processing helix chain 'C' and resid 326 through 345 removed outlier: 3.621A pdb=" N LEU C 331 " --> pdb=" O TRP C 327 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 333 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA C 345 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 366 removed outlier: 3.522A pdb=" N GLY C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 93 through 114 removed outlier: 3.693A pdb=" N ILE D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 145 removed outlier: 3.693A pdb=" N SER D 121 " --> pdb=" O TYR D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 165 through 183 removed outlier: 3.741A pdb=" N ASP D 171 " --> pdb=" O PHE D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 209 removed outlier: 4.159A pdb=" N LEU D 205 " --> pdb=" O PHE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 227 Processing helix chain 'D' and resid 230 through 253 removed outlier: 3.576A pdb=" N ALA D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.765A pdb=" N ALA D 305 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 326 removed outlier: 3.572A pdb=" N GLY D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1641 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: 1.14 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1160 1.31 - 1.43: 2455 1.43 - 1.56: 4603 1.56 - 1.69: 4 1.69 - 1.81: 52 Bond restraints: 8274 Sorted by residual: bond pdb=" C31 9PE A1001 " pdb=" O31 9PE A1001 " ideal model delta sigma weight residual 1.325 1.398 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C31 9PE C1001 " pdb=" O31 9PE C1001 " ideal model delta sigma weight residual 1.325 1.398 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C21 9PE C1001 " pdb=" O21 9PE C1001 " ideal model delta sigma weight residual 1.329 1.398 -0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C21 9PE A1001 " pdb=" O21 9PE A1001 " ideal model delta sigma weight residual 1.329 1.398 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C7 YJ0 B 601 " pdb=" C8 YJ0 B 601 " ideal model delta sigma weight residual 1.561 1.523 0.038 2.00e-02 2.50e+03 3.66e+00 ... (remaining 8269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.67: 11207 9.67 - 19.35: 7 19.35 - 29.02: 0 29.02 - 38.69: 0 38.69 - 48.37: 3 Bond angle restraints: 11217 Sorted by residual: angle pdb=" C22 9PE C1001 " pdb=" C21 9PE C1001 " pdb=" O21 9PE C1001 " ideal model delta sigma weight residual 111.28 159.65 -48.37 3.00e+00 1.11e-01 2.60e+02 angle pdb=" C22 9PE C1001 " pdb=" C21 9PE C1001 " pdb=" O22 9PE C1001 " ideal model delta sigma weight residual 124.92 80.06 44.86 3.00e+00 1.11e-01 2.24e+02 angle pdb=" O21 9PE C1001 " pdb=" C21 9PE C1001 " pdb=" O22 9PE C1001 " ideal model delta sigma weight residual 123.80 79.59 44.21 3.00e+00 1.11e-01 2.17e+02 angle pdb=" C LEU C 229 " pdb=" CA LEU C 229 " pdb=" CB LEU C 229 " ideal model delta sigma weight residual 117.23 110.20 7.03 1.36e+00 5.41e-01 2.68e+01 angle pdb=" C LEU A 229 " pdb=" CA LEU A 229 " pdb=" CB LEU A 229 " ideal model delta sigma weight residual 117.23 110.25 6.98 1.36e+00 5.41e-01 2.63e+01 ... (remaining 11212 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 4646 35.90 - 71.80: 272 71.80 - 107.70: 69 107.70 - 143.60: 59 143.60 - 179.50: 19 Dihedral angle restraints: 5065 sinusoidal: 2281 harmonic: 2784 Sorted by residual: dihedral pdb=" C37 YJ0 B 601 " pdb=" C34 YJ0 B 601 " pdb=" C35 YJ0 B 601 " pdb=" O39 YJ0 B 601 " ideal model delta sinusoidal sigma weight residual -67.37 112.13 -179.50 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O36 YJ0 D 601 " pdb=" C31 YJ0 D 601 " pdb=" C32 YJ0 D 601 " pdb=" O52 YJ0 D 601 " ideal model delta sinusoidal sigma weight residual 124.08 -59.37 -176.55 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O30 YJ0 D 601 " pdb=" C31 YJ0 D 601 " pdb=" C32 YJ0 D 601 " pdb=" O52 YJ0 D 601 " ideal model delta sinusoidal sigma weight residual 234.92 59.27 175.65 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.214: 1254 1.214 - 2.429: 0 2.429 - 3.643: 0 3.643 - 4.858: 4 4.858 - 6.072: 21 Chirality restraints: 1279 Sorted by residual: chirality pdb=" C12 YJ0 D 601 " pdb=" C11 YJ0 D 601 " pdb=" C13 YJ0 D 601 " pdb=" C7 YJ0 D 601 " both_signs ideal model delta sigma weight residual False 3.10 -2.98 6.07 2.00e-01 2.50e+01 9.22e+02 chirality pdb=" C8 YJ0 B 601 " pdb=" C10 YJ0 B 601 " pdb=" C7 YJ0 B 601 " pdb=" O9 YJ0 B 601 " both_signs ideal model delta sigma weight residual False -2.87 2.73 -5.60 2.00e-01 2.50e+01 7.84e+02 chirality pdb=" C16 YJ0 D 601 " pdb=" C11 YJ0 D 601 " pdb=" C15 YJ0 D 601 " pdb=" C17 YJ0 D 601 " both_signs ideal model delta sigma weight residual False -2.82 2.75 -5.57 2.00e-01 2.50e+01 7.74e+02 ... (remaining 1276 not shown) Planarity restraints: 1314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 YJ0 D 601 " -0.120 2.00e-02 2.50e+03 9.94e-02 1.24e+02 pdb=" C18 YJ0 D 601 " 0.148 2.00e-02 2.50e+03 pdb=" C19 YJ0 D 601 " 0.058 2.00e-02 2.50e+03 pdb=" C20 YJ0 D 601 " 0.012 2.00e-02 2.50e+03 pdb=" C24 YJ0 D 601 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 YJ0 B 601 " -0.029 2.00e-02 2.50e+03 2.46e-02 7.55e+00 pdb=" C18 YJ0 B 601 " 0.037 2.00e-02 2.50e+03 pdb=" C19 YJ0 B 601 " 0.014 2.00e-02 2.50e+03 pdb=" C20 YJ0 B 601 " 0.003 2.00e-02 2.50e+03 pdb=" C24 YJ0 B 601 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 77 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" CD GLN D 77 " 0.046 2.00e-02 2.50e+03 pdb=" OE1 GLN D 77 " -0.018 2.00e-02 2.50e+03 pdb=" NE2 GLN D 77 " -0.015 2.00e-02 2.50e+03 ... (remaining 1311 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1026 2.75 - 3.29: 7907 3.29 - 3.82: 13390 3.82 - 4.36: 14381 4.36 - 4.90: 25622 Nonbonded interactions: 62326 Sorted by model distance: nonbonded pdb=" OG1 THR B 273 " pdb=" OH TYR C 319 " model vdw 2.212 3.040 nonbonded pdb=" OH TYR A 319 " pdb=" OG1 THR D 273 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR B 94 " pdb=" OE1 GLU B 139 " model vdw 2.220 3.040 nonbonded pdb=" O ALA D 293 " pdb=" OG1 THR D 297 " model vdw 2.265 3.040 nonbonded pdb=" NH1 ARG D 212 " pdb=" O38 YJ0 D 601 " model vdw 2.276 3.120 ... (remaining 62321 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 70 through 182 or resid 197 through 601)) } 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.490 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8274 Z= 0.213 Angle : 1.142 48.366 11217 Z= 0.450 Chirality : 0.725 6.072 1279 Planarity : 0.005 0.099 1314 Dihedral : 30.563 179.495 3285 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.25 % Favored : 92.44 % Rotamer: Outliers : 0.25 % Allowed : 27.56 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.19 (0.28), residues: 952 helix: 1.72 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -2.74 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 174 TYR 0.028 0.001 TYR D 81 PHE 0.022 0.001 PHE D 79 TRP 0.021 0.001 TRP D 145 HIS 0.003 0.001 HIS D 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 ( 8274) covalent geometry : angle 1.14206 / 0.45 (11217) hydrogen bonds : bond 0.12780 / 8.47 ( 555) hydrogen bonds : angle 5.36865 / 3.76 ( 1641) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.7337 (mmm) cc_final: 0.7087 (tpp) outliers start: 2 outliers final: 2 residues processed: 130 average time/residue: 0.1224 time to fit residues: 20.2860 Evaluate side-chains 129 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain C residue 184 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.0470 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.221103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.166745 restraints weight = 8814.123| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.42 r_work: 0.3240 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8274 Z= 0.146 Angle : 1.257 46.091 11217 Z= 0.468 Chirality : 0.108 2.330 1279 Planarity : 0.004 0.040 1314 Dihedral : 24.913 179.723 1543 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.51 % Favored : 93.17 % Rotamer: Outliers : 2.49 % Allowed : 26.68 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.30 (0.28), residues: 952 helix: 1.77 (0.19), residues: 751 sheet: None (None), residues: 0 loop : -2.82 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 174 TYR 0.015 0.001 TYR D 81 PHE 0.017 0.001 PHE D 99 TRP 0.016 0.001 TRP D 287 HIS 0.002 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 ( 8274) covalent geometry : angle 1.25683 / 0.47 (11217) hydrogen bonds : bond 0.05047 / 3.39 ( 555) hydrogen bonds : angle 4.33002 / 3.10 ( 1641) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 14 residues processed: 134 average time/residue: 0.1154 time to fit residues: 20.1418 Evaluate side-chains 133 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 222 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 56 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 365 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.219720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.169650 restraints weight = 8678.832| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.59 r_work: 0.3201 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8274 Z= 0.153 Angle : 1.232 46.271 11217 Z= 0.460 Chirality : 0.104 2.166 1279 Planarity : 0.004 0.041 1314 Dihedral : 23.178 172.865 1541 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.62 % Favored : 93.17 % Rotamer: Outliers : 5.11 % Allowed : 24.81 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.32 (0.28), residues: 952 helix: 1.78 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -2.79 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 183 TYR 0.023 0.001 TYR C 184 PHE 0.013 0.001 PHE D 79 TRP 0.014 0.001 TRP D 287 HIS 0.003 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 8274) covalent geometry : angle 1.23176 / 0.46 (11217) hydrogen bonds : bond 0.05036 / 3.40 ( 555) hydrogen bonds : angle 4.21872 / 3.03 ( 1641) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 298 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7809 (tt) REVERT: D 77 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: D 145 TRP cc_start: 0.7784 (t60) cc_final: 0.7521 (t60) outliers start: 41 outliers final: 27 residues processed: 148 average time/residue: 0.1132 time to fit residues: 21.7947 Evaluate side-chains 148 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 297 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 91 optimal weight: 3.9990 chunk 12 optimal weight: 0.0050 chunk 50 optimal weight: 2.9990 chunk 81 optimal weight: 0.0060 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 30.0000 chunk 13 optimal weight: 2.9990 overall best weight: 0.9414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 365 GLN D 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.219963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.164466 restraints weight = 8822.863| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.43 r_work: 0.3208 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8274 Z= 0.148 Angle : 1.223 46.323 11217 Z= 0.455 Chirality : 0.101 2.080 1279 Planarity : 0.004 0.038 1314 Dihedral : 22.002 172.393 1538 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.41 % Favored : 93.38 % Rotamer: Outliers : 5.99 % Allowed : 25.19 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.39 (0.28), residues: 952 helix: 1.84 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -2.83 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 212 TYR 0.020 0.001 TYR C 184 PHE 0.014 0.001 PHE D 136 TRP 0.014 0.001 TRP D 287 HIS 0.004 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 8274) covalent geometry : angle 1.22265 / 0.45 (11217) hydrogen bonds : bond 0.04907 / 3.32 ( 555) hydrogen bonds : angle 4.09269 / 2.95 ( 1641) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 123 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 TYR cc_start: 0.7828 (t80) cc_final: 0.7537 (t80) REVERT: D 77 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7447 (tm-30) REVERT: D 251 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8098 (mp) outliers start: 48 outliers final: 33 residues processed: 155 average time/residue: 0.1098 time to fit residues: 22.4999 Evaluate side-chains 156 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 21 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.219386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.168285 restraints weight = 8823.440| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.53 r_work: 0.3207 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8274 Z= 0.148 Angle : 1.216 46.161 11217 Z= 0.453 Chirality : 0.100 2.045 1279 Planarity : 0.004 0.038 1314 Dihedral : 21.740 176.582 1538 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.72 % Favored : 93.07 % Rotamer: Outliers : 5.86 % Allowed : 25.06 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.43 (0.28), residues: 952 helix: 1.88 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -2.85 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 212 TYR 0.018 0.001 TYR C 184 PHE 0.013 0.001 PHE D 136 TRP 0.014 0.001 TRP D 287 HIS 0.003 0.001 HIS D 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 8274) covalent geometry : angle 1.21610 / 0.45 (11217) hydrogen bonds : bond 0.04929 / 3.34 ( 555) hydrogen bonds : angle 4.07748 / 2.93 ( 1641) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 TYR cc_start: 0.7859 (t80) cc_final: 0.7591 (t80) REVERT: B 298 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7849 (tt) REVERT: D 160 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7984 (pp) outliers start: 47 outliers final: 38 residues processed: 152 average time/residue: 0.1152 time to fit residues: 23.0039 Evaluate side-chains 159 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain D residue 82 ASN Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 17 optimal weight: 0.0570 chunk 18 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 48 optimal weight: 0.2980 chunk 42 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.223311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.164303 restraints weight = 8787.671| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.73 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8274 Z= 0.113 Angle : 1.194 46.494 11217 Z= 0.438 Chirality : 0.099 2.031 1279 Planarity : 0.003 0.035 1314 Dihedral : 21.227 176.774 1538 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.99 % Favored : 93.80 % Rotamer: Outliers : 4.24 % Allowed : 26.68 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.64 (0.28), residues: 952 helix: 2.04 (0.19), residues: 751 sheet: None (None), residues: 0 loop : -2.81 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 209 TYR 0.017 0.001 TYR C 184 PHE 0.011 0.001 PHE D 136 TRP 0.017 0.001 TRP D 287 HIS 0.001 0.000 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 ( 8274) covalent geometry : angle 1.19352 / 0.44 (11217) hydrogen bonds : bond 0.04321 / 2.93 ( 555) hydrogen bonds : angle 3.93240 / 2.82 ( 1641) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LYS cc_start: 0.7266 (tptp) cc_final: 0.6740 (pttt) REVERT: B 298 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7744 (tt) REVERT: C 237 MET cc_start: 0.7026 (mmt) cc_final: 0.6790 (mmp) REVERT: C 284 LYS cc_start: 0.7207 (tptp) cc_final: 0.6896 (pttt) REVERT: C 365 GLN cc_start: 0.6660 (OUTLIER) cc_final: 0.5430 (mp10) REVERT: D 77 GLN cc_start: 0.7293 (pp30) cc_final: 0.7083 (pp30) REVERT: D 143 ARG cc_start: 0.7887 (ttm-80) cc_final: 0.7613 (ttp-110) outliers start: 34 outliers final: 21 residues processed: 150 average time/residue: 0.1060 time to fit residues: 20.5855 Evaluate side-chains 141 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 59 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.215421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.160620 restraints weight = 8817.737| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.67 r_work: 0.3122 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8274 Z= 0.253 Angle : 1.260 47.275 11217 Z= 0.481 Chirality : 0.099 2.008 1279 Planarity : 0.004 0.039 1314 Dihedral : 21.152 178.170 1538 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.09 % Favored : 93.70 % Rotamer: Outliers : 4.74 % Allowed : 26.43 % Favored : 68.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.19 (0.28), residues: 952 helix: 1.70 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -2.86 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 364 TYR 0.021 0.002 TYR C 184 PHE 0.015 0.002 PHE C 269 TRP 0.010 0.001 TRP C 176 HIS 0.004 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.25 ( 8274) covalent geometry : angle 1.26011 / 0.48 (11217) hydrogen bonds : bond 0.05821 / 3.93 ( 555) hydrogen bonds : angle 4.22234 / 3.04 ( 1641) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 298 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7957 (tt) REVERT: D 77 GLN cc_start: 0.8031 (pp30) cc_final: 0.7310 (pp30) REVERT: D 85 GLU cc_start: 0.7723 (tt0) cc_final: 0.7519 (tt0) REVERT: D 167 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.6848 (t80) outliers start: 38 outliers final: 32 residues processed: 143 average time/residue: 0.1202 time to fit residues: 22.0224 Evaluate side-chains 154 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 8 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 365 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.219352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.165426 restraints weight = 8749.812| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.47 r_work: 0.3196 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8274 Z= 0.135 Angle : 1.214 47.218 11217 Z= 0.452 Chirality : 0.099 2.026 1279 Planarity : 0.004 0.034 1314 Dihedral : 20.894 177.444 1538 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.41 % Favored : 93.38 % Rotamer: Outliers : 4.36 % Allowed : 26.93 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.40 (0.28), residues: 952 helix: 1.86 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -2.87 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 143 TYR 0.019 0.001 TYR C 184 PHE 0.013 0.001 PHE D 136 TRP 0.013 0.001 TRP D 287 HIS 0.003 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 8274) covalent geometry : angle 1.21440 / 0.45 (11217) hydrogen bonds : bond 0.04751 / 3.23 ( 555) hydrogen bonds : angle 4.09335 / 2.95 ( 1641) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8340 (mmm) cc_final: 0.8069 (mmm) REVERT: B 298 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7956 (tt) REVERT: C 125 TYR cc_start: 0.5528 (OUTLIER) cc_final: 0.4365 (t80) REVERT: C 284 LYS cc_start: 0.7358 (tptp) cc_final: 0.6608 (pttt) REVERT: D 77 GLN cc_start: 0.8030 (pp30) cc_final: 0.7331 (pp30) REVERT: D 167 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.6799 (t80) REVERT: D 251 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8121 (mp) outliers start: 35 outliers final: 26 residues processed: 144 average time/residue: 0.1127 time to fit residues: 21.1472 Evaluate side-chains 148 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 125 TYR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 20.0000 chunk 65 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.218013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.164520 restraints weight = 8748.451| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.52 r_work: 0.3193 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8274 Z= 0.157 Angle : 1.222 47.206 11217 Z= 0.457 Chirality : 0.098 2.011 1279 Planarity : 0.004 0.037 1314 Dihedral : 20.603 174.486 1538 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.41 % Favored : 93.38 % Rotamer: Outliers : 4.74 % Allowed : 27.18 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.41 (0.28), residues: 952 helix: 1.85 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -2.81 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 143 TYR 0.020 0.001 TYR C 184 PHE 0.014 0.001 PHE D 136 TRP 0.013 0.001 TRP D 145 HIS 0.004 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 ( 8274) covalent geometry : angle 1.22236 / 0.46 (11217) hydrogen bonds : bond 0.05032 / 3.42 ( 555) hydrogen bonds : angle 4.06578 / 2.92 ( 1641) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8276 (mmm) cc_final: 0.7996 (mmm) REVERT: B 298 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7956 (tt) REVERT: C 125 TYR cc_start: 0.5545 (OUTLIER) cc_final: 0.4415 (t80) REVERT: C 239 ARG cc_start: 0.7120 (ttp80) cc_final: 0.6749 (tpt90) REVERT: D 77 GLN cc_start: 0.8078 (pp30) cc_final: 0.7368 (pp30) REVERT: D 167 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.6803 (t80) REVERT: D 251 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8124 (mp) outliers start: 38 outliers final: 32 residues processed: 140 average time/residue: 0.1210 time to fit residues: 21.8302 Evaluate side-chains 153 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 125 TYR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 69 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 90 optimal weight: 0.0570 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.219810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.166570 restraints weight = 8745.187| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.39 r_work: 0.3227 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8274 Z= 0.129 Angle : 1.212 47.010 11217 Z= 0.449 Chirality : 0.098 1.999 1279 Planarity : 0.004 0.082 1314 Dihedral : 20.309 174.035 1538 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.51 % Favored : 93.28 % Rotamer: Outliers : 4.36 % Allowed : 27.56 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.53 (0.28), residues: 952 helix: 1.94 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -2.76 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 143 TYR 0.019 0.001 TYR C 184 PHE 0.014 0.001 PHE D 79 TRP 0.015 0.001 TRP D 287 HIS 0.003 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 8274) covalent geometry : angle 1.21179 / 0.45 (11217) hydrogen bonds : bond 0.04624 / 3.15 ( 555) hydrogen bonds : angle 4.01285 / 2.88 ( 1641) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8268 (mmm) cc_final: 0.7991 (mmm) REVERT: A 284 LYS cc_start: 0.7427 (tptp) cc_final: 0.6616 (pttt) REVERT: B 79 PHE cc_start: 0.8572 (t80) cc_final: 0.8370 (t80) REVERT: B 298 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7898 (tt) REVERT: C 125 TYR cc_start: 0.5479 (OUTLIER) cc_final: 0.4359 (t80) REVERT: C 284 LYS cc_start: 0.7327 (tptp) cc_final: 0.6608 (pttt) REVERT: D 77 GLN cc_start: 0.8067 (pp30) cc_final: 0.7346 (pp30) REVERT: D 167 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.6835 (t80) REVERT: D 251 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8072 (mp) outliers start: 35 outliers final: 26 residues processed: 142 average time/residue: 0.1159 time to fit residues: 21.2520 Evaluate side-chains 147 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 125 TYR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 283 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 365 GLN Chi-restraints excluded: chain D residue 167 PHE Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 34 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 68 optimal weight: 0.0670 chunk 21 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.218412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.165605 restraints weight = 8763.193| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.55 r_work: 0.3200 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8274 Z= 0.146 Angle : 1.217 47.125 11217 Z= 0.454 Chirality : 0.098 2.004 1279 Planarity : 0.004 0.075 1314 Dihedral : 20.202 175.718 1538 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.30 % Favored : 93.49 % Rotamer: Outliers : 4.61 % Allowed : 27.43 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.51 (0.28), residues: 952 helix: 1.92 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -2.77 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 143 TYR 0.019 0.001 TYR C 184 PHE 0.029 0.001 PHE D 79 TRP 0.014 0.001 TRP D 145 HIS 0.003 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 8274) covalent geometry : angle 1.21709 / 0.45 (11217) hydrogen bonds : bond 0.04845 / 3.30 ( 555) hydrogen bonds : angle 4.01853 / 2.89 ( 1641) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1985.60 seconds wall clock time: 34 minutes 43.82 seconds (2083.82 seconds total)