Starting phenix.real_space_refine on Fri Sep 11 08:05:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24vl_69843/09_2026/24vl_69843.cif Found real_map, /net/cci-nas-00/data/ceres_data/24vl_69843/09_2026/24vl_69843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/24vl_69843/09_2026/24vl_69843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24vl_69843/09_2026/24vl_69843.map" model { file = "/net/cci-nas-00/data/ceres_data/24vl_69843/09_2026/24vl_69843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24vl_69843/09_2026/24vl_69843.cif" } resolution = 4.05 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= 0.009 sd= 0.072 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 3 5.49 5 S 37 5.16 5 C 5508 2.51 5 N 1319 2.21 5 O 1397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 8264 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: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 2000 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 4, 'TRANS': 241} 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: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 121 Unusual residues: {'9PE': 1, 'YJ0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 121 Unusual residues: {'9PE': 1, 'YJ0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 1.43, per 1000 atoms: 0.17 Number of scatterers: 8264 At special positions: 0 Unit cell: (81.525, 106.526, 115.222, 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 37 16.00 P 3 15.00 O 1397 8.00 N 1319 7.00 C 5508 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: 0.77 Conformation dependent library (CDL) restraints added in 193.4 milliseconds 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1796 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 80.6% alpha, 0.0% 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 112 through 117 removed outlier: 3.560A pdb=" N ARG A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 144 removed outlier: 3.529A pdb=" N LEU A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 178 removed outlier: 3.991A pdb=" N TRP A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 208 Processing helix chain 'A' and resid 230 through 238 removed outlier: 4.430A pdb=" N ILE A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 257 Processing helix chain 'A' and resid 257 through 283 removed outlier: 3.595A pdb=" N LEU A 261 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 289 removed outlier: 3.554A pdb=" N VAL A 289 " --> pdb=" O VAL A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.983A pdb=" N ALA A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 345 removed outlier: 3.614A pdb=" N LEU A 331 " --> pdb=" O TRP A 327 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ILE A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 366 removed outlier: 3.746A pdb=" N LEU A 351 " --> pdb=" O PRO A 347 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 85 removed outlier: 3.575A pdb=" N GLU B 85 " --> pdb=" O TYR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 114 removed outlier: 4.059A pdb=" N HIS B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 147 removed outlier: 3.676A pdb=" N SER B 121 " --> pdb=" O TYR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 Processing helix chain 'B' and resid 165 through 182 removed outlier: 3.528A pdb=" N LEU B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 4.224A pdb=" N ILE B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 removed outlier: 3.530A pdb=" N ALA B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 253 Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 286 through 305 removed outlier: 3.921A pdb=" N ALA B 305 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 326 removed outlier: 3.983A pdb=" N GLY B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU B 311 " --> pdb=" O PRO B 307 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 85 Processing helix chain 'C' and resid 91 through 112 removed outlier: 4.394A pdb=" N HIS C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 147 removed outlier: 3.789A pdb=" N GLY C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 155 through 164 Processing helix chain 'C' and resid 165 through 183 Processing helix chain 'C' and resid 201 through 209 removed outlier: 4.014A pdb=" N LEU C 205 " --> pdb=" O PHE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 227 Processing helix chain 'C' and resid 229 through 253 removed outlier: 3.793A pdb=" N ALA C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 274 Processing helix chain 'C' and resid 288 through 326 removed outlier: 4.079A pdb=" N LEU C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) Proline residue: C 307 - end of helix Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 93 through 114 removed outlier: 3.747A pdb=" N ILE D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 145 removed outlier: 4.048A 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 Processing helix chain 'D' and resid 202 through 209 Processing helix chain 'D' and resid 214 through 227 Processing helix chain 'D' and resid 230 through 253 Processing helix chain 'D' and resid 263 through 275 Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.872A pdb=" N ALA D 305 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 326 removed outlier: 3.592A pdb=" N GLY D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) 566 hydrogen bonds defined for protein. 1695 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: 1.19 Time building geometry restraints manager: 1.01 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: 1165 1.31 - 1.43: 2567 1.43 - 1.56: 4709 1.56 - 1.69: 6 1.69 - 1.81: 50 Bond restraints: 8497 Sorted by residual: bond pdb=" N THR D 233 " pdb=" CA THR D 233 " ideal model delta sigma weight residual 1.459 1.408 0.051 1.18e-02 7.18e+03 1.86e+01 bond pdb=" CA THR D 233 " pdb=" C THR D 233 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.24e-02 6.50e+03 1.58e+01 bond pdb=" CA SER B 302 " pdb=" C SER B 302 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.29e-02 6.01e+03 1.57e+01 bond pdb=" C31 9PE B 902 " pdb=" O31 9PE B 902 " ideal model delta sigma weight residual 1.325 1.399 -0.074 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C31 9PE A1001 " pdb=" O31 9PE A1001 " ideal model delta sigma weight residual 1.325 1.399 -0.074 2.00e-02 2.50e+03 1.39e+01 ... (remaining 8492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 11267 3.16 - 6.33: 206 6.33 - 9.49: 44 9.49 - 12.65: 10 12.65 - 15.82: 1 Bond angle restraints: 11528 Sorted by residual: angle pdb=" C28 YJ0 B 901 " pdb=" C53 YJ0 B 901 " pdb=" O54 YJ0 B 901 " ideal model delta sigma weight residual 103.45 119.27 -15.82 3.00e+00 1.11e-01 2.78e+01 angle pdb=" N GLU B 321 " pdb=" CA GLU B 321 " pdb=" CB GLU B 321 " ideal model delta sigma weight residual 110.28 116.80 -6.52 1.55e+00 4.16e-01 1.77e+01 angle pdb=" O12 9PE B 902 " pdb=" P 9PE B 902 " pdb=" O14 9PE B 902 " ideal model delta sigma weight residual 120.90 108.97 11.93 3.00e+00 1.11e-01 1.58e+01 angle pdb=" N SER B 302 " pdb=" CA SER B 302 " pdb=" C SER B 302 " ideal model delta sigma weight residual 111.40 106.64 4.76 1.22e+00 6.72e-01 1.52e+01 angle pdb=" O12 9PE A1001 " pdb=" P 9PE A1001 " pdb=" O14 9PE A1001 " ideal model delta sigma weight residual 120.90 109.28 11.62 3.00e+00 1.11e-01 1.50e+01 ... (remaining 11523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 4939 35.81 - 71.62: 190 71.62 - 107.43: 108 107.43 - 143.24: 78 143.24 - 179.06: 26 Dihedral angle restraints: 5341 sinusoidal: 2528 harmonic: 2813 Sorted by residual: dihedral pdb=" O30 YJ0 D 901 " pdb=" C31 YJ0 D 901 " pdb=" C32 YJ0 D 901 " pdb=" O52 YJ0 D 901 " ideal model delta sinusoidal sigma weight residual -125.08 53.98 -179.06 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N 9PE A1001 " pdb=" C11 9PE A1001 " pdb=" C12 9PE A1001 " pdb=" O13 9PE A1001 " ideal model delta sinusoidal sigma weight residual -66.84 107.78 -174.62 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O36 YJ0 D 901 " pdb=" C31 YJ0 D 901 " pdb=" C32 YJ0 D 901 " pdb=" O52 YJ0 D 901 " ideal model delta sinusoidal sigma weight residual 124.08 -64.77 -171.15 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 5338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.215: 1285 1.215 - 2.430: 0 2.430 - 3.644: 0 3.644 - 4.859: 4 4.859 - 6.074: 29 Chirality restraints: 1318 Sorted by residual: chirality pdb=" C12 YJ0 D 901 " pdb=" C11 YJ0 D 901 " pdb=" C13 YJ0 D 901 " pdb=" C7 YJ0 D 901 " 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=" C12 YJ0 C 901 " pdb=" C11 YJ0 C 901 " pdb=" C13 YJ0 C 901 " pdb=" C7 YJ0 C 901 " both_signs ideal model delta sigma weight residual False 3.10 -2.95 6.05 2.00e-01 2.50e+01 9.15e+02 chirality pdb=" C8 YJ0 B 901 " pdb=" C10 YJ0 B 901 " pdb=" C7 YJ0 B 901 " pdb=" O9 YJ0 B 901 " both_signs ideal model delta sigma weight residual False -2.87 2.74 -5.61 2.00e-01 2.50e+01 7.86e+02 ... (remaining 1315 not shown) Planarity restraints: 1334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 YJ0 C 901 " -0.176 2.00e-02 2.50e+03 1.48e-01 2.72e+02 pdb=" C18 YJ0 C 901 " 0.215 2.00e-02 2.50e+03 pdb=" C19 YJ0 C 901 " 0.098 2.00e-02 2.50e+03 pdb=" C20 YJ0 C 901 " 0.009 2.00e-02 2.50e+03 pdb=" C24 YJ0 C 901 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 YJ0 D 901 " 0.150 2.00e-02 2.50e+03 1.25e-01 1.95e+02 pdb=" C18 YJ0 D 901 " -0.187 2.00e-02 2.50e+03 pdb=" C19 YJ0 D 901 " -0.073 2.00e-02 2.50e+03 pdb=" C20 YJ0 D 901 " -0.013 2.00e-02 2.50e+03 pdb=" C24 YJ0 D 901 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 301 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C VAL B 301 " 0.060 2.00e-02 2.50e+03 pdb=" O VAL B 301 " -0.022 2.00e-02 2.50e+03 pdb=" N SER B 302 " -0.020 2.00e-02 2.50e+03 ... (remaining 1331 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1203 2.75 - 3.29: 9189 3.29 - 3.82: 14037 3.82 - 4.36: 15312 4.36 - 4.90: 25506 Nonbonded interactions: 65247 Sorted by model distance: nonbonded pdb=" O ALA D 293 " pdb=" OG1 THR D 297 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR B 283 " pdb=" OD1 ASP C 281 " model vdw 2.223 3.040 nonbonded pdb=" O SER C 109 " pdb=" OG SER C 112 " model vdw 2.225 3.040 nonbonded pdb=" NZ LYS B 229 " pdb=" O73 YJ0 C 901 " model vdw 2.232 3.120 nonbonded pdb=" O LEU A 158 " pdb=" OG1 THR A 161 " model vdw 2.245 3.040 ... (remaining 65242 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 'B' and resid 70 through 901) selection = (chain 'C' and (resid 70 through 182 or resid 197 through 901)) selection = (chain 'D' and (resid 70 through 182 or resid 197 through 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.260 Find NCS groups from input model: 0.170 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 : 0.006 0.074 8497 Z= 0.294 Angle : 1.049 15.817 11528 Z= 0.462 Chirality : 0.826 6.074 1318 Planarity : 0.007 0.148 1334 Dihedral : 32.245 179.055 3545 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.84 % Favored : 94.06 % Rotamer: Outliers : 0.12 % Allowed : 0.37 % Favored : 99.51 % 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: 0.65 (0.28), residues: 959 helix: 1.41 (0.19), residues: 732 sheet: None (None), residues: 0 loop : -2.93 (0.36), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 154 TYR 0.022 0.001 TYR B 283 PHE 0.037 0.002 PHE D 79 TRP 0.026 0.001 TRP D 145 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.29 ( 8497) covalent geometry : angle 1.04861 / 0.46 (11528) hydrogen bonds : bond 0.10997 / 6.90 ( 566) hydrogen bonds : angle 5.25557 / 3.78 ( 1695) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 0.311 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: symmetry clash REVERT: A 284 LYS cc_start: 0.8965 (pptt) cc_final: 0.8426 (tttt) REVERT: B 106 LEU cc_start: 0.9062 (mt) cc_final: 0.8850 (mt) REVERT: B 227 HIS cc_start: 0.8992 (m90) cc_final: 0.8580 (m-70) REVERT: B 259 HIS cc_start: 0.8219 (m-70) cc_final: 0.7998 (m90) REVERT: C 141 PHE cc_start: 0.9558 (m-80) cc_final: 0.9190 (m-80) REVERT: C 167 PHE cc_start: 0.8713 (m-10) cc_final: 0.8339 (m-80) REVERT: C 320 GLN cc_start: 0.9309 (tm-30) cc_final: 0.8896 (tm-30) outliers start: 1 outliers final: 1 residues processed: 233 average time/residue: 0.0700 time to fit residues: 23.0559 Evaluate side-chains 176 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 259 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.106817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.079722 restraints weight = 28736.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.082078 restraints weight = 16712.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.083636 restraints weight = 11715.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.084644 restraints weight = 9221.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.085332 restraints weight = 7885.915| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8497 Z= 0.164 Angle : 1.274 36.424 11528 Z= 0.490 Chirality : 0.138 2.365 1318 Planarity : 0.004 0.057 1334 Dihedral : 27.974 177.979 1790 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.80 % Favored : 95.10 % Rotamer: Outliers : 0.37 % Allowed : 6.04 % Favored : 93.59 % 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: 1.02 (0.28), residues: 959 helix: 1.65 (0.19), residues: 739 sheet: None (None), residues: 0 loop : -2.82 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 209 TYR 0.014 0.001 TYR D 73 PHE 0.025 0.002 PHE D 79 TRP 0.012 0.001 TRP D 145 HIS 0.007 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 ( 8497) covalent geometry : angle 1.27364 / 0.49 (11528) hydrogen bonds : bond 0.05146 / 3.38 ( 566) hydrogen bonds : angle 4.34785 / 3.16 ( 1695) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 242 time to evaluate : 0.268 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 PHE cc_start: 0.9201 (m-80) cc_final: 0.8973 (m-80) REVERT: A 241 ASP cc_start: 0.7521 (t70) cc_final: 0.7183 (t0) REVERT: A 280 TYR cc_start: 0.8352 (t80) cc_final: 0.8070 (t80) REVERT: A 362 GLN cc_start: 0.9442 (tm-30) cc_final: 0.9091 (tm-30) REVERT: B 171 ASP cc_start: 0.8836 (m-30) cc_final: 0.8536 (m-30) REVERT: B 227 HIS cc_start: 0.9060 (m90) cc_final: 0.8363 (m90) REVERT: C 122 GLU cc_start: 0.8479 (mp0) cc_final: 0.8253 (mp0) REVERT: C 141 PHE cc_start: 0.9527 (m-80) cc_final: 0.9140 (m-80) REVERT: C 167 PHE cc_start: 0.8856 (m-10) cc_final: 0.8520 (m-80) REVERT: C 173 MET cc_start: 0.8849 (ptt) cc_final: 0.8203 (ppp) REVERT: C 320 GLN cc_start: 0.9322 (tm-30) cc_final: 0.8912 (tm-30) REVERT: D 236 TYR cc_start: 0.8971 (t80) cc_final: 0.8696 (t80) REVERT: D 325 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7544 (tm-30) outliers start: 3 outliers final: 1 residues processed: 244 average time/residue: 0.0756 time to fit residues: 26.2671 Evaluate side-chains 190 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 77 GLN B 259 HIS D 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.106124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.079623 restraints weight = 28430.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.081982 restraints weight = 16459.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.083506 restraints weight = 11417.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.084499 restraints weight = 8936.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.085173 restraints weight = 7613.411| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8497 Z= 0.169 Angle : 1.250 35.475 11528 Z= 0.481 Chirality : 0.131 2.195 1318 Planarity : 0.004 0.031 1334 Dihedral : 26.078 174.399 1790 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.32 % Favored : 94.58 % Rotamer: Outliers : 0.25 % Allowed : 4.93 % Favored : 94.82 % 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: 1.14 (0.28), residues: 959 helix: 1.75 (0.19), residues: 735 sheet: None (None), residues: 0 loop : -2.79 (0.36), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 206 TYR 0.016 0.001 TYR D 73 PHE 0.018 0.001 PHE D 79 TRP 0.012 0.001 TRP D 145 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 ( 8497) covalent geometry : angle 1.25007 / 0.48 (11528) hydrogen bonds : bond 0.04978 / 3.27 ( 566) hydrogen bonds : angle 4.16073 / 3.02 ( 1695) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 245 time to evaluate : 0.188 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: symmetry clash revert: symmetry clash REVERT: A 167 PHE cc_start: 0.9229 (m-10) cc_final: 0.8983 (m-80) REVERT: B 227 HIS cc_start: 0.9092 (m90) cc_final: 0.8849 (m-70) REVERT: B 259 HIS cc_start: 0.8180 (m-70) cc_final: 0.7763 (m90) REVERT: B 283 TYR cc_start: 0.8374 (p90) cc_final: 0.7623 (p90) REVERT: B 318 LYS cc_start: 0.9499 (tppt) cc_final: 0.9114 (tppp) REVERT: B 321 GLU cc_start: 0.9383 (pp20) cc_final: 0.9181 (pp20) REVERT: C 122 GLU cc_start: 0.8502 (mp0) cc_final: 0.8169 (mp0) REVERT: C 141 PHE cc_start: 0.9515 (m-80) cc_final: 0.9131 (m-80) REVERT: C 167 PHE cc_start: 0.8801 (m-10) cc_final: 0.8480 (m-80) REVERT: C 253 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8424 (tp30) REVERT: C 320 GLN cc_start: 0.9353 (tm-30) cc_final: 0.8901 (tm-30) REVERT: D 325 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7510 (tm-30) outliers start: 2 outliers final: 0 residues processed: 246 average time/residue: 0.0764 time to fit residues: 26.2639 Evaluate side-chains 182 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 92 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 0.1980 chunk 58 optimal weight: 8.9990 chunk 89 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 30 optimal weight: 0.0050 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.108903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.082301 restraints weight = 28851.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.084813 restraints weight = 16581.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.086444 restraints weight = 11435.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.087593 restraints weight = 8914.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.088345 restraints weight = 7541.518| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8497 Z= 0.138 Angle : 1.229 35.269 11528 Z= 0.473 Chirality : 0.128 2.152 1318 Planarity : 0.003 0.031 1334 Dihedral : 25.484 173.836 1790 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.01 % Favored : 94.89 % Rotamer: Outliers : 0.25 % Allowed : 3.58 % Favored : 96.18 % 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: 1.28 (0.28), residues: 959 helix: 1.81 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -2.66 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 206 TYR 0.016 0.001 TYR D 73 PHE 0.025 0.001 PHE A 162 TRP 0.016 0.001 TRP A 327 HIS 0.002 0.000 HIS C 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 ( 8497) covalent geometry : angle 1.22864 / 0.47 (11528) hydrogen bonds : bond 0.04703 / 3.12 ( 566) hydrogen bonds : angle 3.97109 / 2.92 ( 1695) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 242 time to evaluate : 0.341 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: A 167 PHE cc_start: 0.9218 (m-10) cc_final: 0.8963 (m-80) REVERT: B 227 HIS cc_start: 0.9060 (m90) cc_final: 0.8643 (m90) REVERT: B 283 TYR cc_start: 0.8384 (p90) cc_final: 0.7634 (p90) REVERT: C 86 ARG cc_start: 0.9094 (ptt90) cc_final: 0.8748 (ptt-90) REVERT: C 122 GLU cc_start: 0.8368 (mp0) cc_final: 0.8049 (mp0) REVERT: C 141 PHE cc_start: 0.9525 (m-80) cc_final: 0.9144 (m-80) REVERT: C 173 MET cc_start: 0.8845 (ptt) cc_final: 0.8219 (ppp) REVERT: C 253 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8263 (tp30) REVERT: C 320 GLN cc_start: 0.9344 (tm-30) cc_final: 0.8472 (tm-30) REVERT: C 321 GLU cc_start: 0.9380 (mm-30) cc_final: 0.8678 (mm-30) REVERT: D 302 SER cc_start: 0.9089 (m) cc_final: 0.8709 (p) REVERT: D 325 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7419 (tm-30) outliers start: 2 outliers final: 0 residues processed: 243 average time/residue: 0.0829 time to fit residues: 28.2749 Evaluate side-chains 195 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 83 optimal weight: 0.1980 chunk 73 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 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 = 0.3832 r_free = 0.3832 target = 0.108703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.082099 restraints weight = 28394.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.084548 restraints weight = 16408.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.086166 restraints weight = 11383.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.087223 restraints weight = 8869.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.087995 restraints weight = 7546.044| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8497 Z= 0.132 Angle : 1.218 35.090 11528 Z= 0.466 Chirality : 0.127 2.112 1318 Planarity : 0.003 0.037 1334 Dihedral : 24.925 173.555 1790 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.32 % Favored : 94.58 % Rotamer: Outliers : 0.12 % Allowed : 1.85 % Favored : 98.03 % 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: 959 helix: 1.82 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -2.58 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 209 TYR 0.017 0.001 TYR A 280 PHE 0.021 0.001 PHE A 162 TRP 0.013 0.001 TRP D 145 HIS 0.002 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 ( 8497) covalent geometry : angle 1.21818 / 0.47 (11528) hydrogen bonds : bond 0.04489 / 2.99 ( 566) hydrogen bonds : angle 3.88113 / 2.84 ( 1695) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 246 time to evaluate : 0.328 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: A 167 PHE cc_start: 0.9234 (m-10) cc_final: 0.9034 (m-80) REVERT: B 106 LEU cc_start: 0.9094 (mt) cc_final: 0.8886 (mt) REVERT: B 206 ARG cc_start: 0.8904 (mpp80) cc_final: 0.8553 (mmt180) REVERT: B 227 HIS cc_start: 0.9107 (m90) cc_final: 0.8729 (m90) REVERT: B 283 TYR cc_start: 0.8473 (p90) cc_final: 0.7733 (p90) REVERT: B 320 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8693 (pp30) REVERT: C 86 ARG cc_start: 0.9095 (ptt90) cc_final: 0.8731 (ptt-90) REVERT: C 122 GLU cc_start: 0.8405 (mp0) cc_final: 0.8062 (mp0) REVERT: C 141 PHE cc_start: 0.9522 (m-80) cc_final: 0.9180 (m-80) REVERT: C 218 LYS cc_start: 0.9361 (mtmm) cc_final: 0.9120 (mttp) REVERT: C 320 GLN cc_start: 0.9352 (tm-30) cc_final: 0.8481 (tm-30) REVERT: C 321 GLU cc_start: 0.9393 (mm-30) cc_final: 0.8717 (mm-30) REVERT: D 201 PHE cc_start: 0.6552 (m-80) cc_final: 0.6319 (m-80) REVERT: D 325 GLN cc_start: 0.7723 (tm-30) cc_final: 0.7397 (tm-30) outliers start: 1 outliers final: 0 residues processed: 246 average time/residue: 0.0782 time to fit residues: 27.4528 Evaluate side-chains 188 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 62 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 33 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.107031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.080693 restraints weight = 28249.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.083089 restraints weight = 16243.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.084680 restraints weight = 11298.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.085770 restraints weight = 8832.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.086439 restraints weight = 7478.006| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8497 Z= 0.155 Angle : 1.225 35.135 11528 Z= 0.474 Chirality : 0.126 2.086 1318 Planarity : 0.004 0.036 1334 Dihedral : 24.585 173.629 1790 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.42 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: 1.36 (0.28), residues: 959 helix: 1.86 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -2.56 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 209 TYR 0.018 0.001 TYR A 280 PHE 0.020 0.001 PHE D 303 TRP 0.042 0.001 TRP A 327 HIS 0.002 0.001 HIS C 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 8497) covalent geometry : angle 1.22545 / 0.47 (11528) hydrogen bonds : bond 0.04662 / 3.12 ( 566) hydrogen bonds : angle 3.99414 / 2.91 ( 1695) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.306 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: symmetry clash revert: symmetry clash REVERT: A 167 PHE cc_start: 0.9253 (m-10) cc_final: 0.9040 (m-80) REVERT: B 106 LEU cc_start: 0.9141 (mt) cc_final: 0.8935 (mt) REVERT: B 206 ARG cc_start: 0.8950 (mpp80) cc_final: 0.8575 (mmt180) REVERT: B 227 HIS cc_start: 0.9179 (m90) cc_final: 0.8908 (m-70) REVERT: B 283 TYR cc_start: 0.8489 (p90) cc_final: 0.7721 (p90) REVERT: C 86 ARG cc_start: 0.9088 (ptt90) cc_final: 0.8732 (ptt-90) REVERT: C 122 GLU cc_start: 0.8443 (mp0) cc_final: 0.8025 (mp0) REVERT: C 141 PHE cc_start: 0.9502 (m-80) cc_final: 0.9174 (m-80) REVERT: C 209 ARG cc_start: 0.8784 (pmt-80) cc_final: 0.8431 (ttp80) REVERT: C 253 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8286 (tp30) REVERT: C 259 HIS cc_start: 0.8881 (m170) cc_final: 0.8521 (m170) REVERT: C 318 LYS cc_start: 0.9708 (tptp) cc_final: 0.9504 (tptt) REVERT: C 320 GLN cc_start: 0.9349 (tm-30) cc_final: 0.8462 (tm-30) REVERT: C 321 GLU cc_start: 0.9406 (mm-30) cc_final: 0.8637 (mm-30) REVERT: D 130 ILE cc_start: 0.9338 (tp) cc_final: 0.9134 (pt) REVERT: D 201 PHE cc_start: 0.6642 (m-80) cc_final: 0.6404 (m-80) REVERT: D 236 TYR cc_start: 0.9082 (t80) cc_final: 0.8859 (t80) REVERT: D 325 GLN cc_start: 0.7748 (tm-30) cc_final: 0.7410 (tm-30) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.0685 time to fit residues: 24.2212 Evaluate side-chains 186 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 82 optimal weight: 0.0060 chunk 41 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.107773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081011 restraints weight = 28744.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.083414 restraints weight = 16695.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.085081 restraints weight = 11636.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.086177 restraints weight = 9061.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.086948 restraints weight = 7668.237| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8497 Z= 0.137 Angle : 1.222 34.868 11528 Z= 0.472 Chirality : 0.125 2.066 1318 Planarity : 0.004 0.068 1334 Dihedral : 24.250 173.206 1790 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.42 % Favored : 94.47 % Rotamer: Outliers : 0.12 % Allowed : 1.85 % Favored : 98.03 % 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: 1.33 (0.28), residues: 959 helix: 1.80 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -2.52 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 209 TYR 0.020 0.001 TYR A 280 PHE 0.017 0.001 PHE A 162 TRP 0.038 0.001 TRP A 327 HIS 0.003 0.001 HIS D 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 8497) covalent geometry : angle 1.22241 / 0.47 (11528) hydrogen bonds : bond 0.04597 / 3.05 ( 566) hydrogen bonds : angle 3.92939 / 2.88 ( 1695) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 0.336 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: symmetry clash REVERT: A 167 PHE cc_start: 0.9217 (m-10) cc_final: 0.8999 (m-80) REVERT: B 106 LEU cc_start: 0.9157 (mt) cc_final: 0.8957 (mt) REVERT: B 227 HIS cc_start: 0.9162 (m90) cc_final: 0.8935 (m-70) REVERT: B 248 LEU cc_start: 0.9438 (mt) cc_final: 0.9231 (mt) REVERT: B 283 TYR cc_start: 0.8505 (p90) cc_final: 0.7752 (p90) REVERT: B 320 GLN cc_start: 0.8962 (tm-30) cc_final: 0.8645 (pp30) REVERT: C 122 GLU cc_start: 0.8375 (mp0) cc_final: 0.7968 (mp0) REVERT: C 141 PHE cc_start: 0.9506 (m-80) cc_final: 0.9182 (m-80) REVERT: C 173 MET cc_start: 0.8828 (ptt) cc_final: 0.8269 (ppp) REVERT: C 209 ARG cc_start: 0.8849 (pmt-80) cc_final: 0.8422 (ttp80) REVERT: C 218 LYS cc_start: 0.9336 (mtmm) cc_final: 0.9100 (mttp) REVERT: C 259 HIS cc_start: 0.8913 (m170) cc_final: 0.8570 (m170) REVERT: C 318 LYS cc_start: 0.9705 (tptp) cc_final: 0.9504 (tptt) REVERT: C 320 GLN cc_start: 0.9361 (tm-30) cc_final: 0.8496 (tm-30) REVERT: C 321 GLU cc_start: 0.9414 (mm-30) cc_final: 0.8642 (mm-30) REVERT: D 201 PHE cc_start: 0.6677 (m-80) cc_final: 0.6462 (m-80) REVERT: D 325 GLN cc_start: 0.7743 (tm-30) cc_final: 0.7393 (tm-30) outliers start: 1 outliers final: 0 residues processed: 244 average time/residue: 0.0760 time to fit residues: 26.6884 Evaluate side-chains 193 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 31 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.107838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.081064 restraints weight = 28509.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.083480 restraints weight = 16559.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.085092 restraints weight = 11555.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.086165 restraints weight = 9065.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.086881 restraints weight = 7709.662| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 8497 Z= 0.144 Angle : 1.222 34.752 11528 Z= 0.474 Chirality : 0.125 2.051 1318 Planarity : 0.004 0.039 1334 Dihedral : 24.051 173.399 1790 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.11 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 959 helix: 1.76 (0.19), residues: 745 sheet: None (None), residues: 0 loop : -2.47 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 206 TYR 0.021 0.001 TYR A 280 PHE 0.013 0.001 PHE D 303 TRP 0.026 0.001 TRP A 327 HIS 0.003 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 8497) covalent geometry : angle 1.22210 / 0.47 (11528) hydrogen bonds : bond 0.04558 / 3.03 ( 566) hydrogen bonds : angle 3.94394 / 2.88 ( 1695) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.307 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: symmetry clash revert: symmetry clash REVERT: A 167 PHE cc_start: 0.9251 (m-10) cc_final: 0.8997 (m-80) REVERT: A 280 TYR cc_start: 0.8517 (t80) cc_final: 0.7614 (t80) REVERT: A 296 MET cc_start: 0.7341 (tmm) cc_final: 0.7126 (tmm) REVERT: B 106 LEU cc_start: 0.9194 (mt) cc_final: 0.8990 (mt) REVERT: B 206 ARG cc_start: 0.9024 (ptp-110) cc_final: 0.8590 (ptp-110) REVERT: B 283 TYR cc_start: 0.8530 (p90) cc_final: 0.7733 (p90) REVERT: C 122 GLU cc_start: 0.8369 (mp0) cc_final: 0.7973 (mp0) REVERT: C 141 PHE cc_start: 0.9498 (m-80) cc_final: 0.9169 (m-80) REVERT: C 173 MET cc_start: 0.8872 (ptt) cc_final: 0.8271 (ppp) REVERT: C 209 ARG cc_start: 0.9092 (pmt-80) cc_final: 0.8641 (ttp80) REVERT: C 210 MET cc_start: 0.7273 (tmm) cc_final: 0.7001 (tmm) REVERT: C 218 LYS cc_start: 0.9347 (mtmm) cc_final: 0.9142 (ptpt) REVERT: C 253 GLU cc_start: 0.8729 (tp30) cc_final: 0.8384 (tp30) REVERT: C 259 HIS cc_start: 0.8732 (m170) cc_final: 0.8368 (m170) REVERT: C 320 GLN cc_start: 0.9327 (tm-30) cc_final: 0.8851 (tm-30) REVERT: D 201 PHE cc_start: 0.6703 (m-80) cc_final: 0.6483 (m-80) REVERT: D 325 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7425 (tm-30) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.0758 time to fit residues: 25.8839 Evaluate side-chains 194 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.103752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.077115 restraints weight = 29425.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.079374 restraints weight = 17107.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.080886 restraints weight = 11916.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.081918 restraints weight = 9361.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.082528 restraints weight = 7954.215| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 8497 Z= 0.233 Angle : 1.276 35.176 11528 Z= 0.511 Chirality : 0.125 2.033 1318 Planarity : 0.004 0.045 1334 Dihedral : 23.991 172.978 1790 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.84 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: 0.85 (0.28), residues: 959 helix: 1.48 (0.19), residues: 739 sheet: None (None), residues: 0 loop : -2.70 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 239 TYR 0.022 0.002 TYR A 280 PHE 0.034 0.002 PHE B 136 TRP 0.036 0.002 TRP A 327 HIS 0.005 0.001 HIS B 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.23 ( 8497) covalent geometry : angle 1.27596 / 0.51 (11528) hydrogen bonds : bond 0.05212 / 3.48 ( 566) hydrogen bonds : angle 4.34773 / 3.18 ( 1695) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.261 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: A 167 PHE cc_start: 0.9248 (m-10) cc_final: 0.9032 (m-80) REVERT: A 280 TYR cc_start: 0.8646 (t80) cc_final: 0.7686 (t80) REVERT: B 129 GLU cc_start: 0.8898 (pm20) cc_final: 0.8638 (pm20) REVERT: B 206 ARG cc_start: 0.9105 (ptp-110) cc_final: 0.8899 (ptp90) REVERT: B 227 HIS cc_start: 0.9100 (m90) cc_final: 0.8596 (m90) REVERT: B 283 TYR cc_start: 0.8569 (p90) cc_final: 0.7691 (p90) REVERT: B 303 PHE cc_start: 0.8806 (m-80) cc_final: 0.8347 (m-80) REVERT: C 141 PHE cc_start: 0.9507 (m-80) cc_final: 0.9186 (m-80) REVERT: C 218 LYS cc_start: 0.9315 (mtmm) cc_final: 0.9046 (mttp) REVERT: C 318 LYS cc_start: 0.9717 (tptp) cc_final: 0.9515 (tptp) REVERT: C 320 GLN cc_start: 0.9327 (tm-30) cc_final: 0.8857 (tm-30) REVERT: D 201 PHE cc_start: 0.6730 (m-80) cc_final: 0.6420 (m-80) REVERT: D 325 GLN cc_start: 0.7659 (tm-30) cc_final: 0.7355 (tm-30) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.0694 time to fit residues: 23.1922 Evaluate side-chains 173 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 22 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 259 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.106705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.080237 restraints weight = 28548.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.082669 restraints weight = 16436.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.084278 restraints weight = 11356.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.085370 restraints weight = 8852.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.085985 restraints weight = 7510.649| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8497 Z= 0.146 Angle : 1.242 35.807 11528 Z= 0.487 Chirality : 0.125 2.117 1318 Planarity : 0.003 0.033 1334 Dihedral : 23.749 173.522 1790 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.84 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 1.05 (0.28), residues: 959 helix: 1.59 (0.19), residues: 743 sheet: None (None), residues: 0 loop : -2.57 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 239 TYR 0.020 0.001 TYR A 280 PHE 0.029 0.001 PHE B 136 TRP 0.023 0.001 TRP A 327 HIS 0.008 0.001 HIS C 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 ( 8497) covalent geometry : angle 1.24196 / 0.49 (11528) hydrogen bonds : bond 0.04833 / 3.19 ( 566) hydrogen bonds : angle 4.12709 / 3.04 ( 1695) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.245 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: symmetry clash REVERT: A 167 PHE cc_start: 0.9245 (m-10) cc_final: 0.9006 (m-80) REVERT: A 237 MET cc_start: 0.9503 (mmm) cc_final: 0.9048 (tpp) REVERT: A 280 TYR cc_start: 0.8572 (t80) cc_final: 0.7653 (t80) REVERT: A 305 ASP cc_start: 0.8845 (m-30) cc_final: 0.8613 (m-30) REVERT: B 129 GLU cc_start: 0.8939 (pm20) cc_final: 0.8687 (pm20) REVERT: B 227 HIS cc_start: 0.9063 (m90) cc_final: 0.8517 (m90) REVERT: B 248 LEU cc_start: 0.9463 (mt) cc_final: 0.9238 (mt) REVERT: B 283 TYR cc_start: 0.8561 (p90) cc_final: 0.7737 (p90) REVERT: C 141 PHE cc_start: 0.9482 (m-80) cc_final: 0.9164 (m-80) REVERT: C 173 MET cc_start: 0.8675 (ptt) cc_final: 0.8167 (ppp) REVERT: C 320 GLN cc_start: 0.9337 (tm-30) cc_final: 0.8905 (tm-30) REVERT: C 325 GLN cc_start: 0.7624 (tp40) cc_final: 0.7424 (tp40) REVERT: D 236 TYR cc_start: 0.8983 (t80) cc_final: 0.8584 (t80) REVERT: D 302 SER cc_start: 0.9239 (m) cc_final: 0.8828 (p) REVERT: D 325 GLN cc_start: 0.7758 (tm-30) cc_final: 0.7446 (tm-30) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.0731 time to fit residues: 24.5699 Evaluate side-chains 187 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 0.0980 chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 259 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.105737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.079472 restraints weight = 28833.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.081832 restraints weight = 16637.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.083422 restraints weight = 11533.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.084392 restraints weight = 9026.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.085119 restraints weight = 7705.126| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8497 Z= 0.164 Angle : 1.241 35.116 11528 Z= 0.489 Chirality : 0.125 2.074 1318 Planarity : 0.004 0.034 1334 Dihedral : 23.638 173.016 1790 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 1.01 (0.28), residues: 959 helix: 1.59 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -2.62 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 239 TYR 0.020 0.001 TYR A 280 PHE 0.037 0.002 PHE A 204 TRP 0.025 0.001 TRP A 327 HIS 0.008 0.001 HIS C 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 ( 8497) covalent geometry : angle 1.24056 / 0.49 (11528) hydrogen bonds : bond 0.04858 / 3.20 ( 566) hydrogen bonds : angle 4.14379 / 3.05 ( 1695) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1467.84 seconds wall clock time: 26 minutes 2.05 seconds (1562.05 seconds total)