Starting phenix.real_space_refine on Fri Sep 11 06:53:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24vq_69848/09_2026/24vq_69848.cif Found real_map, /net/cci-nas-00/data/ceres_data/24vq_69848/09_2026/24vq_69848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/24vq_69848/09_2026/24vq_69848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24vq_69848/09_2026/24vq_69848.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/24vq_69848/09_2026/24vq_69848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24vq_69848/09_2026/24vq_69848.map" } resolution = 3.48 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= 0.088 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 5373 2.51 5 N 1299 2.21 5 O 1362 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 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: 8074 Number of models: 1 Model: "" Number of chains: 7 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: 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: "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: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'9PE': 1} Classifications: {'undetermined': 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: 2.03, per 1000 atoms: 0.25 Number of scatterers: 8074 At special positions: 0 Unit cell: (84.0294, 108.807, 114.194, 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 1362 8.00 N 1299 7.00 C 5373 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: 0.73 Conformation dependent library (CDL) restraints added in 421.9 milliseconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1786 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 0 sheets defined 78.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 124 through 143 Processing helix chain 'A' and resid 149 through 178 removed outlier: 3.869A pdb=" N TRP A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 208 removed outlier: 3.593A pdb=" N ALA A 208 " --> pdb=" O PHE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 239 Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.526A pdb=" N LYS A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU A 250 " --> pdb=" O THR A 246 " (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: 3.790A pdb=" N ALA A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 366 removed outlier: 3.733A pdb=" N GLY A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 366 " --> pdb=" O GLN A 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'B' and resid 149 through 178 removed outlier: 3.948A pdb=" N TRP B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 195 Processing helix chain 'B' and resid 196 through 208 Processing helix chain 'B' and resid 229 through 238 removed outlier: 4.160A pdb=" N GLN B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 removed outlier: 4.019A pdb=" N LEU B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 283 removed outlier: 3.762A pdb=" N ILE B 262 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 326 through 345 removed outlier: 4.245A pdb=" N ILE B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 366 removed outlier: 3.704A pdb=" N GLY B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 85 Processing helix chain 'C' and resid 91 through 112 removed outlier: 4.334A pdb=" N HIS C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 147 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 163 Processing helix chain 'C' and resid 165 through 183 Processing helix chain 'C' and resid 201 through 210 removed outlier: 4.105A pdb=" N LEU C 205 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N MET C 210 " --> pdb=" O ARG C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 227 Processing helix chain 'C' and resid 227 through 253 removed outlier: 4.056A pdb=" N LEU C 231 " --> pdb=" O HIS C 227 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 275 Processing helix chain 'C' and resid 289 through 326 Proline residue: C 307 - end of helix removed outlier: 3.853A pdb=" N GLY C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 93 through 114 removed outlier: 3.539A pdb=" N ILE D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 145 Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 165 through 183 removed outlier: 3.572A pdb=" N ALA D 183 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 210 removed outlier: 3.935A pdb=" N MET D 210 " --> pdb=" O ARG D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 227 Processing helix chain 'D' and resid 228 through 253 Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 286 through 305 removed outlier: 3.796A pdb=" N ALA D 305 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 326 removed outlier: 3.723A pdb=" N SER D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) 559 hydrogen bonds defined for protein. 1671 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: 1.02 Time building geometry restraints manager: 0.97 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: 1163 1.31 - 1.43: 2452 1.43 - 1.56: 4620 1.56 - 1.69: 5 1.69 - 1.81: 52 Bond restraints: 8292 Sorted by residual: bond pdb=" C31 9PE C 602 " pdb=" O31 9PE C 602 " ideal model delta sigma weight residual 1.325 1.400 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C31 9PE B1001 " pdb=" O31 9PE B1001 " ideal model delta sigma weight residual 1.325 1.398 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C21 9PE C 602 " pdb=" O21 9PE C 602 " ideal model delta sigma weight residual 1.329 1.400 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C21 9PE B1001 " pdb=" O21 9PE B1001 " ideal model delta sigma weight residual 1.329 1.398 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C55 YJ0 C 601 " pdb=" O60 YJ0 C 601 " ideal model delta sigma weight residual 1.455 1.414 0.041 2.00e-02 2.50e+03 4.18e+00 ... (remaining 8287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 10963 2.68 - 5.35: 206 5.35 - 8.03: 49 8.03 - 10.71: 19 10.71 - 13.38: 5 Bond angle restraints: 11242 Sorted by residual: angle pdb=" C LEU D 196 " pdb=" CA LEU D 196 " pdb=" CB LEU D 196 " ideal model delta sigma weight residual 116.54 110.30 6.24 1.15e+00 7.56e-01 2.94e+01 angle pdb=" CA LYS C 165 " pdb=" CB LYS C 165 " pdb=" CG LYS C 165 " ideal model delta sigma weight residual 114.10 122.38 -8.28 2.00e+00 2.50e-01 1.71e+01 angle pdb=" O12 9PE B1001 " pdb=" P 9PE B1001 " pdb=" O14 9PE B1001 " ideal model delta sigma weight residual 120.90 108.96 11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" CB LYS A 146 " pdb=" CG LYS A 146 " pdb=" CD LYS A 146 " ideal model delta sigma weight residual 111.30 120.36 -9.06 2.30e+00 1.89e-01 1.55e+01 angle pdb=" O12 9PE C 602 " pdb=" P 9PE C 602 " pdb=" O14 9PE C 602 " ideal model delta sigma weight residual 120.90 109.24 11.66 3.00e+00 1.11e-01 1.51e+01 ... (remaining 11237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 4667 35.40 - 70.79: 273 70.79 - 106.19: 63 106.19 - 141.58: 54 141.58 - 176.98: 19 Dihedral angle restraints: 5076 sinusoidal: 2283 harmonic: 2793 Sorted by residual: 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 -58.94 -176.98 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C78 YJ0 C 601 " pdb=" C12 YJ0 C 601 " pdb=" C7 YJ0 C 601 " pdb=" C8 YJ0 C 601 " ideal model delta sinusoidal sigma weight residual 85.32 -88.91 174.23 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 60.77 174.15 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.215: 1263 1.215 - 2.429: 0 2.429 - 3.644: 0 3.644 - 4.859: 1 4.859 - 6.073: 19 Chirality restraints: 1283 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=" C12 YJ0 C 601 " pdb=" C11 YJ0 C 601 " pdb=" C13 YJ0 C 601 " pdb=" C7 YJ0 C 601 " both_signs ideal model delta sigma weight residual False 3.10 -2.96 6.05 2.00e-01 2.50e+01 9.16e+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 2.77 -5.59 2.00e-01 2.50e+01 7.80e+02 ... (remaining 1280 not shown) Planarity restraints: 1317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 YJ0 C 601 " -0.164 2.00e-02 2.50e+03 1.37e-01 2.36e+02 pdb=" C18 YJ0 C 601 " 0.197 2.00e-02 2.50e+03 pdb=" C19 YJ0 C 601 " 0.098 2.00e-02 2.50e+03 pdb=" C20 YJ0 C 601 " 0.008 2.00e-02 2.50e+03 pdb=" C24 YJ0 C 601 " -0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 YJ0 D 601 " 0.102 2.00e-02 2.50e+03 8.45e-02 8.93e+01 pdb=" C18 YJ0 D 601 " -0.125 2.00e-02 2.50e+03 pdb=" C19 YJ0 D 601 " -0.050 2.00e-02 2.50e+03 pdb=" C20 YJ0 D 601 " -0.011 2.00e-02 2.50e+03 pdb=" C24 YJ0 D 601 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 276 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C THR C 276 " -0.033 2.00e-02 2.50e+03 pdb=" O THR C 276 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE C 277 " 0.011 2.00e-02 2.50e+03 ... (remaining 1314 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 620 2.74 - 3.28: 8411 3.28 - 3.82: 13443 3.82 - 4.36: 14692 4.36 - 4.90: 25464 Nonbonded interactions: 62630 Sorted by model distance: nonbonded pdb=" OH TYR A 319 " pdb=" OG1 THR D 273 " model vdw 2.197 3.040 nonbonded pdb=" O TYR C 117 " pdb=" OG SER C 121 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR A 313 " pdb=" OH TYR B 319 " model vdw 2.216 3.040 nonbonded pdb=" O ARG A 364 " pdb=" NH1 ARG A 364 " model vdw 2.280 3.120 nonbonded pdb=" N GLU C 230 " pdb=" OE1 GLU C 230 " model vdw 2.308 3.120 ... (remaining 62625 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 'B' and resid 110 through 366) } ncs_group { reference = (chain 'C' and resid 70 through 601) selection = (chain 'D' and (resid 70 through 183 or resid 195 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: 1.350 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 8.760 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 8292 Z= 0.226 Angle : 0.960 13.384 11242 Z= 0.429 Chirality : 0.659 6.073 1283 Planarity : 0.006 0.137 1317 Dihedral : 29.858 176.981 3290 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.81 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 29.51 % Favored : 70.49 % 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: 0.84 (0.28), residues: 955 helix: 1.52 (0.19), residues: 731 sheet: None (None), residues: 0 loop : -2.82 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 143 TYR 0.019 0.001 TYR D 81 PHE 0.023 0.001 PHE C 99 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 0.00465 / 0.23 ( 8292) covalent geometry : angle 0.96013 / 0.43 (11242) hydrogen bonds : bond 0.14175 / 9.37 ( 559) hydrogen bonds : angle 5.50298 / 3.92 ( 1671) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 PHE cc_start: 0.5823 (m-80) cc_final: 0.5621 (m-80) REVERT: B 174 ARG cc_start: 0.7059 (mmp80) cc_final: 0.6230 (mmp80) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1066 time to fit residues: 25.1506 Evaluate side-chains 171 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.0010 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.0170 overall best weight: 0.5024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 257 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.211885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.152733 restraints weight = 10638.891| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.61 r_work: 0.3435 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8292 Z= 0.143 Angle : 1.159 35.634 11242 Z= 0.447 Chirality : 0.114 2.220 1283 Planarity : 0.004 0.044 1317 Dihedral : 25.141 174.369 1541 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.86 % Favored : 94.03 % Rotamer: Outliers : 2.86 % Allowed : 25.65 % Favored : 71.48 % 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: 1.06 (0.28), residues: 955 helix: 1.68 (0.19), residues: 743 sheet: None (None), residues: 0 loop : -2.97 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 364 TYR 0.012 0.001 TYR C 236 PHE 0.015 0.001 PHE A 162 TRP 0.011 0.001 TRP D 287 HIS 0.008 0.001 HIS D 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 8292) covalent geometry : angle 1.15899 / 0.45 (11242) hydrogen bonds : bond 0.04830 / 3.18 ( 559) hydrogen bonds : angle 4.37043 / 3.07 ( 1671) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 145 PHE cc_start: 0.6332 (m-80) cc_final: 0.6077 (m-80) REVERT: B 200 MET cc_start: 0.6872 (mpp) cc_final: 0.6583 (mpp) REVERT: D 75 LYS cc_start: 0.9018 (mtmm) cc_final: 0.8783 (mtmm) REVERT: D 81 TYR cc_start: 0.7916 (t80) cc_final: 0.7588 (t80) REVERT: D 208 ILE cc_start: 0.7751 (mt) cc_final: 0.7514 (mp) outliers start: 23 outliers final: 14 residues processed: 197 average time/residue: 0.0931 time to fit residues: 24.4901 Evaluate side-chains 180 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 313 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 253 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 2 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 233 GLN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.208066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147580 restraints weight = 10789.911| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 3.00 r_work: 0.3335 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8292 Z= 0.198 Angle : 1.156 33.810 11242 Z= 0.457 Chirality : 0.115 2.163 1283 Planarity : 0.004 0.046 1317 Dihedral : 23.576 175.585 1541 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.39 % Favored : 93.51 % Rotamer: Outliers : 4.23 % Allowed : 24.91 % Favored : 70.86 % 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: 1.00 (0.28), residues: 955 helix: 1.60 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -2.86 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 364 TYR 0.017 0.001 TYR C 236 PHE 0.018 0.002 PHE C 99 TRP 0.012 0.001 TRP C 287 HIS 0.005 0.001 HIS D 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 ( 8292) covalent geometry : angle 1.15560 / 0.46 (11242) hydrogen bonds : bond 0.05173 / 3.41 ( 559) hydrogen bonds : angle 4.33466 / 3.08 ( 1671) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 HIS cc_start: 0.6922 (m-70) cc_final: 0.6711 (m-70) REVERT: A 262 ILE cc_start: 0.8862 (tp) cc_final: 0.8607 (tp) REVERT: B 145 PHE cc_start: 0.6478 (m-80) cc_final: 0.6137 (m-80) REVERT: B 200 MET cc_start: 0.7106 (mpp) cc_final: 0.6858 (mpp) REVERT: B 202 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7886 (p0) REVERT: D 208 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7636 (mp) REVERT: D 210 MET cc_start: 0.7020 (mpp) cc_final: 0.6703 (mpp) REVERT: D 240 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8617 (mm) outliers start: 34 outliers final: 22 residues processed: 194 average time/residue: 0.0876 time to fit residues: 23.1114 Evaluate side-chains 186 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 162 PHE Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 276 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 0.0470 chunk 4 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 GLN C 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.210419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149447 restraints weight = 10931.861| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.91 r_work: 0.3405 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8292 Z= 0.142 Angle : 1.129 34.501 11242 Z= 0.438 Chirality : 0.112 2.090 1283 Planarity : 0.003 0.044 1317 Dihedral : 22.802 174.883 1541 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.60 % Favored : 93.30 % Rotamer: Outliers : 3.74 % Allowed : 26.77 % Favored : 69.49 % 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: 1.16 (0.28), residues: 955 helix: 1.73 (0.19), residues: 744 sheet: None (None), residues: 0 loop : -2.87 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 364 TYR 0.013 0.001 TYR C 236 PHE 0.028 0.001 PHE C 201 TRP 0.010 0.001 TRP C 287 HIS 0.003 0.001 HIS D 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 8292) covalent geometry : angle 1.12897 / 0.44 (11242) hydrogen bonds : bond 0.04600 / 3.01 ( 559) hydrogen bonds : angle 4.18174 / 2.96 ( 1671) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 HIS cc_start: 0.6818 (m-70) cc_final: 0.6567 (m-70) REVERT: A 170 GLU cc_start: 0.6313 (pp20) cc_final: 0.5971 (pp20) REVERT: A 262 ILE cc_start: 0.8882 (tp) cc_final: 0.8665 (tp) REVERT: B 145 PHE cc_start: 0.6499 (m-80) cc_final: 0.6057 (m-80) REVERT: B 200 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6758 (mpp) REVERT: C 311 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8903 (mt) REVERT: D 86 ARG cc_start: 0.8649 (ptt-90) cc_final: 0.8313 (ptt90) REVERT: D 206 ARG cc_start: 0.8466 (mmp-170) cc_final: 0.8254 (mmp-170) REVERT: D 208 ILE cc_start: 0.7860 (mt) cc_final: 0.7475 (mp) REVERT: D 210 MET cc_start: 0.7072 (mpp) cc_final: 0.5901 (mpp) outliers start: 30 outliers final: 19 residues processed: 192 average time/residue: 0.0943 time to fit residues: 24.2715 Evaluate side-chains 178 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 162 PHE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 276 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 71 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 89 optimal weight: 0.3980 chunk 80 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 22 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.208401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147716 restraints weight = 10824.242| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.83 r_work: 0.3362 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8292 Z= 0.178 Angle : 1.145 34.095 11242 Z= 0.451 Chirality : 0.113 2.066 1283 Planarity : 0.004 0.045 1317 Dihedral : 22.302 175.897 1541 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.49 % Favored : 93.40 % Rotamer: Outliers : 4.23 % Allowed : 25.65 % Favored : 70.11 % 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: 1.09 (0.28), residues: 955 helix: 1.63 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -2.73 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 364 TYR 0.017 0.001 TYR C 236 PHE 0.022 0.002 PHE C 99 TRP 0.011 0.001 TRP C 287 HIS 0.004 0.001 HIS D 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 ( 8292) covalent geometry : angle 1.14472 / 0.45 (11242) hydrogen bonds : bond 0.04994 / 3.28 ( 559) hydrogen bonds : angle 4.17841 / 2.96 ( 1671) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 HIS cc_start: 0.6638 (m-70) cc_final: 0.6429 (m-70) REVERT: B 200 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6744 (mpp) REVERT: B 246 THR cc_start: 0.8287 (p) cc_final: 0.8059 (t) REVERT: D 206 ARG cc_start: 0.8520 (mmp-170) cc_final: 0.8283 (mmp-170) REVERT: D 208 ILE cc_start: 0.8037 (mt) cc_final: 0.7803 (mp) outliers start: 34 outliers final: 24 residues processed: 192 average time/residue: 0.0847 time to fit residues: 21.9091 Evaluate side-chains 184 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 162 PHE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 276 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 30 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 83 optimal weight: 0.0270 chunk 58 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.211046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149891 restraints weight = 10700.657| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.87 r_work: 0.3370 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8292 Z= 0.141 Angle : 1.136 33.897 11242 Z= 0.444 Chirality : 0.112 2.068 1283 Planarity : 0.004 0.047 1317 Dihedral : 22.081 175.697 1541 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.39 % Favored : 93.51 % Rotamer: Outliers : 3.24 % Allowed : 27.27 % Favored : 69.49 % 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: 1.25 (0.28), residues: 955 helix: 1.76 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -2.76 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 364 TYR 0.020 0.001 TYR D 81 PHE 0.017 0.001 PHE C 99 TRP 0.011 0.001 TRP D 287 HIS 0.004 0.001 HIS D 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 8292) covalent geometry : angle 1.13616 / 0.44 (11242) hydrogen bonds : bond 0.04551 / 2.99 ( 559) hydrogen bonds : angle 4.10069 / 2.90 ( 1671) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 HIS cc_start: 0.6646 (m-70) cc_final: 0.6413 (m-70) REVERT: A 262 ILE cc_start: 0.8983 (tp) cc_final: 0.8723 (tp) REVERT: A 296 MET cc_start: 0.2251 (tpt) cc_final: 0.1957 (ptt) REVERT: B 200 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6768 (mpp) REVERT: B 246 THR cc_start: 0.8262 (p) cc_final: 0.8050 (t) REVERT: C 175 LEU cc_start: 0.9018 (mt) cc_final: 0.8810 (mm) REVERT: D 208 ILE cc_start: 0.7941 (mt) cc_final: 0.7525 (mp) REVERT: D 210 MET cc_start: 0.7150 (mpp) cc_final: 0.5898 (mpp) outliers start: 26 outliers final: 22 residues processed: 188 average time/residue: 0.0937 time to fit residues: 23.7255 Evaluate side-chains 185 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 162 PHE Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 276 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 0.0870 chunk 63 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 233 GLN C 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.209878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.149792 restraints weight = 10828.898| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.89 r_work: 0.3398 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8292 Z= 0.140 Angle : 1.145 33.838 11242 Z= 0.445 Chirality : 0.112 2.058 1283 Planarity : 0.003 0.043 1317 Dihedral : 21.975 175.553 1541 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.18 % Favored : 93.72 % Rotamer: Outliers : 3.49 % Allowed : 27.90 % Favored : 68.62 % 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: 955 helix: 1.82 (0.19), residues: 745 sheet: None (None), residues: 0 loop : -2.75 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 364 TYR 0.011 0.001 TYR C 236 PHE 0.016 0.001 PHE C 99 TRP 0.009 0.001 TRP D 287 HIS 0.004 0.001 HIS D 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 8292) covalent geometry : angle 1.14467 / 0.45 (11242) hydrogen bonds : bond 0.04488 / 2.94 ( 559) hydrogen bonds : angle 4.05708 / 2.87 ( 1671) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 HIS cc_start: 0.6628 (m-70) cc_final: 0.6417 (m-70) REVERT: A 296 MET cc_start: 0.2391 (tpt) cc_final: 0.2174 (ptt) REVERT: B 200 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6753 (mpp) REVERT: B 259 LYS cc_start: 0.8813 (tppt) cc_final: 0.8404 (tptm) REVERT: C 115 LYS cc_start: 0.8396 (mtmm) cc_final: 0.8188 (mtmm) REVERT: C 175 LEU cc_start: 0.9020 (mt) cc_final: 0.8812 (mm) REVERT: D 210 MET cc_start: 0.7214 (mpp) cc_final: 0.5904 (mpp) outliers start: 28 outliers final: 21 residues processed: 189 average time/residue: 0.0995 time to fit residues: 25.0500 Evaluate side-chains 189 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 162 PHE Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 272 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 11 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 233 GLN C 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.210060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.153866 restraints weight = 10757.136| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.77 r_work: 0.3351 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8292 Z= 0.171 Angle : 1.157 33.918 11242 Z= 0.456 Chirality : 0.112 2.044 1283 Planarity : 0.004 0.044 1317 Dihedral : 21.971 175.692 1541 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.81 % Favored : 93.09 % Rotamer: Outliers : 3.24 % Allowed : 27.90 % Favored : 68.87 % 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: 1.26 (0.28), residues: 955 helix: 1.76 (0.19), residues: 745 sheet: None (None), residues: 0 loop : -2.70 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 364 TYR 0.022 0.001 TYR D 81 PHE 0.018 0.001 PHE C 99 TRP 0.011 0.001 TRP B 121 HIS 0.007 0.001 HIS D 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 8292) covalent geometry : angle 1.15726 / 0.46 (11242) hydrogen bonds : bond 0.04799 / 3.16 ( 559) hydrogen bonds : angle 4.10561 / 2.92 ( 1671) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 MET cc_start: 0.8751 (tmm) cc_final: 0.7746 (mpp) REVERT: A 296 MET cc_start: 0.2714 (tpt) cc_final: 0.2287 (ptt) REVERT: B 200 MET cc_start: 0.7202 (mpp) cc_final: 0.6820 (mpp) REVERT: C 175 LEU cc_start: 0.9054 (mt) cc_final: 0.8847 (mm) REVERT: C 320 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: D 210 MET cc_start: 0.7304 (mpp) cc_final: 0.6036 (mpp) REVERT: D 230 GLU cc_start: 0.8058 (mp0) cc_final: 0.7742 (mp0) outliers start: 26 outliers final: 22 residues processed: 194 average time/residue: 0.1024 time to fit residues: 26.1729 Evaluate side-chains 191 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 162 PHE Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 320 GLN Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 272 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 83 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 233 GLN C 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.209605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.148828 restraints weight = 10816.791| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.89 r_work: 0.3386 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8292 Z= 0.146 Angle : 1.149 33.784 11242 Z= 0.450 Chirality : 0.112 2.043 1283 Planarity : 0.003 0.044 1317 Dihedral : 21.942 175.778 1541 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.49 % Favored : 93.40 % Rotamer: Outliers : 3.24 % Allowed : 28.02 % Favored : 68.74 % 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: 1.35 (0.28), residues: 955 helix: 1.82 (0.19), residues: 745 sheet: None (None), residues: 0 loop : -2.66 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 364 TYR 0.012 0.001 TYR C 236 PHE 0.026 0.001 PHE C 201 TRP 0.010 0.001 TRP D 287 HIS 0.005 0.001 HIS D 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 8292) covalent geometry : angle 1.14904 / 0.45 (11242) hydrogen bonds : bond 0.04520 / 2.97 ( 559) hydrogen bonds : angle 4.05954 / 2.88 ( 1671) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8116 (mmmm) cc_final: 0.7528 (tppp) REVERT: A 200 MET cc_start: 0.8762 (tmm) cc_final: 0.7971 (mtm) REVERT: A 262 ILE cc_start: 0.8983 (tp) cc_final: 0.8728 (tp) REVERT: A 296 MET cc_start: 0.2531 (tpt) cc_final: 0.2250 (ptt) REVERT: B 174 ARG cc_start: 0.7429 (mmp80) cc_final: 0.6690 (mmp80) REVERT: B 200 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6834 (mpp) REVERT: B 202 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7503 (m-30) REVERT: C 175 LEU cc_start: 0.9052 (mt) cc_final: 0.8849 (mm) REVERT: C 320 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7993 (tt0) REVERT: D 171 ASP cc_start: 0.8666 (m-30) cc_final: 0.8273 (p0) REVERT: D 210 MET cc_start: 0.7334 (mpp) cc_final: 0.7011 (mpp) REVERT: D 230 GLU cc_start: 0.8056 (mp0) cc_final: 0.7757 (mp0) outliers start: 26 outliers final: 20 residues processed: 189 average time/residue: 0.1022 time to fit residues: 25.4871 Evaluate side-chains 194 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 162 PHE Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 320 GLN Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 272 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 69 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 0.0870 chunk 9 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 233 GLN C 323 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.210476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.149096 restraints weight = 10790.917| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.05 r_work: 0.3402 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8292 Z= 0.142 Angle : 1.150 33.730 11242 Z= 0.449 Chirality : 0.112 2.038 1283 Planarity : 0.003 0.043 1317 Dihedral : 21.905 175.735 1541 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.18 % Favored : 93.72 % Rotamer: Outliers : 3.11 % Allowed : 28.27 % Favored : 68.62 % 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: 955 helix: 1.88 (0.19), residues: 745 sheet: None (None), residues: 0 loop : -2.61 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 364 TYR 0.023 0.001 TYR D 81 PHE 0.026 0.001 PHE C 201 TRP 0.010 0.001 TRP D 287 HIS 0.005 0.001 HIS D 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 8292) covalent geometry : angle 1.15034 / 0.45 (11242) hydrogen bonds : bond 0.04434 / 2.90 ( 559) hydrogen bonds : angle 4.03278 / 2.86 ( 1671) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8096 (mmmm) cc_final: 0.7323 (tppp) REVERT: A 200 MET cc_start: 0.8773 (tmm) cc_final: 0.7940 (mtp) REVERT: A 262 ILE cc_start: 0.8977 (tp) cc_final: 0.8694 (tp) REVERT: A 296 MET cc_start: 0.2913 (tpt) cc_final: 0.2529 (ptt) REVERT: B 200 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6837 (mpp) REVERT: B 202 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7551 (m-30) REVERT: C 175 LEU cc_start: 0.9060 (mt) cc_final: 0.8855 (mm) REVERT: C 320 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: D 171 ASP cc_start: 0.8682 (m-30) cc_final: 0.8274 (p0) REVERT: D 210 MET cc_start: 0.7368 (mpp) cc_final: 0.6712 (mtm) REVERT: D 230 GLU cc_start: 0.8070 (mp0) cc_final: 0.7781 (mp0) outliers start: 25 outliers final: 20 residues processed: 186 average time/residue: 0.0948 time to fit residues: 23.4580 Evaluate side-chains 195 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 162 PHE Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 320 GLN Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 272 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 5 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.0670 chunk 67 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.211081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.150729 restraints weight = 10767.441| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.88 r_work: 0.3404 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8292 Z= 0.141 Angle : 1.154 33.665 11242 Z= 0.452 Chirality : 0.112 2.031 1283 Planarity : 0.003 0.043 1317 Dihedral : 21.876 175.787 1541 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.39 % Favored : 93.51 % Rotamer: Outliers : 2.74 % Allowed : 28.14 % Favored : 69.12 % 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: 1.50 (0.28), residues: 955 helix: 1.91 (0.19), residues: 745 sheet: None (None), residues: 0 loop : -2.52 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 364 TYR 0.021 0.001 TYR C 153 PHE 0.026 0.001 PHE C 201 TRP 0.010 0.001 TRP D 287 HIS 0.004 0.001 HIS D 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 8292) covalent geometry : angle 1.15364 / 0.45 (11242) hydrogen bonds : bond 0.04363 / 2.86 ( 559) hydrogen bonds : angle 4.00697 / 2.83 ( 1671) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1999.08 seconds wall clock time: 34 minutes 57.55 seconds (2097.55 seconds total)