Starting phenix.real_space_refine on Tue Aug 4 16:19:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21vl_68036/08_2026/21vl_68036.cif Found real_map, /net/cci-nas-00/data/ceres_data/21vl_68036/08_2026/21vl_68036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21vl_68036/08_2026/21vl_68036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21vl_68036/08_2026/21vl_68036.map" model { file = "/net/cci-nas-00/data/ceres_data/21vl_68036/08_2026/21vl_68036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21vl_68036/08_2026/21vl_68036.cif" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.510 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 3021 2.51 5 N 796 2.21 5 O 919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4754 Number of models: 1 Model: "" Number of chains: 2 Chain: "H" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3390 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 23, 'TRANS': 400} Chain breaks: 1 Chain: "E" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1364 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Time building chain proxies: 1.17, per 1000 atoms: 0.25 Number of scatterers: 4754 At special positions: 0 Unit cell: (94.6, 75.9, 191.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 919 8.00 N 796 7.00 C 3021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 111.3 milliseconds 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1112 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 6 sheets defined 49.4% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'H' and resid 64 through 76 removed outlier: 4.667A pdb=" N ILE H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ARG H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 96 removed outlier: 4.205A pdb=" N ALA H 87 " --> pdb=" O THR H 83 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR H 88 " --> pdb=" O ALA H 84 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR H 89 " --> pdb=" O LEU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 123 removed outlier: 3.696A pdb=" N ARG H 111 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 136 removed outlier: 3.867A pdb=" N TYR H 131 " --> pdb=" O PRO H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 142 Processing helix chain 'H' and resid 239 through 243 removed outlier: 3.759A pdb=" N ALA H 243 " --> pdb=" O PRO H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 264 removed outlier: 3.526A pdb=" N TRP H 248 " --> pdb=" O VAL H 244 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU H 253 " --> pdb=" O ARG H 249 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER H 263 " --> pdb=" O VAL H 259 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS H 264 " --> pdb=" O VAL H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 283 removed outlier: 4.058A pdb=" N LEU H 279 " --> pdb=" O PRO H 275 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER H 283 " --> pdb=" O LEU H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 303 removed outlier: 3.794A pdb=" N ASN H 303 " --> pdb=" O ALA H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 359 removed outlier: 4.043A pdb=" N LEU H 346 " --> pdb=" O ASP H 342 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG H 357 " --> pdb=" O ASP H 353 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE H 358 " --> pdb=" O ILE H 354 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY H 359 " --> pdb=" O TYR H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 402 removed outlier: 3.914A pdb=" N HIS H 385 " --> pdb=" O THR H 381 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE H 386 " --> pdb=" O LEU H 382 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG H 389 " --> pdb=" O HIS H 385 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP H 390 " --> pdb=" O PHE H 386 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL H 391 " --> pdb=" O ILE H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 402 through 410 removed outlier: 3.852A pdb=" N LEU H 406 " --> pdb=" O VAL H 402 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 445 removed outlier: 3.556A pdb=" N LYS H 437 " --> pdb=" O GLU H 433 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA H 445 " --> pdb=" O GLN H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 463 Processing helix chain 'H' and resid 469 through 475 removed outlier: 3.592A pdb=" N ASP H 475 " --> pdb=" O ASP H 471 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 487 Processing helix chain 'E' and resid 7 through 15 removed outlier: 3.667A pdb=" N ILE E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE E 13 " --> pdb=" O PRO E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 39 removed outlier: 3.705A pdb=" N GLN E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP E 35 " --> pdb=" O ILE E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 73 removed outlier: 3.790A pdb=" N VAL E 49 " --> pdb=" O ASN E 45 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN E 70 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN E 72 " --> pdb=" O ASN E 68 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR E 73 " --> pdb=" O HIS E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 125 through 129 Processing helix chain 'E' and resid 136 through 145 removed outlier: 3.606A pdb=" N ILE E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 172 removed outlier: 3.675A pdb=" N TYR E 168 " --> pdb=" O ASN E 165 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 99 through 102 removed outlier: 3.674A pdb=" N LYS H 102 " --> pdb=" O LYS H 421 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 164 through 171 removed outlier: 5.346A pdb=" N LEU H 166 " --> pdb=" O GLU H 151 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU H 151 " --> pdb=" O LEU H 166 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS H 168 " --> pdb=" O VAL H 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 183 through 185 removed outlier: 6.857A pdb=" N THR H 184 " --> pdb=" O LEU H 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 270 through 273 removed outlier: 3.943A pdb=" N ASP H 328 " --> pdb=" O MET H 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 318 through 319 Processing sheet with id=AA6, first strand: chain 'E' and resid 78 through 83 190 hydrogen bonds defined for protein. 537 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.39 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1585 1.34 - 1.46: 1024 1.46 - 1.58: 2206 1.58 - 1.70: 0 1.70 - 1.81: 34 Bond restraints: 4849 Sorted by residual: bond pdb=" N ASN H 104 " pdb=" CA ASN H 104 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.30e-02 5.92e+03 7.57e+00 bond pdb=" N ASP H 470 " pdb=" CA ASP H 470 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.20e-02 6.94e+03 6.84e+00 bond pdb=" N ASP E 42 " pdb=" CA ASP E 42 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.43e+00 bond pdb=" N TYR H 103 " pdb=" CA TYR H 103 " ideal model delta sigma weight residual 1.457 1.494 -0.038 1.53e-02 4.27e+03 6.02e+00 bond pdb=" N ASP H 471 " pdb=" CA ASP H 471 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.01e+00 ... (remaining 4844 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 6486 2.46 - 4.93: 81 4.93 - 7.39: 8 7.39 - 9.85: 2 9.85 - 12.32: 1 Bond angle restraints: 6578 Sorted by residual: angle pdb=" CB MET E 1 " pdb=" CG MET E 1 " pdb=" SD MET E 1 " ideal model delta sigma weight residual 112.70 125.02 -12.32 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C MET E 1 " pdb=" CA MET E 1 " pdb=" CB MET E 1 " ideal model delta sigma weight residual 110.10 117.65 -7.55 1.90e+00 2.77e-01 1.58e+01 angle pdb=" CA ASP H 471 " pdb=" CB ASP H 471 " pdb=" CG ASP H 471 " ideal model delta sigma weight residual 112.60 115.89 -3.29 1.00e+00 1.00e+00 1.08e+01 angle pdb=" C VAL H 402 " pdb=" N ILE H 403 " pdb=" CA ILE H 403 " ideal model delta sigma weight residual 120.33 122.90 -2.57 8.00e-01 1.56e+00 1.03e+01 angle pdb=" CA MET E 1 " pdb=" CB MET E 1 " pdb=" CG MET E 1 " ideal model delta sigma weight residual 114.10 120.46 -6.36 2.00e+00 2.50e-01 1.01e+01 ... (remaining 6573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 2546 17.74 - 35.48: 288 35.48 - 53.22: 72 53.22 - 70.96: 12 70.96 - 88.70: 4 Dihedral angle restraints: 2922 sinusoidal: 1184 harmonic: 1738 Sorted by residual: dihedral pdb=" CA GLY H 307 " pdb=" C GLY H 307 " pdb=" N GLU H 308 " pdb=" CA GLU H 308 " ideal model delta harmonic sigma weight residual 180.00 160.61 19.39 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ASP H 390 " pdb=" CB ASP H 390 " pdb=" CG ASP H 390 " pdb=" OD1 ASP H 390 " ideal model delta sinusoidal sigma weight residual -30.00 -88.65 58.65 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CB GLU H 258 " pdb=" CG GLU H 258 " pdb=" CD GLU H 258 " pdb=" OE1 GLU H 258 " ideal model delta sinusoidal sigma weight residual 0.00 88.70 -88.70 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 2919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 486 0.031 - 0.063: 160 0.063 - 0.094: 49 0.094 - 0.126: 29 0.126 - 0.157: 7 Chirality restraints: 731 Sorted by residual: chirality pdb=" CA ILE E 117 " pdb=" N ILE E 117 " pdb=" C ILE E 117 " pdb=" CB ILE E 117 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA VAL E 135 " pdb=" N VAL E 135 " pdb=" C VAL E 135 " pdb=" CB VAL E 135 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE H 224 " pdb=" N ILE H 224 " pdb=" C ILE H 224 " pdb=" CB ILE H 224 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 728 not shown) Planarity restraints: 865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 23 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO E 24 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO E 24 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 24 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 8 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO E 9 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 9 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 9 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 25 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.36e+00 pdb=" C ASP E 25 " 0.027 2.00e-02 2.50e+03 pdb=" O ASP E 25 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA E 26 " -0.009 2.00e-02 2.50e+03 ... (remaining 862 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1053 2.78 - 3.31: 4209 3.31 - 3.84: 6754 3.84 - 4.37: 7067 4.37 - 4.90: 12976 Nonbonded interactions: 32059 Sorted by model distance: nonbonded pdb=" O ASP E 141 " pdb=" OG SER E 145 " model vdw 2.253 3.040 nonbonded pdb=" OG SER H 186 " pdb=" O ASP H 188 " model vdw 2.262 3.040 nonbonded pdb=" O GLU E 21 " pdb=" OG1 THR E 22 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR H 225 " pdb=" O PRO H 235 " model vdw 2.302 3.040 nonbonded pdb=" O ALA E 48 " pdb=" ND2 ASN E 52 " model vdw 2.309 3.120 ... (remaining 32054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.940 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 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 0.042 4849 Z= 0.184 Angle : 0.682 12.319 6578 Z= 0.385 Chirality : 0.041 0.157 731 Planarity : 0.005 0.065 865 Dihedral : 15.947 88.701 1810 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.84 % Allowed : 5.04 % Favored : 94.12 % Rotamer: Outliers : 0.38 % Allowed : 18.01 % Favored : 81.61 % 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: 0.04 (0.34), residues: 595 helix: 2.21 (0.32), residues: 243 sheet: 0.07 (0.64), residues: 56 loop : -2.00 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 124 TYR 0.008 0.001 TYR H 103 PHE 0.006 0.001 PHE H 482 TRP 0.013 0.001 TRP H 248 HIS 0.002 0.001 HIS E 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.18 ( 4849) covalent geometry : angle 0.68175 / 0.38 ( 6578) hydrogen bonds : bond 0.18353 / 12.44 ( 190) hydrogen bonds : angle 5.99368 / 3.86 ( 537) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 0.105 Fit side-chains REVERT: E 129 LYS cc_start: 0.8145 (mttm) cc_final: 0.6560 (tptt) outliers start: 2 outliers final: 0 residues processed: 149 average time/residue: 0.0602 time to fit residues: 10.9016 Evaluate side-chains 88 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 0.2980 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 0.4980 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.125270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.108599 restraints weight = 11222.031| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.61 r_work: 0.3314 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4849 Z= 0.124 Angle : 0.574 6.103 6578 Z= 0.310 Chirality : 0.043 0.163 731 Planarity : 0.004 0.043 865 Dihedral : 4.285 18.661 657 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.67 % Allowed : 5.38 % Favored : 93.95 % Rotamer: Outliers : 4.02 % Allowed : 18.77 % Favored : 77.20 % 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: 0.27 (0.35), residues: 595 helix: 2.40 (0.32), residues: 246 sheet: 0.39 (0.68), residues: 54 loop : -1.96 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 94 TYR 0.010 0.001 TYR H 327 PHE 0.010 0.001 PHE H 161 TRP 0.009 0.001 TRP H 248 HIS 0.002 0.001 HIS E 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 4849) covalent geometry : angle 0.57425 / 0.31 ( 6578) hydrogen bonds : bond 0.04948 / 3.26 ( 190) hydrogen bonds : angle 4.61362 / 2.94 ( 537) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.217 Fit side-chains REVERT: H 389 ARG cc_start: 0.4275 (mtt180) cc_final: 0.4030 (mtt90) REVERT: H 478 LYS cc_start: 0.8482 (mmtm) cc_final: 0.8035 (mptt) REVERT: E 2 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8106 (tp) REVERT: E 30 GLN cc_start: 0.8045 (pt0) cc_final: 0.7677 (pp30) REVERT: E 138 ARG cc_start: 0.8391 (mtm-85) cc_final: 0.7822 (mpt180) REVERT: E 177 TYR cc_start: 0.4970 (OUTLIER) cc_final: 0.4387 (p90) outliers start: 21 outliers final: 7 residues processed: 109 average time/residue: 0.0859 time to fit residues: 11.5515 Evaluate side-chains 87 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 61 TYR Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain E residue 5 SER Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 177 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 36 optimal weight: 0.0770 chunk 34 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 42 optimal weight: 0.0670 chunk 24 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 50 optimal weight: 0.2980 chunk 21 optimal weight: 4.9990 overall best weight: 1.4880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 87 GLN E 162 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.124468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.107841 restraints weight = 11332.779| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.67 r_work: 0.3305 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4849 Z= 0.111 Angle : 0.527 5.086 6578 Z= 0.285 Chirality : 0.042 0.146 731 Planarity : 0.004 0.036 865 Dihedral : 4.151 18.277 657 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.72 % Favored : 92.61 % Rotamer: Outliers : 3.64 % Allowed : 19.54 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.36), residues: 595 helix: 2.58 (0.33), residues: 245 sheet: 0.44 (0.73), residues: 52 loop : -1.94 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 161 TYR 0.011 0.001 TYR H 245 PHE 0.008 0.001 PHE H 482 TRP 0.010 0.001 TRP H 248 HIS 0.015 0.003 HIS E 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 4849) covalent geometry : angle 0.52683 / 0.28 ( 6578) hydrogen bonds : bond 0.04541 / 3.02 ( 190) hydrogen bonds : angle 4.22793 / 2.70 ( 537) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.116 Fit side-chains REVERT: H 393 ILE cc_start: 0.8587 (mt) cc_final: 0.8327 (mt) REVERT: H 413 PHE cc_start: 0.7124 (t80) cc_final: 0.6617 (t80) REVERT: H 478 LYS cc_start: 0.8507 (mmtm) cc_final: 0.8063 (mptt) REVERT: E 2 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8283 (tp) REVERT: E 30 GLN cc_start: 0.8085 (pt0) cc_final: 0.7885 (tm-30) REVERT: E 79 ARG cc_start: 0.8735 (mtp-110) cc_final: 0.7796 (tpm170) REVERT: E 138 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.7891 (mpt180) REVERT: E 177 TYR cc_start: 0.4952 (OUTLIER) cc_final: 0.4512 (p90) outliers start: 19 outliers final: 5 residues processed: 101 average time/residue: 0.0631 time to fit residues: 7.8622 Evaluate side-chains 86 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 130 GLN Chi-restraints excluded: chain H residue 408 ARG Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 177 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 43 optimal weight: 0.0770 chunk 28 optimal weight: 6.9990 overall best weight: 1.2940 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.123937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.107213 restraints weight = 11194.842| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.66 r_work: 0.3298 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4849 Z= 0.102 Angle : 0.503 4.800 6578 Z= 0.271 Chirality : 0.041 0.145 731 Planarity : 0.004 0.032 865 Dihedral : 4.018 17.628 657 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.67 % Allowed : 5.55 % Favored : 93.78 % Rotamer: Outliers : 2.68 % Allowed : 19.73 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.36), residues: 595 helix: 2.63 (0.33), residues: 246 sheet: 0.33 (0.73), residues: 52 loop : -1.93 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 94 TYR 0.010 0.001 TYR H 245 PHE 0.009 0.001 PHE E 92 TRP 0.009 0.001 TRP H 248 HIS 0.001 0.000 HIS H 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 4849) covalent geometry : angle 0.50319 / 0.27 ( 6578) hydrogen bonds : bond 0.04117 / 2.73 ( 190) hydrogen bonds : angle 4.07141 / 2.60 ( 537) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.119 Fit side-chains REVERT: H 389 ARG cc_start: 0.4457 (mtt180) cc_final: 0.4167 (mtt180) REVERT: H 393 ILE cc_start: 0.8487 (mt) cc_final: 0.8194 (mt) REVERT: H 413 PHE cc_start: 0.7197 (t80) cc_final: 0.6666 (t80) REVERT: E 2 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8283 (tp) REVERT: E 30 GLN cc_start: 0.8093 (pt0) cc_final: 0.7637 (pp30) REVERT: E 79 ARG cc_start: 0.8746 (mtp-110) cc_final: 0.7764 (tpm170) REVERT: E 138 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.7894 (mpt180) REVERT: E 177 TYR cc_start: 0.4930 (OUTLIER) cc_final: 0.4372 (p90) outliers start: 14 outliers final: 8 residues processed: 93 average time/residue: 0.0817 time to fit residues: 9.3072 Evaluate side-chains 87 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 408 ARG Chi-restraints excluded: chain E residue 2 LEU Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 177 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 25 optimal weight: 0.2980 chunk 57 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 0.0570 chunk 33 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.126392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109831 restraints weight = 11388.129| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.62 r_work: 0.3336 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4849 Z= 0.092 Angle : 0.484 5.141 6578 Z= 0.258 Chirality : 0.040 0.157 731 Planarity : 0.003 0.030 865 Dihedral : 3.783 16.118 657 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.88 % Favored : 93.61 % Rotamer: Outliers : 1.92 % Allowed : 21.65 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.36), residues: 595 helix: 2.73 (0.33), residues: 247 sheet: 0.47 (0.76), residues: 50 loop : -1.92 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 94 TYR 0.009 0.001 TYR H 245 PHE 0.008 0.001 PHE H 482 TRP 0.008 0.001 TRP H 248 HIS 0.012 0.002 HIS E 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.09 ( 4849) covalent geometry : angle 0.48396 / 0.26 ( 6578) hydrogen bonds : bond 0.03184 / 2.11 ( 190) hydrogen bonds : angle 3.93890 / 2.51 ( 537) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.207 Fit side-chains REVERT: H 393 ILE cc_start: 0.8460 (mt) cc_final: 0.8152 (mt) REVERT: H 413 PHE cc_start: 0.7109 (t80) cc_final: 0.6596 (t80) REVERT: E 30 GLN cc_start: 0.8163 (pt0) cc_final: 0.7675 (pp30) REVERT: E 79 ARG cc_start: 0.8704 (mtp-110) cc_final: 0.7768 (tpm170) REVERT: E 138 ARG cc_start: 0.8361 (mtm-85) cc_final: 0.7870 (mpt180) REVERT: E 174 PRO cc_start: 0.7317 (Cg_endo) cc_final: 0.7008 (Cg_exo) REVERT: E 177 TYR cc_start: 0.4771 (OUTLIER) cc_final: 0.4301 (p90) outliers start: 10 outliers final: 5 residues processed: 97 average time/residue: 0.0812 time to fit residues: 9.8619 Evaluate side-chains 88 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 470 ASP Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 177 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.119356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102341 restraints weight = 11190.248| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.65 r_work: 0.3215 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4849 Z= 0.179 Angle : 0.595 5.555 6578 Z= 0.326 Chirality : 0.044 0.148 731 Planarity : 0.004 0.031 865 Dihedral : 4.454 21.481 657 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.39 % Favored : 92.94 % Rotamer: Outliers : 3.83 % Allowed : 20.69 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.35), residues: 595 helix: 2.53 (0.32), residues: 246 sheet: 0.42 (0.74), residues: 50 loop : -2.09 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 94 TYR 0.014 0.001 TYR H 245 PHE 0.010 0.002 PHE H 141 TRP 0.010 0.002 TRP H 248 HIS 0.001 0.000 HIS H 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 4849) covalent geometry : angle 0.59452 / 0.33 ( 6578) hydrogen bonds : bond 0.06489 / 4.27 ( 190) hydrogen bonds : angle 4.23678 / 2.75 ( 537) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.180 Fit side-chains REVERT: H 393 ILE cc_start: 0.8635 (mt) cc_final: 0.8365 (mt) REVERT: H 413 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6748 (t80) REVERT: E 30 GLN cc_start: 0.8206 (pt0) cc_final: 0.8000 (tm-30) REVERT: E 79 ARG cc_start: 0.8787 (mtp-110) cc_final: 0.7791 (tpm170) REVERT: E 138 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.7875 (mpt180) REVERT: E 174 PRO cc_start: 0.7576 (Cg_endo) cc_final: 0.7290 (Cg_exo) REVERT: E 177 TYR cc_start: 0.4801 (OUTLIER) cc_final: 0.4264 (p90) outliers start: 20 outliers final: 12 residues processed: 95 average time/residue: 0.0814 time to fit residues: 9.7318 Evaluate side-chains 91 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 322 THR Chi-restraints excluded: chain H residue 413 PHE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 177 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 441 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.120669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103652 restraints weight = 11187.582| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.65 r_work: 0.3240 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4849 Z= 0.135 Angle : 0.547 5.173 6578 Z= 0.299 Chirality : 0.043 0.148 731 Planarity : 0.004 0.033 865 Dihedral : 4.356 20.776 657 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.06 % Favored : 92.27 % Rotamer: Outliers : 2.68 % Allowed : 22.80 % Favored : 74.52 % 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: 0.33 (0.36), residues: 595 helix: 2.65 (0.32), residues: 244 sheet: 0.56 (0.76), residues: 50 loop : -2.09 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 94 TYR 0.013 0.001 TYR H 245 PHE 0.019 0.001 PHE H 161 TRP 0.012 0.002 TRP H 248 HIS 0.001 0.000 HIS H 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 4849) covalent geometry : angle 0.54663 / 0.30 ( 6578) hydrogen bonds : bond 0.05289 / 3.48 ( 190) hydrogen bonds : angle 4.14202 / 2.67 ( 537) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.113 Fit side-chains REVERT: H 161 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7734 (m-10) REVERT: H 393 ILE cc_start: 0.8632 (mt) cc_final: 0.8356 (mt) REVERT: H 413 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6673 (t80) REVERT: E 79 ARG cc_start: 0.8723 (mtp-110) cc_final: 0.7792 (tpm170) REVERT: E 138 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.7914 (mpt180) REVERT: E 174 PRO cc_start: 0.7245 (Cg_endo) cc_final: 0.6968 (Cg_exo) REVERT: E 177 TYR cc_start: 0.4987 (OUTLIER) cc_final: 0.4382 (p90) outliers start: 14 outliers final: 9 residues processed: 90 average time/residue: 0.0740 time to fit residues: 8.3174 Evaluate side-chains 87 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 161 PHE Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 413 PHE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 177 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.121896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105002 restraints weight = 11236.634| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.64 r_work: 0.3260 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4849 Z= 0.112 Angle : 0.521 6.128 6578 Z= 0.283 Chirality : 0.042 0.146 731 Planarity : 0.004 0.031 865 Dihedral : 4.155 19.009 657 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.39 % Favored : 92.10 % Rotamer: Outliers : 2.30 % Allowed : 23.18 % Favored : 74.52 % 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: 0.50 (0.36), residues: 595 helix: 2.81 (0.32), residues: 246 sheet: 0.73 (0.77), residues: 50 loop : -2.07 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 94 TYR 0.011 0.001 TYR H 245 PHE 0.013 0.001 PHE H 161 TRP 0.012 0.001 TRP H 248 HIS 0.001 0.000 HIS H 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 4849) covalent geometry : angle 0.52113 / 0.28 ( 6578) hydrogen bonds : bond 0.04421 / 2.93 ( 190) hydrogen bonds : angle 4.04012 / 2.59 ( 537) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.120 Fit side-chains REVERT: H 161 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7331 (m-10) REVERT: H 393 ILE cc_start: 0.8592 (mt) cc_final: 0.8304 (mt) REVERT: H 413 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6648 (t80) REVERT: E 79 ARG cc_start: 0.8722 (mtp-110) cc_final: 0.7777 (tpm170) REVERT: E 138 ARG cc_start: 0.8337 (mtm-85) cc_final: 0.7913 (mpt180) REVERT: E 174 PRO cc_start: 0.7155 (Cg_endo) cc_final: 0.6862 (Cg_exo) REVERT: E 177 TYR cc_start: 0.5022 (OUTLIER) cc_final: 0.4400 (p90) outliers start: 12 outliers final: 9 residues processed: 86 average time/residue: 0.0823 time to fit residues: 8.8066 Evaluate side-chains 90 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 161 PHE Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 322 THR Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 413 PHE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 148 ASN Chi-restraints excluded: chain E residue 177 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.120352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.103477 restraints weight = 11025.188| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.61 r_work: 0.3239 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4849 Z= 0.134 Angle : 0.548 7.422 6578 Z= 0.297 Chirality : 0.042 0.148 731 Planarity : 0.004 0.032 865 Dihedral : 4.284 20.060 657 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.39 % Favored : 92.27 % Rotamer: Outliers : 3.26 % Allowed : 22.61 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.36), residues: 595 helix: 2.70 (0.32), residues: 247 sheet: 0.74 (0.78), residues: 50 loop : -2.09 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 94 TYR 0.012 0.001 TYR H 245 PHE 0.012 0.001 PHE H 161 TRP 0.011 0.001 TRP H 248 HIS 0.001 0.000 HIS H 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 4849) covalent geometry : angle 0.54780 / 0.30 ( 6578) hydrogen bonds : bond 0.05280 / 3.48 ( 190) hydrogen bonds : angle 4.11102 / 2.64 ( 537) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.108 Fit side-chains REVERT: H 161 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7222 (m-10) REVERT: H 393 ILE cc_start: 0.8629 (mt) cc_final: 0.8349 (mt) REVERT: H 413 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.6440 (t80) REVERT: E 79 ARG cc_start: 0.8710 (mtp-110) cc_final: 0.7764 (tpm170) REVERT: E 138 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.7925 (mpt180) REVERT: E 174 PRO cc_start: 0.7168 (Cg_endo) cc_final: 0.6868 (Cg_exo) outliers start: 17 outliers final: 12 residues processed: 90 average time/residue: 0.0676 time to fit residues: 7.6924 Evaluate side-chains 91 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain H residue 158 SER Chi-restraints excluded: chain H residue 161 PHE Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 322 THR Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 413 PHE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 148 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 56 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 7 optimal weight: 0.0870 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.0270 chunk 20 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.124448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.107781 restraints weight = 11048.358| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.64 r_work: 0.3309 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4849 Z= 0.098 Angle : 0.510 8.456 6578 Z= 0.272 Chirality : 0.041 0.175 731 Planarity : 0.004 0.032 865 Dihedral : 3.914 16.602 657 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.89 % Favored : 92.77 % Rotamer: Outliers : 1.72 % Allowed : 23.75 % Favored : 74.52 % 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: 0.63 (0.37), residues: 595 helix: 2.87 (0.32), residues: 247 sheet: 0.74 (0.81), residues: 47 loop : -1.93 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 94 TYR 0.010 0.001 TYR H 245 PHE 0.009 0.001 PHE H 482 TRP 0.012 0.001 TRP H 248 HIS 0.001 0.000 HIS E 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 ( 4849) covalent geometry : angle 0.50979 / 0.27 ( 6578) hydrogen bonds : bond 0.03142 / 2.08 ( 190) hydrogen bonds : angle 3.97548 / 2.53 ( 537) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.173 Fit side-chains REVERT: H 161 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7559 (m-10) REVERT: H 389 ARG cc_start: 0.4648 (mtt180) cc_final: 0.4359 (mtt180) REVERT: H 393 ILE cc_start: 0.8494 (mt) cc_final: 0.8185 (mt) REVERT: H 413 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.6368 (t80) REVERT: E 79 ARG cc_start: 0.8722 (mtp-110) cc_final: 0.7780 (tpm170) REVERT: E 138 ARG cc_start: 0.8285 (mtm-85) cc_final: 0.7888 (mpt180) REVERT: E 174 PRO cc_start: 0.7128 (Cg_endo) cc_final: 0.6824 (Cg_exo) outliers start: 9 outliers final: 4 residues processed: 87 average time/residue: 0.0777 time to fit residues: 8.4432 Evaluate side-chains 86 residues out of total 522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 161 PHE Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 413 PHE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 148 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.120333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.103412 restraints weight = 11306.435| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.66 r_work: 0.3231 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4849 Z= 0.140 Angle : 0.558 9.939 6578 Z= 0.300 Chirality : 0.043 0.191 731 Planarity : 0.004 0.034 865 Dihedral : 4.192 19.596 657 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.90 % Favored : 91.76 % Rotamer: Outliers : 2.11 % Allowed : 23.37 % Favored : 74.52 % 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: 0.50 (0.36), residues: 595 helix: 2.76 (0.32), residues: 247 sheet: 0.77 (0.77), residues: 50 loop : -2.04 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 94 TYR 0.012 0.001 TYR H 245 PHE 0.008 0.001 PHE H 65 TRP 0.010 0.001 TRP H 248 HIS 0.001 0.000 HIS H 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 4849) covalent geometry : angle 0.55828 / 0.30 ( 6578) hydrogen bonds : bond 0.05262 / 3.47 ( 190) hydrogen bonds : angle 4.05542 / 2.60 ( 537) =============================================================================== Job complete usr+sys time: 1327.82 seconds wall clock time: 23 minutes 25.47 seconds (1405.47 seconds total)