Starting phenix.real_space_refine on Sat Oct 24 02:47:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11br_75606/10_2026/11br_75606.cif Found real_map, /net/cci-nas-00/data/ceres_data/11br_75606/10_2026/11br_75606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11br_75606/10_2026/11br_75606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11br_75606/10_2026/11br_75606.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11br_75606/10_2026/11br_75606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11br_75606/10_2026/11br_75606.map" } resolution = 3.37 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= 0.021 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 3830 2.51 5 N 910 2.21 5 O 968 1.98 5 H 5814 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s 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: 11560 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5780 Classifications: {'peptide': 363} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 340} Chain: "B" Number of atoms: 5780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 5780 Classifications: {'peptide': 363} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 22, 'TRANS': 340} Time building chain proxies: 2.10, per 1000 atoms: 0.18 Number of scatterers: 11560 At special positions: 0 Unit cell: (82.566, 83.4, 103.416, 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 968 8.00 N 910 7.00 C 3830 6.00 H 5814 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: 1.15 Conformation dependent library (CDL) restraints added in 223.3 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: 40 helices and 0 sheets defined 84.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 removed outlier: 3.838A pdb=" N ALA A 6 " --> pdb=" O SER A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 28 removed outlier: 3.684A pdb=" N VAL A 19 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 28 " --> pdb=" O ASN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 54 removed outlier: 3.882A pdb=" N VAL A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 85 removed outlier: 3.825A pdb=" N VAL A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 105 through 132 removed outlier: 4.223A pdb=" N TYR A 120 " --> pdb=" O GLY A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 161 removed outlier: 3.652A pdb=" N TYR A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.057A pdb=" N ALA A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 190 Processing helix chain 'A' and resid 199 through 209 removed outlier: 3.637A pdb=" N LYS A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) 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: 4.020A 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: 3.594A pdb=" N GLN A 307 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 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 361 Processing helix chain 'B' and resid 2 through 15 removed outlier: 3.902A pdb=" N ALA B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 28 removed outlier: 3.656A pdb=" N HIS B 25 " --> pdb=" O TYR B 21 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B 28 " --> pdb=" O ASN B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 54 removed outlier: 3.590A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 85 removed outlier: 4.011A pdb=" N VAL B 66 " --> pdb=" O PRO B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 101 through 104 Processing helix chain 'B' and resid 105 through 132 removed outlier: 4.745A pdb=" N TYR B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 160 Proline residue: B 156 - end of helix Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 173 through 190 removed outlier: 4.211A pdb=" N ALA B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 199 through 209 removed outlier: 3.836A pdb=" N LYS B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) 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 288 removed outlier: 4.112A pdb=" N VAL B 276 " --> pdb=" O MET B 272 " (cutoff:3.500A) Proline residue: B 277 - end of helix removed outlier: 3.614A pdb=" N VAL B 287 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 318 removed outlier: 3.693A pdb=" N GLN B 307 " --> pdb=" O GLY B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 326 Processing helix chain 'B' and resid 328 through 355 removed outlier: 4.401A pdb=" N ILE B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) Proline residue: B 346 - end of helix Processing helix chain 'B' and resid 356 through 361 removed outlier: 4.097A pdb=" N PHE B 359 " --> pdb=" O LYS B 356 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1191 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: 2.82 Time building geometry restraints manager: 1.55 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: 5796 1.03 - 1.23: 19 1.23 - 1.42: 2543 1.42 - 1.62: 3322 1.62 - 1.81: 58 Bond restraints: 11738 Sorted by residual: bond pdb=" N GLU B 98 " pdb=" CA GLU B 98 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.17e+00 bond pdb=" CA ILE A 175 " pdb=" CB ILE A 175 " ideal model delta sigma weight residual 1.539 1.545 -0.006 5.40e-03 3.43e+04 1.16e+00 bond pdb=" CB LYS A 57 " pdb=" CG LYS A 57 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.19e-01 bond pdb=" N SER A 117 " pdb=" CA SER A 117 " ideal model delta sigma weight residual 1.468 1.459 0.009 1.24e-02 6.50e+03 5.72e-01 bond pdb=" C SER A 117 " pdb=" O SER A 117 " ideal model delta sigma weight residual 1.234 1.240 -0.006 8.30e-03 1.45e+04 5.10e-01 ... (remaining 11733 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 19667 1.07 - 2.14: 1458 2.14 - 3.20: 68 3.20 - 4.27: 34 4.27 - 5.34: 7 Bond angle restraints: 21234 Sorted by residual: angle pdb=" N VAL B 276 " pdb=" CA VAL B 276 " pdb=" C VAL B 276 " ideal model delta sigma weight residual 112.35 108.99 3.36 1.20e+00 6.94e-01 7.83e+00 angle pdb=" C GLU B 98 " pdb=" CA GLU B 98 " pdb=" CB GLU B 98 " ideal model delta sigma weight residual 110.42 115.76 -5.34 1.99e+00 2.53e-01 7.20e+00 angle pdb=" C GLY A 116 " pdb=" N SER A 117 " pdb=" CA SER A 117 " ideal model delta sigma weight residual 121.71 118.70 3.01 1.39e+00 5.18e-01 4.68e+00 angle pdb=" CB LYS A 57 " pdb=" CG LYS A 57 " pdb=" CD LYS A 57 " ideal model delta sigma weight residual 111.30 116.12 -4.82 2.30e+00 1.89e-01 4.39e+00 angle pdb=" CA VAL B 276 " pdb=" C VAL B 276 " pdb=" N PRO B 277 " ideal model delta sigma weight residual 120.83 119.62 1.21 6.10e-01 2.69e+00 3.94e+00 ... (remaining 21229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 5058 16.07 - 32.14: 315 32.14 - 48.21: 113 48.21 - 64.29: 92 64.29 - 80.36: 14 Dihedral angle restraints: 5592 sinusoidal: 2908 harmonic: 2684 Sorted by residual: dihedral pdb=" CA PHE A 252 " pdb=" C PHE A 252 " pdb=" N GLN A 253 " pdb=" CA GLN A 253 " ideal model delta harmonic sigma weight residual -180.00 -162.80 -17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ASP A 89 " pdb=" CB ASP A 89 " pdb=" CG ASP A 89 " pdb=" OD1 ASP A 89 " ideal model delta sinusoidal sigma weight residual -30.00 -89.30 59.30 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA PHE A 171 " pdb=" C PHE A 171 " pdb=" N PHE A 172 " pdb=" CA PHE A 172 " ideal model delta harmonic sigma weight residual -180.00 -163.14 -16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 567 0.026 - 0.052: 212 0.052 - 0.079: 91 0.079 - 0.105: 37 0.105 - 0.131: 9 Chirality restraints: 916 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 2.57 -0.13 2.00e-01 2.50e+01 4.30e-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 3.92e-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 2.56 -0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 913 not shown) Planarity restraints: 1680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 115 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C ASP A 115 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP A 115 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 116 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 115 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C ASP B 115 " -0.031 2.00e-02 2.50e+03 pdb=" O ASP B 115 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY B 116 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 180 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+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 1677 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 658 2.21 - 2.81: 23733 2.81 - 3.40: 33099 3.40 - 4.00: 41001 4.00 - 4.60: 63803 Nonbonded interactions: 162294 Sorted by model distance: nonbonded pdb=" O ASP B 31 " pdb=" HG1 THR B 34 " model vdw 1.610 2.450 nonbonded pdb="HH11 ARG A 214 " pdb=" OD2 ASP A 217 " model vdw 1.618 2.450 nonbonded pdb=" O TYR A 102 " pdb=" HG1 THR A 105 " model vdw 1.634 2.450 nonbonded pdb=" OE1 GLU B 330 " pdb=" H GLU B 330 " model vdw 1.640 2.450 nonbonded pdb=" O LEU A 12 " pdb=" HG SER A 15 " model vdw 1.642 2.450 ... (remaining 162289 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' } 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: 3.970 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.570 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 0.030 5924 Z= 0.133 Angle : 0.529 5.339 8096 Z= 0.300 Chirality : 0.037 0.131 916 Planarity : 0.004 0.031 1000 Dihedral : 11.885 80.357 2070 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.66 % Allowed : 5.81 % Favored : 93.52 % 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: 2.43 (0.32), residues: 722 helix: 1.65 (0.22), residues: 528 sheet: None (None), residues: 0 loop : 1.83 (0.55), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 213 TYR 0.012 0.001 TYR A 196 PHE 0.008 0.001 PHE B 154 TRP 0.006 0.001 TRP B 183 HIS 0.002 0.001 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 5924) covalent geometry : angle 0.52893 / 0.30 ( 8096) hydrogen bonds : bond 0.12198 / 8.17 ( 417) hydrogen bonds : angle 4.94568 / 3.63 ( 1191) *********************** 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 63 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8686 (m-30) cc_final: 0.8302 (m-30) REVERT: A 240 ASP cc_start: 0.9281 (t0) cc_final: 0.9076 (t0) REVERT: B 353 CYS cc_start: 0.9008 (m) cc_final: 0.8791 (m) outliers start: 4 outliers final: 3 residues processed: 61 average time/residue: 0.1109 time to fit residues: 10.1857 Evaluate side-chains 56 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 305 LEU 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: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.069711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.058683 restraints weight = 64516.742| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.40 r_work: 0.2874 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5924 Z= 0.133 Angle : 0.510 5.072 8096 Z= 0.271 Chirality : 0.037 0.132 916 Planarity : 0.004 0.037 1000 Dihedral : 5.019 52.727 812 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.16 % Allowed : 7.64 % Favored : 91.20 % 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 (0.32), residues: 722 helix: 1.84 (0.22), residues: 536 sheet: None (None), residues: 0 loop : 1.91 (0.57), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 352 TYR 0.015 0.001 TYR A 21 PHE 0.008 0.001 PHE B 64 TRP 0.007 0.001 TRP B 33 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 5924) covalent geometry : angle 0.50976 / 0.27 ( 8096) hydrogen bonds : bond 0.04898 / 3.29 ( 417) hydrogen bonds : angle 4.36611 / 3.21 ( 1191) *********************** 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 61 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.9040 (t80) cc_final: 0.8826 (t80) REVERT: A 85 ASP cc_start: 0.8617 (m-30) cc_final: 0.8174 (m-30) REVERT: B 353 CYS cc_start: 0.8973 (m) cc_final: 0.8676 (m) outliers start: 7 outliers final: 6 residues processed: 57 average time/residue: 0.1051 time to fit residues: 8.8363 Evaluate side-chains 58 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 237 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [52, 3, 16, 57, 51, 56, 65, 58, 40, 66, 61] chunk 52 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 0.0020 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.071882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.061474 restraints weight = 62342.210| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.21 r_work: 0.2953 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5924 Z= 0.111 Angle : 0.471 4.584 8096 Z= 0.245 Chirality : 0.036 0.133 916 Planarity : 0.004 0.036 1000 Dihedral : 4.521 52.115 810 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.16 % Allowed : 7.48 % Favored : 91.36 % 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: 2.97 (0.32), residues: 722 helix: 2.11 (0.22), residues: 536 sheet: None (None), residues: 0 loop : 1.82 (0.55), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 352 TYR 0.010 0.001 TYR A 21 PHE 0.006 0.001 PHE B 64 TRP 0.005 0.001 TRP B 183 HIS 0.004 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 5924) covalent geometry : angle 0.47111 / 0.24 ( 8096) hydrogen bonds : bond 0.04273 / 2.87 ( 417) hydrogen bonds : angle 4.07620 / 3.00 ( 1191) *********************** 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 64 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.9023 (t80) cc_final: 0.8803 (t80) REVERT: A 85 ASP cc_start: 0.8530 (m-30) cc_final: 0.8319 (m-30) outliers start: 7 outliers final: 6 residues processed: 60 average time/residue: 0.1104 time to fit residues: 9.9745 Evaluate side-chains 58 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 237 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [70, 24, 34, 40, 43, 8, 25, 0, 42, 6, 45] chunk 70 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.070745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.060239 restraints weight = 62420.015| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.25 r_work: 0.2926 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5924 Z= 0.172 Angle : 0.498 4.659 8096 Z= 0.262 Chirality : 0.037 0.127 916 Planarity : 0.004 0.036 1000 Dihedral : 4.419 50.520 810 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.16 % Allowed : 8.31 % Favored : 90.53 % 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: 2.96 (0.32), residues: 722 helix: 2.13 (0.22), residues: 536 sheet: None (None), residues: 0 loop : 1.73 (0.55), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 352 TYR 0.014 0.001 TYR A 21 PHE 0.006 0.001 PHE A 252 TRP 0.005 0.001 TRP B 183 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 ( 5924) covalent geometry : angle 0.49762 / 0.26 ( 8096) hydrogen bonds : bond 0.04166 / 2.80 ( 417) hydrogen bonds : angle 4.16104 / 3.06 ( 1191) *********************** 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 60 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.9030 (t80) cc_final: 0.8827 (t80) outliers start: 7 outliers final: 4 residues processed: 57 average time/residue: 0.1145 time to fit residues: 9.8229 Evaluate side-chains 55 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 237 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [27, 40, 41, 29, 11, 49, 36, 31, 18, 53, 26] chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 53 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.071548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.061135 restraints weight = 61934.416| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.25 r_work: 0.2937 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5924 Z= 0.144 Angle : 0.477 4.762 8096 Z= 0.250 Chirality : 0.036 0.131 916 Planarity : 0.004 0.037 1000 Dihedral : 3.700 15.006 806 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.83 % Allowed : 8.64 % Favored : 90.53 % 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: 3.13 (0.32), residues: 722 helix: 2.19 (0.22), residues: 542 sheet: None (None), residues: 0 loop : 1.97 (0.55), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 214 TYR 0.009 0.001 TYR A 67 PHE 0.007 0.001 PHE B 64 TRP 0.005 0.001 TRP B 183 HIS 0.004 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 5924) covalent geometry : angle 0.47664 / 0.25 ( 8096) hydrogen bonds : bond 0.04012 / 2.70 ( 417) hydrogen bonds : angle 4.06429 / 3.00 ( 1191) *********************** 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 58 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8506 (m-30) cc_final: 0.8137 (m-30) outliers start: 5 outliers final: 4 residues processed: 56 average time/residue: 0.1099 time to fit residues: 9.1837 Evaluate side-chains 56 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 237 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [59, 27, 64, 53, 40, 25, 22, 62, 19, 0, 2] chunk 59 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 64 optimal weight: 0.0020 chunk 53 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 339 ASN ** 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 = 0.3330 r_free = 0.3330 target = 0.071926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.061477 restraints weight = 61862.241| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.27 r_work: 0.2940 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5924 Z= 0.127 Angle : 0.472 5.519 8096 Z= 0.244 Chirality : 0.036 0.132 916 Planarity : 0.004 0.036 1000 Dihedral : 3.640 14.875 806 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.16 % Allowed : 8.47 % Favored : 90.37 % 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: 3.22 (0.32), residues: 722 helix: 2.26 (0.22), residues: 542 sheet: None (None), residues: 0 loop : 1.98 (0.54), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 214 TYR 0.008 0.001 TYR A 278 PHE 0.006 0.001 PHE A 64 TRP 0.004 0.001 TRP B 183 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 5924) covalent geometry : angle 0.47248 / 0.24 ( 8096) hydrogen bonds : bond 0.03883 / 2.61 ( 417) hydrogen bonds : angle 3.99594 / 2.94 ( 1191) *********************** 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 65 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8476 (m-30) cc_final: 0.8094 (m-30) outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 0.1127 time to fit residues: 10.5620 Evaluate side-chains 57 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 237 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [63, 14, 27, 30, 3, 2, 37, 19, 24, 45, 20] chunk 63 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 19 optimal weight: 0.0030 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.072583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.062036 restraints weight = 61837.645| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.25 r_work: 0.2952 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5924 Z= 0.111 Angle : 0.459 4.263 8096 Z= 0.238 Chirality : 0.036 0.134 916 Planarity : 0.004 0.036 1000 Dihedral : 3.559 14.723 806 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.83 % Allowed : 9.30 % Favored : 89.87 % 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: 3.33 (0.32), residues: 722 helix: 2.35 (0.22), residues: 542 sheet: None (None), residues: 0 loop : 1.98 (0.53), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 214 TYR 0.008 0.001 TYR A 278 PHE 0.006 0.001 PHE A 64 TRP 0.004 0.001 TRP B 183 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 5924) covalent geometry : angle 0.45920 / 0.24 ( 8096) hydrogen bonds : bond 0.03744 / 2.52 ( 417) hydrogen bonds : angle 3.90218 / 2.87 ( 1191) *********************** 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 62 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8445 (m-30) cc_final: 0.8107 (m-30) outliers start: 5 outliers final: 4 residues processed: 60 average time/residue: 0.1214 time to fit residues: 11.0460 Evaluate side-chains 59 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 237 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [46, 13, 68, 55, 30, 34, 37, 57, 50, 4, 45] chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 339 ASN ** 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 = 0.3330 r_free = 0.3330 target = 0.071862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.061509 restraints weight = 61404.749| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.20 r_work: 0.2942 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5924 Z= 0.132 Angle : 0.469 4.281 8096 Z= 0.243 Chirality : 0.036 0.131 916 Planarity : 0.004 0.035 1000 Dihedral : 3.525 14.586 806 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.83 % Allowed : 9.30 % Favored : 89.87 % 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: 3.33 (0.32), residues: 722 helix: 2.37 (0.22), residues: 542 sheet: None (None), residues: 0 loop : 1.93 (0.53), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 214 TYR 0.009 0.001 TYR A 67 PHE 0.006 0.001 PHE A 64 TRP 0.004 0.001 TRP A 143 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 5924) covalent geometry : angle 0.46855 / 0.24 ( 8096) hydrogen bonds : bond 0.03727 / 2.51 ( 417) hydrogen bonds : angle 3.92583 / 2.89 ( 1191) *********************** 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 61 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8466 (m-30) cc_final: 0.8087 (m-30) outliers start: 5 outliers final: 5 residues processed: 59 average time/residue: 0.1162 time to fit residues: 10.2885 Evaluate side-chains 60 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 268 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [3, 17, 8, 65, 14, 27, 63, 5, 66, 62, 54] chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 339 ASN ** 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 = 0.3339 r_free = 0.3339 target = 0.072672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.062127 restraints weight = 61806.204| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.22 r_work: 0.2956 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5924 Z= 0.112 Angle : 0.457 4.298 8096 Z= 0.237 Chirality : 0.036 0.134 916 Planarity : 0.004 0.036 1000 Dihedral : 3.479 14.705 806 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.83 % Allowed : 9.63 % Favored : 89.53 % 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: 3.40 (0.32), residues: 722 helix: 2.43 (0.22), residues: 542 sheet: None (None), residues: 0 loop : 1.93 (0.53), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 214 TYR 0.009 0.001 TYR A 278 PHE 0.006 0.001 PHE A 64 TRP 0.004 0.001 TRP B 114 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 5924) covalent geometry : angle 0.45715 / 0.24 ( 8096) hydrogen bonds : bond 0.03625 / 2.43 ( 417) hydrogen bonds : angle 3.85711 / 2.84 ( 1191) *********************** 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 62 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.8900 (m100) cc_final: 0.8543 (m100) outliers start: 5 outliers final: 5 residues processed: 60 average time/residue: 0.1196 time to fit residues: 10.7887 Evaluate side-chains 61 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 268 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [69, 16, 21, 56, 68, 23, 19, 38, 31, 32, 64] chunk 69 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 23 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 339 ASN ** 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 = 0.3338 r_free = 0.3338 target = 0.072611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.062036 restraints weight = 62393.155| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.24 r_work: 0.2955 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5924 Z= 0.110 Angle : 0.461 4.714 8096 Z= 0.237 Chirality : 0.036 0.133 916 Planarity : 0.004 0.036 1000 Dihedral : 3.442 14.623 806 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.83 % Allowed : 9.63 % Favored : 89.53 % 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: 3.43 (0.32), residues: 722 helix: 2.45 (0.22), residues: 542 sheet: None (None), residues: 0 loop : 1.95 (0.52), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 214 TYR 0.010 0.001 TYR A 67 PHE 0.005 0.001 PHE A 64 TRP 0.004 0.001 TRP B 132 HIS 0.002 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 5924) covalent geometry : angle 0.46131 / 0.24 ( 8096) hydrogen bonds : bond 0.03562 / 2.40 ( 417) hydrogen bonds : angle 3.83534 / 2.82 ( 1191) ********************** 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 62 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.8899 (m100) cc_final: 0.8547 (m100) outliers start: 5 outliers final: 5 residues processed: 60 average time/residue: 0.1183 time to fit residues: 10.6066 Evaluate side-chains 60 residues out of total 602 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 268 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: [47, 25, 34, 3, 26, 36, 30, 17, 7, 51, 10] chunk 47 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 339 ASN ** 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 = 0.3346 r_free = 0.3346 target = 0.072892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.062320 restraints weight = 62530.825| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.23 r_work: 0.2956 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5924 Z= 0.117 Angle : 0.460 4.642 8096 Z= 0.238 Chirality : 0.036 0.133 916 Planarity : 0.004 0.035 1000 Dihedral : 3.419 14.623 806 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.83 % Allowed : 9.63 % Favored : 89.53 % 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: 3.45 (0.32), residues: 722 helix: 2.45 (0.22), residues: 544 sheet: None (None), residues: 0 loop : 2.00 (0.52), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 214 TYR 0.011 0.001 TYR A 67 PHE 0.005 0.001 PHE A 64 TRP 0.005 0.001 TRP B 114 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 5924) covalent geometry : angle 0.46010 / 0.24 ( 8096) hydrogen bonds : bond 0.03556 / 2.39 ( 417) hydrogen bonds : angle 3.83681 / 2.82 ( 1191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2347.15 seconds wall clock time: 40 minutes 36.56 seconds (2436.56 seconds total)