Starting phenix.real_space_refine on Sat Oct 24 03:18:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10up_75471/10_2026/10up_75471_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/10up_75471/10_2026/10up_75471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10up_75471/10_2026/10up_75471.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10up_75471/10_2026/10up_75471.map" model { file = "/net/cci-nas-00/data/ceres_data/10up_75471/10_2026/10up_75471_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10up_75471/10_2026/10up_75471_trim.cif" } resolution = 2.86 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= 0.032 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 S 38 5.16 5 C 3898 2.51 5 N 912 2.21 5 O 976 1.98 5 H 5825 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11649 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5796 Classifications: {'peptide': 363} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 340} Chain: "B" Number of atoms: 5797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5797 Classifications: {'peptide': 363} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 340} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.09, per 1000 atoms: 0.18 Number of scatterers: 11649 At special positions: 0 Unit cell: (80.442, 75.276, 101.844, 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 O 976 8.00 N 912 7.00 C 3898 6.00 H 5825 1.00 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: 0.83 Conformation dependent library (CDL) restraints added in 197.4 milliseconds 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1360 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 86.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 removed outlier: 3.900A pdb=" N ALA A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 28 removed outlier: 3.603A pdb=" N VAL A 19 " --> pdb=" O SER A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 54 removed outlier: 3.520A pdb=" N VAL A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 85 removed outlier: 4.002A pdb=" N VAL A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 105 through 132 removed outlier: 3.845A pdb=" N HIS A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR A 120 " --> pdb=" O GLY A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 161 Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.929A pdb=" N ILE A 167 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 174 through 190 Proline residue: A 181 - end of helix removed outlier: 3.579A pdb=" N ASN A 190 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'A' and resid 210 through 213 Processing helix chain 'A' and resid 214 through 239 Processing helix chain 'A' and resid 243 through 253 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 262 through 286 removed outlier: 3.949A pdb=" N VAL A 276 " --> pdb=" O MET A 272 " (cutoff:3.500A) Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 293 through 318 removed outlier: 3.685A pdb=" N LEU A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 331 through 356 Proline residue: A 346 - end of helix Processing helix chain 'A' and resid 357 through 360 Processing helix chain 'B' and resid 2 through 15 removed outlier: 3.961A pdb=" N ALA B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 28 removed outlier: 3.536A pdb=" N VAL B 19 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 21 " --> pdb=" O ILE B 17 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS B 25 " --> pdb=" O TYR B 21 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 54 removed outlier: 3.730A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 85 removed outlier: 3.970A pdb=" N VAL B 66 " --> pdb=" O PRO B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 99 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 105 through 132 removed outlier: 3.810A pdb=" N HIS B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 161 Proline residue: B 156 - end of helix removed outlier: 3.565A pdb=" N ILE B 159 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 175 through 190 Proline residue: B 181 - end of helix removed outlier: 3.687A pdb=" N ASN B 190 " --> pdb=" O PHE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 208 Processing helix chain 'B' and resid 210 through 213 Processing helix chain 'B' and resid 214 through 239 Processing helix chain 'B' and resid 243 through 253 Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 262 through 286 removed outlier: 3.929A pdb=" N VAL B 276 " --> pdb=" O MET B 272 " (cutoff:3.500A) Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 293 through 317 removed outlier: 3.604A pdb=" N LEU B 317 " --> pdb=" O ILE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 326 Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 331 through 356 Proline residue: B 346 - end of helix Processing helix chain 'B' and resid 357 through 361 removed outlier: 3.555A pdb=" N ILE B 361 " --> pdb=" O GLU B 358 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1197 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: 2.47 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5807 1.03 - 1.23: 18 1.23 - 1.42: 2568 1.42 - 1.62: 3384 1.62 - 1.81: 58 Bond restraints: 11835 Sorted by residual: bond pdb=" CA VAL B 276 " pdb=" CB VAL B 276 " ideal model delta sigma weight residual 1.539 1.545 -0.006 5.40e-03 3.43e+04 1.22e+00 bond pdb=" C LEU B 180 " pdb=" O LEU B 180 " ideal model delta sigma weight residual 1.244 1.236 0.007 9.80e-03 1.04e+04 5.46e-01 bond pdb=" C GLY A 303 " pdb=" O GLY A 303 " ideal model delta sigma weight residual 1.234 1.242 -0.009 1.20e-02 6.94e+03 5.15e-01 bond pdb=" C GLY B 303 " pdb=" O GLY B 303 " ideal model delta sigma weight residual 1.234 1.242 -0.008 1.20e-02 6.94e+03 4.58e-01 bond pdb=" CA ILE A 354 " pdb=" CB ILE A 354 " ideal model delta sigma weight residual 1.538 1.547 -0.009 1.42e-02 4.96e+03 4.00e-01 ... (remaining 11830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 19567 1.02 - 2.05: 1721 2.05 - 3.07: 61 3.07 - 4.09: 28 4.09 - 5.12: 7 Bond angle restraints: 21384 Sorted by residual: angle pdb=" N VAL A 276 " pdb=" CA VAL A 276 " pdb=" C VAL A 276 " ideal model delta sigma weight residual 112.35 108.50 3.85 1.20e+00 6.94e-01 1.03e+01 angle pdb=" N ILE B 17 " pdb=" CA ILE B 17 " pdb=" CB ILE B 17 " ideal model delta sigma weight residual 110.45 112.77 -2.32 7.80e-01 1.64e+00 8.84e+00 angle pdb=" N VAL A 287 " pdb=" CA VAL A 287 " pdb=" C VAL A 287 " ideal model delta sigma weight residual 111.90 109.58 2.32 8.10e-01 1.52e+00 8.18e+00 angle pdb=" C ILE B 17 " pdb=" CA ILE B 17 " pdb=" CB ILE B 17 " ideal model delta sigma weight residual 114.00 110.51 3.49 1.31e+00 5.83e-01 7.10e+00 angle pdb=" N ILE B 17 " pdb=" CA ILE B 17 " pdb=" C ILE B 17 " ideal model delta sigma weight residual 112.35 109.19 3.16 1.20e+00 6.94e-01 6.93e+00 ... (remaining 21379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5270 17.87 - 35.75: 283 35.75 - 53.62: 119 53.62 - 71.50: 63 71.50 - 89.37: 8 Dihedral angle restraints: 5743 sinusoidal: 3048 harmonic: 2695 Sorted by residual: dihedral pdb=" CA ASP A 240 " pdb=" CB ASP A 240 " pdb=" CG ASP A 240 " pdb=" OD1 ASP A 240 " ideal model delta sinusoidal sigma weight residual -30.00 -88.32 58.32 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA PRO A 260 " pdb=" C PRO A 260 " pdb=" N ALA A 261 " pdb=" CA ALA A 261 " ideal model delta harmonic sigma weight residual 180.00 163.95 16.05 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" N TYR B 102 " pdb=" CA TYR B 102 " pdb=" CB TYR B 102 " pdb=" CG TYR B 102 " ideal model delta sinusoidal sigma weight residual 60.00 2.34 57.66 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 5740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 597 0.027 - 0.054: 201 0.054 - 0.081: 89 0.081 - 0.108: 34 0.108 - 0.135: 11 Chirality restraints: 932 Sorted by residual: chirality pdb=" CA VAL A 327 " pdb=" N VAL A 327 " pdb=" C VAL A 327 " pdb=" CB VAL A 327 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA VAL A 288 " pdb=" N VAL A 288 " pdb=" C VAL A 288 " pdb=" CB VAL A 288 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 929 not shown) Planarity restraints: 1684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 180 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO B 181 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 181 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 181 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 294 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO A 295 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 180 " 0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO A 181 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " 0.018 5.00e-02 4.00e+02 ... (remaining 1681 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 420 2.18 - 2.78: 22542 2.78 - 3.39: 33531 3.39 - 3.99: 42107 3.99 - 4.60: 66778 Nonbonded interactions: 165378 Sorted by model distance: nonbonded pdb=" OD2 ASP A 85 " pdb=" HH TYR A 113 " model vdw 1.575 2.450 nonbonded pdb=" O MET A 1 " pdb=" HG SER A 4 " model vdw 1.587 2.450 nonbonded pdb="HD21 ASN B 77 " pdb=" OD2 ASP B 115 " model vdw 1.596 2.450 nonbonded pdb=" OD2 ASP B 85 " pdb=" HH TYR B 113 " model vdw 1.612 2.450 nonbonded pdb=" O LEU A 12 " pdb=" HG SER A 15 " model vdw 1.614 2.450 ... (remaining 165373 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 1 through 118 or (resid 119 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 120 through 401)) } 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: 3.720 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.380 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.002 0.024 6010 Z= 0.126 Angle : 0.497 5.119 8224 Z= 0.289 Chirality : 0.037 0.135 932 Planarity : 0.004 0.036 1004 Dihedral : 12.096 89.373 2212 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.15 % Allowed : 4.77 % Favored : 94.08 % 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: 2.17 (0.32), residues: 722 helix: 1.42 (0.22), residues: 556 sheet: None (None), residues: 0 loop : 1.96 (0.53), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 214 TYR 0.009 0.001 TYR B 278 PHE 0.012 0.001 PHE B 64 TRP 0.007 0.001 TRP A 183 HIS 0.003 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 ( 6010) covalent geometry : angle 0.49744 / 0.29 ( 8224) hydrogen bonds : bond 0.12143 / 8.22 ( 423) hydrogen bonds : angle 4.99857 / 3.69 ( 1197) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 TYR cc_start: 0.7205 (t80) cc_final: 0.6689 (t80) REVERT: B 211 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7398 (tt) REVERT: B 358 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6530 (mp0) outliers start: 7 outliers final: 4 residues processed: 87 average time/residue: 0.8078 time to fit residues: 74.9843 Evaluate side-chains 81 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 358 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 27] chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.164922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130614 restraints weight = 17865.778| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.95 r_work: 0.3431 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6010 Z= 0.134 Angle : 0.478 4.693 8224 Z= 0.258 Chirality : 0.037 0.135 932 Planarity : 0.005 0.033 1004 Dihedral : 5.826 62.998 949 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.81 % Allowed : 5.92 % Favored : 92.27 % 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: 2.25 (0.32), residues: 722 helix: 1.47 (0.22), residues: 562 sheet: None (None), residues: 0 loop : 1.98 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 352 TYR 0.010 0.001 TYR B 177 PHE 0.011 0.001 PHE B 64 TRP 0.008 0.001 TRP B 33 HIS 0.012 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 6010) covalent geometry : angle 0.47809 / 0.26 ( 8224) hydrogen bonds : bond 0.05472 / 3.86 ( 423) hydrogen bonds : angle 4.41197 / 3.22 ( 1197) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 TYR cc_start: 0.7448 (t80) cc_final: 0.6962 (t80) REVERT: B 51 ARG cc_start: 0.6003 (OUTLIER) cc_final: 0.5068 (ttt180) REVERT: B 211 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7553 (tt) REVERT: B 356 LYS cc_start: 0.7777 (mtmt) cc_final: 0.7250 (mtmt) outliers start: 11 outliers final: 5 residues processed: 79 average time/residue: 0.7716 time to fit residues: 65.4026 Evaluate side-chains 80 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 219 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [16, 23, 48, 21, 25, 54, 67, 5, 22, 2, 4] chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 54 optimal weight: 0.0270 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 0.0170 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.165039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.130209 restraints weight = 17814.010| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.97 r_work: 0.3428 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6010 Z= 0.107 Angle : 0.443 4.697 8224 Z= 0.233 Chirality : 0.036 0.134 932 Planarity : 0.004 0.032 1004 Dihedral : 5.057 52.157 946 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.32 % Allowed : 6.74 % Favored : 91.94 % 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: 2.29 (0.31), residues: 722 helix: 1.61 (0.22), residues: 568 sheet: None (None), residues: 0 loop : 1.55 (0.54), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 320 TYR 0.009 0.001 TYR B 177 PHE 0.010 0.001 PHE B 64 TRP 0.005 0.001 TRP B 33 HIS 0.004 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 ( 6010) covalent geometry : angle 0.44296 / 0.23 ( 8224) hydrogen bonds : bond 0.04704 / 3.33 ( 423) hydrogen bonds : angle 4.09122 / 2.99 ( 1197) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 TYR cc_start: 0.7449 (t80) cc_final: 0.6924 (t80) REVERT: B 51 ARG cc_start: 0.5996 (OUTLIER) cc_final: 0.5411 (ttp-170) REVERT: B 211 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7564 (tt) REVERT: B 356 LYS cc_start: 0.7699 (mtmt) cc_final: 0.7121 (mtmt) outliers start: 8 outliers final: 3 residues processed: 81 average time/residue: 0.8241 time to fit residues: 71.2763 Evaluate side-chains 82 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 219 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [59, 9, 53, 14, 24, 12, 13, 67, 2, 44, 21] chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 53 optimal weight: 0.0970 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.156267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.121213 restraints weight = 17907.787| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.02 r_work: 0.3317 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6010 Z= 0.120 Angle : 0.449 4.630 8224 Z= 0.236 Chirality : 0.037 0.136 932 Planarity : 0.004 0.033 1004 Dihedral : 4.866 50.673 944 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.32 % Allowed : 6.91 % Favored : 91.78 % 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: 2.27 (0.31), residues: 722 helix: 1.58 (0.21), residues: 568 sheet: None (None), residues: 0 loop : 1.59 (0.53), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 213 TYR 0.010 0.001 TYR B 278 PHE 0.011 0.001 PHE B 64 TRP 0.004 0.001 TRP B 183 HIS 0.005 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 6010) covalent geometry : angle 0.44851 / 0.24 ( 8224) hydrogen bonds : bond 0.04729 / 3.37 ( 423) hydrogen bonds : angle 4.04027 / 2.95 ( 1197) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3225 (tpt) cc_final: 0.2798 (ptm) REVERT: B 21 TYR cc_start: 0.7274 (t80) cc_final: 0.6731 (t80) REVERT: B 51 ARG cc_start: 0.5778 (OUTLIER) cc_final: 0.5193 (ttp-170) REVERT: B 211 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7433 (tt) REVERT: B 356 LYS cc_start: 0.7510 (mtmt) cc_final: 0.6918 (mtmt) REVERT: B 358 GLU cc_start: 0.7621 (mp0) cc_final: 0.7390 (mp0) outliers start: 8 outliers final: 4 residues processed: 80 average time/residue: 0.7840 time to fit residues: 66.8409 Evaluate side-chains 83 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 219 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [16, 69, 68, 24, 63, 22, 14, 9, 35, 36, 27] chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.155928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121450 restraints weight = 17852.871| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.97 r_work: 0.3317 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6010 Z= 0.120 Angle : 0.445 4.608 8224 Z= 0.234 Chirality : 0.037 0.137 932 Planarity : 0.004 0.036 1004 Dihedral : 4.837 50.372 944 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.64 % Allowed : 6.74 % Favored : 91.61 % 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: 2.66 (0.31), residues: 722 helix: 1.80 (0.22), residues: 550 sheet: None (None), residues: 0 loop : 1.99 (0.50), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 213 TYR 0.010 0.001 TYR B 278 PHE 0.011 0.001 PHE B 64 TRP 0.004 0.001 TRP B 183 HIS 0.006 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 6010) covalent geometry : angle 0.44493 / 0.23 ( 8224) hydrogen bonds : bond 0.04706 / 3.35 ( 423) hydrogen bonds : angle 3.99087 / 2.90 ( 1197) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 TYR cc_start: 0.7332 (t80) cc_final: 0.6785 (t80) REVERT: B 51 ARG cc_start: 0.5881 (OUTLIER) cc_final: 0.5307 (ttp-170) REVERT: B 211 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7461 (tt) REVERT: B 356 LYS cc_start: 0.7564 (mtmt) cc_final: 0.6990 (mtmt) outliers start: 10 outliers final: 6 residues processed: 84 average time/residue: 0.8077 time to fit residues: 72.4858 Evaluate side-chains 84 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 219 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [22, 30, 49, 66, 68, 37, 71, 53, 46, 48, 31] chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.156393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.121603 restraints weight = 17939.228| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.01 r_work: 0.3321 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6010 Z= 0.112 Angle : 0.444 4.571 8224 Z= 0.231 Chirality : 0.036 0.137 932 Planarity : 0.004 0.035 1004 Dihedral : 4.776 50.729 944 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.32 % Allowed : 8.06 % Favored : 90.62 % 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: 2.59 (0.31), residues: 722 helix: 1.79 (0.22), residues: 558 sheet: None (None), residues: 0 loop : 1.80 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 213 TYR 0.009 0.001 TYR B 278 PHE 0.010 0.001 PHE B 64 TRP 0.004 0.001 TRP B 143 HIS 0.006 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 6010) covalent geometry : angle 0.44360 / 0.23 ( 8224) hydrogen bonds : bond 0.04533 / 3.23 ( 423) hydrogen bonds : angle 3.94009 / 2.86 ( 1197) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5748 (tpt) cc_final: 0.5057 (tpp) REVERT: B 21 TYR cc_start: 0.7336 (t80) cc_final: 0.6779 (t80) REVERT: B 51 ARG cc_start: 0.5891 (OUTLIER) cc_final: 0.5319 (ttp-170) REVERT: B 211 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7483 (tt) REVERT: B 356 LYS cc_start: 0.7558 (mtmt) cc_final: 0.6969 (mtmt) outliers start: 8 outliers final: 5 residues processed: 80 average time/residue: 0.7947 time to fit residues: 68.0418 Evaluate side-chains 84 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 219 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [16, 9, 58, 71, 8, 45, 5, 26, 13, 46, 2] chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.154716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.119816 restraints weight = 17944.479| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.02 r_work: 0.3299 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6010 Z= 0.137 Angle : 0.456 4.538 8224 Z= 0.240 Chirality : 0.037 0.139 932 Planarity : 0.005 0.039 1004 Dihedral : 4.856 53.499 944 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.48 % Allowed : 8.39 % Favored : 90.13 % 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: 2.61 (0.31), residues: 722 helix: 1.78 (0.22), residues: 550 sheet: None (None), residues: 0 loop : 1.92 (0.50), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 320 TYR 0.011 0.001 TYR B 278 PHE 0.011 0.001 PHE B 64 TRP 0.004 0.001 TRP B 143 HIS 0.005 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 6010) covalent geometry : angle 0.45576 / 0.24 ( 8224) hydrogen bonds : bond 0.04859 / 3.47 ( 423) hydrogen bonds : angle 3.98299 / 2.89 ( 1197) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3360 (tpt) cc_final: 0.3012 (ptm) REVERT: B 21 TYR cc_start: 0.7272 (t80) cc_final: 0.6704 (t80) REVERT: B 51 ARG cc_start: 0.5902 (OUTLIER) cc_final: 0.5336 (ttp-170) REVERT: B 211 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7452 (tt) REVERT: B 356 LYS cc_start: 0.7503 (mtmt) cc_final: 0.6879 (mtmt) outliers start: 9 outliers final: 6 residues processed: 79 average time/residue: 0.7648 time to fit residues: 64.6622 Evaluate side-chains 81 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 162 LYS Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 219 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [12, 28, 38, 60, 36, 61, 44, 9, 37, 1, 49] chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 0.0070 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 0.0070 chunk 36 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 44 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.2216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.158110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.123664 restraints weight = 17730.413| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.97 r_work: 0.3356 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6010 Z= 0.097 Angle : 0.437 6.183 8224 Z= 0.226 Chirality : 0.036 0.138 932 Planarity : 0.004 0.033 1004 Dihedral : 4.632 50.327 944 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.48 % Allowed : 7.89 % Favored : 90.62 % 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: 2.80 (0.31), residues: 722 helix: 1.95 (0.22), residues: 560 sheet: None (None), residues: 0 loop : 1.83 (0.51), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 214 TYR 0.009 0.001 TYR B 177 PHE 0.010 0.001 PHE A 91 TRP 0.005 0.001 TRP B 143 HIS 0.006 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 ( 6010) covalent geometry : angle 0.43694 / 0.23 ( 8224) hydrogen bonds : bond 0.04124 / 2.94 ( 423) hydrogen bonds : angle 3.83794 / 2.79 ( 1197) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3482 (tpt) cc_final: 0.3126 (ptm) REVERT: A 53 LEU cc_start: 0.7253 (tp) cc_final: 0.6996 (tp) REVERT: A 359 PHE cc_start: 0.8943 (t80) cc_final: 0.8732 (t80) REVERT: B 1 MET cc_start: 0.5647 (tpt) cc_final: 0.4929 (tpp) REVERT: B 21 TYR cc_start: 0.7272 (t80) cc_final: 0.6698 (t80) REVERT: B 51 ARG cc_start: 0.5854 (OUTLIER) cc_final: 0.5412 (ttp-170) REVERT: B 219 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6018 (mtt) REVERT: B 356 LYS cc_start: 0.7474 (mtmt) cc_final: 0.6894 (mtmt) outliers start: 9 outliers final: 4 residues processed: 82 average time/residue: 0.7741 time to fit residues: 67.9675 Evaluate side-chains 84 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 219 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [25, 69, 47, 50, 63, 57, 2, 54, 18, 37, 27] chunk 25 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 54 optimal weight: 0.0770 chunk 18 optimal weight: 0.5980 chunk 37 optimal weight: 0.0470 chunk 27 optimal weight: 1.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.157594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.123269 restraints weight = 17679.180| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.97 r_work: 0.3344 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6010 Z= 0.100 Angle : 0.434 4.546 8224 Z= 0.224 Chirality : 0.036 0.136 932 Planarity : 0.004 0.033 1004 Dihedral : 4.373 50.516 942 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.99 % Allowed : 8.55 % Favored : 90.46 % 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: 2.83 (0.31), residues: 722 helix: 1.97 (0.22), residues: 560 sheet: None (None), residues: 0 loop : 1.84 (0.51), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 56 TYR 0.009 0.001 TYR A 177 PHE 0.009 0.001 PHE B 64 TRP 0.004 0.001 TRP B 143 HIS 0.007 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 6010) covalent geometry : angle 0.43351 / 0.22 ( 8224) hydrogen bonds : bond 0.04211 / 3.00 ( 423) hydrogen bonds : angle 3.84065 / 2.79 ( 1197) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3577 (tpt) cc_final: 0.3217 (ptm) REVERT: A 53 LEU cc_start: 0.7332 (tp) cc_final: 0.7102 (tp) REVERT: B 21 TYR cc_start: 0.7321 (t80) cc_final: 0.6794 (t80) REVERT: B 51 ARG cc_start: 0.5918 (OUTLIER) cc_final: 0.5485 (ttp-170) REVERT: B 219 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6112 (mtt) REVERT: B 356 LYS cc_start: 0.7521 (mtmt) cc_final: 0.6951 (mtmt) outliers start: 6 outliers final: 3 residues processed: 80 average time/residue: 0.7772 time to fit residues: 66.6867 Evaluate side-chains 81 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 219 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [26, 42, 68, 4, 45, 65, 20, 11, 59, 36, 53] chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.154500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.120165 restraints weight = 18006.106| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.98 r_work: 0.3304 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 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 : 0.004 0.030 6010 Z= 0.153 Angle : 0.470 4.537 8224 Z= 0.247 Chirality : 0.038 0.135 932 Planarity : 0.005 0.037 1004 Dihedral : 4.618 54.667 942 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.99 % Allowed : 8.88 % Favored : 90.13 % 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: 2.66 (0.31), residues: 722 helix: 1.82 (0.22), residues: 550 sheet: None (None), residues: 0 loop : 1.90 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 213 TYR 0.012 0.001 TYR B 278 PHE 0.013 0.001 PHE A 230 TRP 0.004 0.001 TRP B 143 HIS 0.006 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 6010) covalent geometry : angle 0.47031 / 0.25 ( 8224) hydrogen bonds : bond 0.04939 / 3.53 ( 423) hydrogen bonds : angle 3.98061 / 2.89 ( 1197) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3587 (tpt) cc_final: 0.2837 (ptt) REVERT: A 53 LEU cc_start: 0.7286 (tp) cc_final: 0.7056 (tp) REVERT: B 1 MET cc_start: 0.6294 (tpt) cc_final: 0.5607 (tpp) REVERT: B 21 TYR cc_start: 0.7330 (t80) cc_final: 0.6766 (t80) REVERT: B 51 ARG cc_start: 0.5882 (OUTLIER) cc_final: 0.5333 (ttp-170) REVERT: B 356 LYS cc_start: 0.7526 (mtmt) cc_final: 0.6949 (mtmt) outliers start: 6 outliers final: 4 residues processed: 78 average time/residue: 0.8108 time to fit residues: 67.4777 Evaluate side-chains 78 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 HIS Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 113 TYR Chi-restraints excluded: chain B residue 219 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [65, 30, 62, 26, 1, 3, 56, 51, 42, 45, 4] chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120651 restraints weight = 18023.323| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.98 r_work: 0.3308 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6010 Z= 0.131 Angle : 0.455 4.547 8224 Z= 0.238 Chirality : 0.037 0.135 932 Planarity : 0.004 0.037 1004 Dihedral : 4.609 54.911 942 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.99 % Allowed : 9.21 % Favored : 89.80 % 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: 2.68 (0.31), residues: 722 helix: 1.84 (0.22), residues: 550 sheet: None (None), residues: 0 loop : 1.90 (0.49), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 213 TYR 0.011 0.001 TYR B 278 PHE 0.011 0.001 PHE B 64 TRP 0.005 0.001 TRP B 143 HIS 0.006 0.001 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 6010) covalent geometry : angle 0.45459 / 0.24 ( 8224) hydrogen bonds : bond 0.04772 / 3.41 ( 423) hydrogen bonds : angle 3.95370 / 2.87 ( 1197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3474.98 seconds wall clock time: 59 minutes 32.77 seconds (3572.77 seconds total)