Starting phenix.real_space_refine on Tue Mar 3 13:18:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l0b_62694/03_2026/9l0b_62694.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l0b_62694/03_2026/9l0b_62694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l0b_62694/03_2026/9l0b_62694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l0b_62694/03_2026/9l0b_62694.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l0b_62694/03_2026/9l0b_62694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l0b_62694/03_2026/9l0b_62694.map" } resolution = 3.7 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= -0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 3175 2.51 5 N 763 2.21 5 O 857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4826 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2971 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 18, 'TRANS': 368} Chain breaks: 1 Chain: "B" Number of atoms: 1855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1855 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 8, 'TRANS': 223} Time building chain proxies: 1.12, per 1000 atoms: 0.23 Number of scatterers: 4826 At special positions: 0 Unit cell: (79.6955, 114.929, 78.0177, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 857 8.00 N 763 7.00 C 3175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 88 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 237 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 280.1 milliseconds 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1138 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 64.0% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 16 through 40 removed outlier: 4.038A pdb=" N PHE A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Proline residue: A 37 - end of helix Processing helix chain 'A' and resid 42 through 52 removed outlier: 4.492A pdb=" N GLU A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 removed outlier: 4.044A pdb=" N ILE A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 81 removed outlier: 4.087A pdb=" N SER A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 85 through 105 removed outlier: 3.572A pdb=" N PHE A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 118 through 139 Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 142 through 173 removed outlier: 3.561A pdb=" N ALA A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Proline residue: A 155 - end of helix removed outlier: 4.048A pdb=" N ALA A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.770A pdb=" N ASN A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 194 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 removed outlier: 4.019A pdb=" N LYS A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 258 removed outlier: 3.761A pdb=" N ILE A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 removed outlier: 4.293A pdb=" N ILE A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 4.200A pdb=" N LYS A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 305 removed outlier: 3.806A pdb=" N PHE A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 312 through 331 Processing helix chain 'A' and resid 336 through 353 removed outlier: 3.889A pdb=" N LEU A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 367 removed outlier: 4.183A pdb=" N MET A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 400 removed outlier: 3.794A pdb=" N ALA A 374 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) Proline residue: A 385 - end of helix Proline residue: A 390 - end of helix Processing helix chain 'A' and resid 403 through 436 removed outlier: 3.905A pdb=" N ALA A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.893A pdb=" N GLN B 136 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 257 through 286 Proline residue: B 263 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 56 through 64 removed outlier: 6.096A pdb=" N SER B 56 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ASN B 85 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLU B 58 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N THR B 87 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS B 60 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N GLN B 89 " --> pdb=" O HIS B 60 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE B 62 " --> pdb=" O GLN B 89 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N THR B 91 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 64 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 72 through 77 Processing sheet with id=AA3, first strand: chain 'B' and resid 168 through 171 removed outlier: 6.104A pdb=" N LEU B 168 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU B 255 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER B 170 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 175 through 180 314 hydrogen bonds defined for protein. 900 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.66 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 776 1.32 - 1.45: 1370 1.45 - 1.57: 2756 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 4950 Sorted by residual: bond pdb=" C VAL B 271 " pdb=" O VAL B 271 " ideal model delta sigma weight residual 1.237 1.200 0.037 1.17e-02 7.31e+03 9.90e+00 bond pdb=" CA ALA A 59 " pdb=" CB ALA A 59 " ideal model delta sigma weight residual 1.530 1.484 0.046 1.64e-02 3.72e+03 7.86e+00 bond pdb=" C HIS A 328 " pdb=" O HIS A 328 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.16e-02 7.43e+03 7.64e+00 bond pdb=" N CYS A 189 " pdb=" CA CYS A 189 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.83e+00 bond pdb=" CA ALA A 191 " pdb=" CB ALA A 191 " ideal model delta sigma weight residual 1.530 1.491 0.039 1.69e-02 3.50e+03 5.21e+00 ... (remaining 4945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 6548 2.03 - 4.07: 131 4.07 - 6.10: 32 6.10 - 8.14: 8 8.14 - 10.17: 4 Bond angle restraints: 6723 Sorted by residual: angle pdb=" N TRP A 60 " pdb=" CA TRP A 60 " pdb=" C TRP A 60 " ideal model delta sigma weight residual 112.89 102.72 10.17 1.24e+00 6.50e-01 6.73e+01 angle pdb=" N ALA A 191 " pdb=" CA ALA A 191 " pdb=" C ALA A 191 " ideal model delta sigma weight residual 113.19 105.77 7.42 1.19e+00 7.06e-01 3.89e+01 angle pdb=" C CYS A 327 " pdb=" N HIS A 328 " pdb=" CA HIS A 328 " ideal model delta sigma weight residual 120.44 112.01 8.43 1.36e+00 5.41e-01 3.84e+01 angle pdb=" C ILE A 58 " pdb=" N ALA A 59 " pdb=" CA ALA A 59 " ideal model delta sigma weight residual 122.65 114.48 8.17 1.60e+00 3.91e-01 2.61e+01 angle pdb=" N VAL A 190 " pdb=" CA VAL A 190 " pdb=" C VAL A 190 " ideal model delta sigma weight residual 110.62 105.57 5.05 1.02e+00 9.61e-01 2.45e+01 ... (remaining 6718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 2592 16.79 - 33.58: 231 33.58 - 50.37: 58 50.37 - 67.17: 1 67.17 - 83.96: 4 Dihedral angle restraints: 2886 sinusoidal: 1101 harmonic: 1785 Sorted by residual: dihedral pdb=" CA LEU A 128 " pdb=" C LEU A 128 " pdb=" N GLN A 129 " pdb=" CA GLN A 129 " ideal model delta harmonic sigma weight residual -180.00 -163.78 -16.22 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA PHE A 359 " pdb=" C PHE A 359 " pdb=" N GLU A 360 " pdb=" CA GLU A 360 " ideal model delta harmonic sigma weight residual 180.00 164.02 15.98 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CB GLU B 149 " pdb=" CG GLU B 149 " pdb=" CD GLU B 149 " pdb=" OE1 GLU B 149 " ideal model delta sinusoidal sigma weight residual 0.00 83.96 -83.96 1 3.00e+01 1.11e-03 9.54e+00 ... (remaining 2883 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 650 0.058 - 0.115: 96 0.115 - 0.173: 16 0.173 - 0.230: 2 0.230 - 0.288: 2 Chirality restraints: 766 Sorted by residual: chirality pdb=" CA VAL B 271 " pdb=" N VAL B 271 " pdb=" C VAL B 271 " pdb=" CB VAL B 271 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CB VAL B 271 " pdb=" CA VAL B 271 " pdb=" CG1 VAL B 271 " pdb=" CG2 VAL B 271 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA GLU B 270 " pdb=" N GLU B 270 " pdb=" C GLU B 270 " pdb=" CB GLU B 270 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 763 not shown) Planarity restraints: 834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 188 " 0.023 2.00e-02 2.50e+03 4.54e-02 2.06e+01 pdb=" C ALA A 188 " -0.079 2.00e-02 2.50e+03 pdb=" O ALA A 188 " 0.029 2.00e-02 2.50e+03 pdb=" N CYS A 189 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 58 " -0.018 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C ILE A 58 " 0.060 2.00e-02 2.50e+03 pdb=" O ILE A 58 " -0.022 2.00e-02 2.50e+03 pdb=" N ALA A 59 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 269 " -0.035 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO A 270 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " -0.030 5.00e-02 4.00e+02 ... (remaining 831 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 456 2.74 - 3.28: 4829 3.28 - 3.82: 7933 3.82 - 4.36: 8886 4.36 - 4.90: 15176 Nonbonded interactions: 37280 Sorted by model distance: nonbonded pdb=" O GLU A 57 " pdb=" OH TYR A 113 " model vdw 2.205 3.040 nonbonded pdb=" O PHE A 172 " pdb=" OH TYR B 171 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASP A 336 " pdb=" OG1 THR A 338 " model vdw 2.264 3.040 nonbonded pdb=" O SER A 108 " pdb=" OG SER A 108 " model vdw 2.282 3.040 nonbonded pdb=" ND2 ASN A 254 " pdb=" OE2 GLU A 382 " model vdw 2.291 3.120 ... (remaining 37275 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.910 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.980 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4952 Z= 0.204 Angle : 0.749 10.172 6727 Z= 0.434 Chirality : 0.046 0.288 766 Planarity : 0.005 0.054 834 Dihedral : 13.607 83.958 1742 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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 (0.35), residues: 613 helix: 1.05 (0.29), residues: 361 sheet: 1.70 (0.44), residues: 107 loop : -0.96 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 196 TYR 0.021 0.001 TYR A 343 PHE 0.027 0.001 PHE A 27 TRP 0.016 0.001 TRP B 192 HIS 0.010 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 4950) covalent geometry : angle 0.74898 ( 6723) SS BOND : bond 0.00271 ( 2) SS BOND : angle 0.49631 ( 4) hydrogen bonds : bond 0.10726 ( 314) hydrogen bonds : angle 4.93806 ( 900) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 382 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7914 (mt-10) REVERT: B 174 ASP cc_start: 0.8543 (m-30) cc_final: 0.8074 (m-30) REVERT: B 231 ASP cc_start: 0.7940 (m-30) cc_final: 0.7592 (m-30) REVERT: B 245 GLU cc_start: 0.7153 (pp20) cc_final: 0.6745 (pp20) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0522 time to fit residues: 8.3461 Evaluate side-chains 95 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.187717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.139320 restraints weight = 7096.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.143624 restraints weight = 3148.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.146381 restraints weight = 1796.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.147882 restraints weight = 1241.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.148312 restraints weight = 995.274| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4952 Z= 0.139 Angle : 0.604 6.633 6727 Z= 0.309 Chirality : 0.041 0.146 766 Planarity : 0.005 0.046 834 Dihedral : 4.197 16.556 663 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.71 % Allowed : 12.14 % Favored : 86.15 % 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 (0.35), residues: 613 helix: 1.16 (0.29), residues: 362 sheet: 1.66 (0.44), residues: 107 loop : -1.03 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 196 TYR 0.014 0.001 TYR A 337 PHE 0.029 0.001 PHE A 27 TRP 0.007 0.001 TRP B 192 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 4950) covalent geometry : angle 0.60402 ( 6723) SS BOND : bond 0.00308 ( 2) SS BOND : angle 0.38481 ( 4) hydrogen bonds : bond 0.04288 ( 314) hydrogen bonds : angle 4.42366 ( 900) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.137 Fit side-chains REVERT: A 392 LEU cc_start: 0.7409 (tt) cc_final: 0.7200 (mp) REVERT: B 137 MET cc_start: 0.4511 (mtt) cc_final: 0.3377 (tpp) REVERT: B 174 ASP cc_start: 0.8718 (m-30) cc_final: 0.8384 (m-30) REVERT: B 278 ILE cc_start: 0.8480 (mp) cc_final: 0.8235 (mp) outliers start: 9 outliers final: 8 residues processed: 114 average time/residue: 0.0573 time to fit residues: 8.7979 Evaluate side-chains 103 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 284 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 17 optimal weight: 0.0270 chunk 33 optimal weight: 4.9990 chunk 55 optimal weight: 0.0870 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 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 = 0.4183 r_free = 0.4183 target = 0.183830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134291 restraints weight = 7239.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.138443 restraints weight = 3282.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.141080 restraints weight = 1925.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.142556 restraints weight = 1356.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.143606 restraints weight = 1103.140| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4952 Z= 0.155 Angle : 0.616 11.343 6727 Z= 0.313 Chirality : 0.042 0.158 766 Planarity : 0.005 0.047 834 Dihedral : 4.263 18.121 663 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.61 % Allowed : 16.32 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.34), residues: 613 helix: 1.20 (0.29), residues: 354 sheet: 1.51 (0.44), residues: 107 loop : -1.07 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 196 TYR 0.016 0.001 TYR A 343 PHE 0.027 0.001 PHE A 27 TRP 0.033 0.002 TRP B 192 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 4950) covalent geometry : angle 0.61593 ( 6723) SS BOND : bond 0.00283 ( 2) SS BOND : angle 0.46134 ( 4) hydrogen bonds : bond 0.04412 ( 314) hydrogen bonds : angle 4.43033 ( 900) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 172 VAL cc_start: 0.8066 (t) cc_final: 0.7861 (m) REVERT: B 174 ASP cc_start: 0.8752 (m-30) cc_final: 0.8420 (m-30) REVERT: B 207 MET cc_start: 0.6440 (pmm) cc_final: 0.6181 (pmm) REVERT: B 222 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8176 (tp) REVERT: B 278 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8157 (mp) outliers start: 19 outliers final: 14 residues processed: 107 average time/residue: 0.0539 time to fit residues: 7.9222 Evaluate side-chains 109 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 278 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.183623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.132699 restraints weight = 7407.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.137071 restraints weight = 3338.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.139864 restraints weight = 1955.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.141349 restraints weight = 1381.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.142268 restraints weight = 1130.453| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4952 Z= 0.131 Angle : 0.597 12.917 6727 Z= 0.301 Chirality : 0.041 0.161 766 Planarity : 0.005 0.047 834 Dihedral : 4.228 17.126 663 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.04 % Allowed : 18.41 % Favored : 78.56 % 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 (0.34), residues: 613 helix: 1.37 (0.29), residues: 348 sheet: 1.81 (0.45), residues: 101 loop : -1.27 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 238 TYR 0.011 0.001 TYR A 337 PHE 0.027 0.001 PHE A 27 TRP 0.015 0.001 TRP B 192 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4950) covalent geometry : angle 0.59709 ( 6723) SS BOND : bond 0.00289 ( 2) SS BOND : angle 0.37235 ( 4) hydrogen bonds : bond 0.04108 ( 314) hydrogen bonds : angle 4.31395 ( 900) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.110 Fit side-chains REVERT: A 237 LEU cc_start: 0.3415 (OUTLIER) cc_final: 0.3062 (mp) REVERT: B 174 ASP cc_start: 0.8737 (m-30) cc_final: 0.8443 (m-30) REVERT: B 207 MET cc_start: 0.6472 (pmm) cc_final: 0.6173 (pmm) REVERT: B 278 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8153 (mp) outliers start: 16 outliers final: 10 residues processed: 107 average time/residue: 0.0436 time to fit residues: 6.7124 Evaluate side-chains 105 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 278 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 26 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 0.0470 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.183640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.132760 restraints weight = 7554.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137111 restraints weight = 3434.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.139819 restraints weight = 2008.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.141593 restraints weight = 1429.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.142462 restraints weight = 1147.796| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4952 Z= 0.129 Angle : 0.612 14.287 6727 Z= 0.306 Chirality : 0.041 0.141 766 Planarity : 0.005 0.047 834 Dihedral : 4.249 17.057 663 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.42 % Allowed : 20.68 % Favored : 75.90 % 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: 1.11 (0.34), residues: 613 helix: 1.36 (0.29), residues: 349 sheet: 1.76 (0.44), residues: 101 loop : -1.30 (0.45), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 238 TYR 0.010 0.001 TYR B 210 PHE 0.027 0.001 PHE A 27 TRP 0.039 0.002 TRP B 192 HIS 0.002 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4950) covalent geometry : angle 0.61248 ( 6723) SS BOND : bond 0.00267 ( 2) SS BOND : angle 0.42819 ( 4) hydrogen bonds : bond 0.04063 ( 314) hydrogen bonds : angle 4.28391 ( 900) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.180 Fit side-chains REVERT: A 237 LEU cc_start: 0.3481 (OUTLIER) cc_final: 0.3074 (mp) REVERT: A 382 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7581 (mt-10) REVERT: B 171 TYR cc_start: 0.8353 (m-10) cc_final: 0.8119 (m-10) REVERT: B 174 ASP cc_start: 0.8770 (m-30) cc_final: 0.8457 (m-30) REVERT: B 207 MET cc_start: 0.6505 (pmm) cc_final: 0.6277 (pmm) REVERT: B 278 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8165 (mp) outliers start: 18 outliers final: 14 residues processed: 103 average time/residue: 0.0489 time to fit residues: 7.1549 Evaluate side-chains 107 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 284 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 39 optimal weight: 30.0000 chunk 32 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 254 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.183095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.132393 restraints weight = 7539.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.136788 restraints weight = 3381.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.139592 restraints weight = 1965.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.141108 restraints weight = 1379.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.142036 restraints weight = 1122.097| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4952 Z= 0.132 Angle : 0.603 14.407 6727 Z= 0.303 Chirality : 0.041 0.139 766 Planarity : 0.005 0.047 834 Dihedral : 4.278 19.237 663 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.98 % Allowed : 20.30 % Favored : 75.71 % 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: 1.15 (0.34), residues: 613 helix: 1.38 (0.29), residues: 349 sheet: 1.83 (0.45), residues: 101 loop : -1.29 (0.45), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 238 TYR 0.012 0.001 TYR A 271 PHE 0.027 0.001 PHE A 27 TRP 0.050 0.002 TRP B 192 HIS 0.001 0.000 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 4950) covalent geometry : angle 0.60349 ( 6723) SS BOND : bond 0.00292 ( 2) SS BOND : angle 0.53206 ( 4) hydrogen bonds : bond 0.04115 ( 314) hydrogen bonds : angle 4.34543 ( 900) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.119 Fit side-chains REVERT: A 237 LEU cc_start: 0.3494 (OUTLIER) cc_final: 0.3081 (mp) REVERT: A 363 MET cc_start: 0.8326 (tpp) cc_final: 0.8072 (mpp) REVERT: A 382 GLU cc_start: 0.7785 (mt-10) cc_final: 0.6758 (mt-10) REVERT: B 171 TYR cc_start: 0.8319 (m-10) cc_final: 0.8069 (m-10) REVERT: B 174 ASP cc_start: 0.8768 (m-30) cc_final: 0.8458 (m-30) REVERT: B 207 MET cc_start: 0.6693 (pmm) cc_final: 0.6387 (pmm) REVERT: B 278 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8152 (mp) outliers start: 21 outliers final: 14 residues processed: 103 average time/residue: 0.0508 time to fit residues: 7.3169 Evaluate side-chains 106 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 284 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 1 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.181729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.131006 restraints weight = 7534.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.135222 restraints weight = 3462.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137945 restraints weight = 2069.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.139219 restraints weight = 1476.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.140283 restraints weight = 1227.919| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4952 Z= 0.142 Angle : 0.647 15.417 6727 Z= 0.320 Chirality : 0.042 0.160 766 Planarity : 0.005 0.047 834 Dihedral : 4.334 21.664 663 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.61 % Allowed : 21.06 % Favored : 75.33 % 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 (0.34), residues: 613 helix: 1.48 (0.29), residues: 343 sheet: 1.63 (0.46), residues: 102 loop : -1.28 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 238 TYR 0.011 0.001 TYR A 271 PHE 0.027 0.001 PHE A 27 TRP 0.057 0.002 TRP B 192 HIS 0.001 0.000 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4950) covalent geometry : angle 0.64738 ( 6723) SS BOND : bond 0.00332 ( 2) SS BOND : angle 0.80281 ( 4) hydrogen bonds : bond 0.04141 ( 314) hydrogen bonds : angle 4.43603 ( 900) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.162 Fit side-chains REVERT: A 100 MET cc_start: 0.8272 (tpt) cc_final: 0.7836 (tpt) REVERT: A 237 LEU cc_start: 0.3512 (OUTLIER) cc_final: 0.3076 (mp) REVERT: A 382 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7146 (mt-10) REVERT: B 174 ASP cc_start: 0.8751 (m-30) cc_final: 0.8448 (m-30) REVERT: B 207 MET cc_start: 0.6759 (pmm) cc_final: 0.6492 (pmm) REVERT: B 278 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8181 (mp) outliers start: 19 outliers final: 13 residues processed: 101 average time/residue: 0.0498 time to fit residues: 7.0892 Evaluate side-chains 108 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 284 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 18 optimal weight: 0.0270 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 12 optimal weight: 0.0770 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.184029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.133556 restraints weight = 7604.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137916 restraints weight = 3465.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.140671 restraints weight = 2048.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.142244 restraints weight = 1453.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.143408 restraints weight = 1183.069| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4952 Z= 0.123 Angle : 0.630 15.691 6727 Z= 0.310 Chirality : 0.041 0.159 766 Planarity : 0.005 0.047 834 Dihedral : 4.342 26.325 663 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.66 % Allowed : 22.96 % Favored : 74.38 % 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 (0.34), residues: 613 helix: 1.51 (0.29), residues: 343 sheet: 1.43 (0.47), residues: 104 loop : -1.24 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 238 TYR 0.010 0.001 TYR B 210 PHE 0.027 0.001 PHE A 27 TRP 0.057 0.002 TRP B 192 HIS 0.001 0.000 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4950) covalent geometry : angle 0.62961 ( 6723) SS BOND : bond 0.00413 ( 2) SS BOND : angle 1.16530 ( 4) hydrogen bonds : bond 0.03830 ( 314) hydrogen bonds : angle 4.39289 ( 900) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.152 Fit side-chains REVERT: A 237 LEU cc_start: 0.3524 (OUTLIER) cc_final: 0.3152 (mp) REVERT: A 382 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7122 (mt-10) REVERT: B 174 ASP cc_start: 0.8735 (m-30) cc_final: 0.8442 (m-30) REVERT: B 207 MET cc_start: 0.6743 (pmm) cc_final: 0.6485 (pmm) REVERT: B 278 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8139 (mp) outliers start: 14 outliers final: 10 residues processed: 104 average time/residue: 0.0494 time to fit residues: 7.2366 Evaluate side-chains 103 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 284 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 59 optimal weight: 0.3980 chunk 41 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.183720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.133413 restraints weight = 7620.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.137481 restraints weight = 3540.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.139771 restraints weight = 2133.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.141456 restraints weight = 1564.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.142129 restraints weight = 1279.675| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4952 Z= 0.146 Angle : 0.662 16.199 6727 Z= 0.324 Chirality : 0.043 0.164 766 Planarity : 0.005 0.049 834 Dihedral : 4.359 26.240 663 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.04 % Allowed : 23.53 % Favored : 73.43 % 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: 1.12 (0.34), residues: 613 helix: 1.42 (0.29), residues: 349 sheet: 1.59 (0.47), residues: 102 loop : -1.33 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 238 TYR 0.014 0.001 TYR A 343 PHE 0.027 0.001 PHE A 27 TRP 0.049 0.002 TRP B 192 HIS 0.001 0.000 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4950) covalent geometry : angle 0.66148 ( 6723) SS BOND : bond 0.00478 ( 2) SS BOND : angle 1.03960 ( 4) hydrogen bonds : bond 0.04205 ( 314) hydrogen bonds : angle 4.47771 ( 900) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.193 Fit side-chains REVERT: A 53 THR cc_start: 0.8252 (p) cc_final: 0.8038 (p) REVERT: A 100 MET cc_start: 0.8497 (tpp) cc_final: 0.7772 (tpt) REVERT: A 237 LEU cc_start: 0.3524 (OUTLIER) cc_final: 0.3085 (mp) REVERT: A 382 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7088 (mt-10) REVERT: B 174 ASP cc_start: 0.8693 (m-30) cc_final: 0.8455 (m-30) REVERT: B 207 MET cc_start: 0.6779 (pmm) cc_final: 0.6507 (pmm) REVERT: B 222 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7253 (tp) REVERT: B 278 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8202 (mp) outliers start: 16 outliers final: 9 residues processed: 100 average time/residue: 0.0478 time to fit residues: 6.7136 Evaluate side-chains 105 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 284 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 58 optimal weight: 0.0570 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.184705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.134423 restraints weight = 7657.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.138539 restraints weight = 3536.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.141046 restraints weight = 2126.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.142457 restraints weight = 1538.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.143446 restraints weight = 1273.654| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4952 Z= 0.137 Angle : 0.677 16.311 6727 Z= 0.328 Chirality : 0.042 0.166 766 Planarity : 0.005 0.050 834 Dihedral : 4.362 25.169 663 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.47 % Allowed : 24.67 % Favored : 72.87 % 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: 1.12 (0.34), residues: 613 helix: 1.39 (0.29), residues: 349 sheet: 1.62 (0.47), residues: 102 loop : -1.29 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 238 TYR 0.014 0.001 TYR A 343 PHE 0.026 0.001 PHE A 27 TRP 0.042 0.002 TRP B 192 HIS 0.001 0.000 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4950) covalent geometry : angle 0.67699 ( 6723) SS BOND : bond 0.00443 ( 2) SS BOND : angle 1.07251 ( 4) hydrogen bonds : bond 0.04011 ( 314) hydrogen bonds : angle 4.44565 ( 900) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.130 Fit side-chains REVERT: A 53 THR cc_start: 0.8211 (p) cc_final: 0.7983 (p) REVERT: A 100 MET cc_start: 0.8492 (tpp) cc_final: 0.7764 (tpt) REVERT: A 237 LEU cc_start: 0.3496 (OUTLIER) cc_final: 0.3066 (mp) REVERT: A 363 MET cc_start: 0.8296 (tpp) cc_final: 0.7861 (mmt) REVERT: A 382 GLU cc_start: 0.7296 (mt-10) cc_final: 0.7060 (mt-10) REVERT: B 174 ASP cc_start: 0.8693 (m-30) cc_final: 0.8433 (m-30) REVERT: B 207 MET cc_start: 0.6817 (pmm) cc_final: 0.6527 (pmm) REVERT: B 222 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7311 (tp) REVERT: B 238 ARG cc_start: 0.7367 (tmt170) cc_final: 0.6689 (ttm170) REVERT: B 278 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8167 (mp) outliers start: 13 outliers final: 8 residues processed: 100 average time/residue: 0.0532 time to fit residues: 7.4592 Evaluate side-chains 106 residues out of total 527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TRP Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 284 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 42 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.182683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132222 restraints weight = 7682.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.136238 restraints weight = 3566.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.138739 restraints weight = 2142.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.140378 restraints weight = 1546.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.140995 restraints weight = 1258.975| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4952 Z= 0.150 Angle : 0.680 16.258 6727 Z= 0.331 Chirality : 0.043 0.166 766 Planarity : 0.005 0.050 834 Dihedral : 4.413 26.308 663 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.66 % Allowed : 24.67 % Favored : 72.68 % 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 (0.34), residues: 613 helix: 1.36 (0.29), residues: 349 sheet: 1.60 (0.47), residues: 102 loop : -1.33 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 238 TYR 0.014 0.001 TYR A 343 PHE 0.026 0.001 PHE A 27 TRP 0.037 0.002 TRP B 192 HIS 0.001 0.000 HIS B 162 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 4950) covalent geometry : angle 0.68009 ( 6723) SS BOND : bond 0.00478 ( 2) SS BOND : angle 1.11010 ( 4) hydrogen bonds : bond 0.04272 ( 314) hydrogen bonds : angle 4.49864 ( 900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1001.82 seconds wall clock time: 17 minutes 54.39 seconds (1074.39 seconds total)