Starting phenix.real_space_refine on Wed Jul 1 21:46:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wl5_66046/07_2026/9wl5_66046.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wl5_66046/07_2026/9wl5_66046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wl5_66046/07_2026/9wl5_66046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wl5_66046/07_2026/9wl5_66046.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wl5_66046/07_2026/9wl5_66046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wl5_66046/07_2026/9wl5_66046.map" } resolution = 1.96 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= 0.000 sd= 0.004 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 24 5.16 5 C 1923 2.51 5 N 558 2.21 5 O 561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3066 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1022 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 123} Restraints were copied for chains: B, C Time building chain proxies: 0.84, per 1000 atoms: 0.27 Number of scatterers: 3066 At special positions: 0 Unit cell: (92.07, 81.84, 36.27, 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 24 16.00 O 561 8.00 N 558 7.00 C 1923 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 42 " distance=2.03 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 23 " distance=2.03 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 124 " distance=2.02 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 42 " distance=2.04 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 42 " distance=2.04 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS C 18 " - pdb=" SG CYS C 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 124 " distance=2.02 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 124 " distance=2.02 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: 0.30 Conformation dependent library (CDL) restraints added in 125.7 milliseconds 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 708 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6 removed outlier: 8.967A pdb=" N TRP A 3 " --> pdb=" O ALA B 4 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N ILE B 6 " --> pdb=" O TRP A 3 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ASN A 5 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA A 4 " --> pdb=" O TRP C 3 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASN C 5 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 19 removed outlier: 6.275A pdb=" N SER A 12 " --> pdb=" O ASN B 13 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE B 15 " --> pdb=" O SER A 12 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU A 14 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N THR B 17 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG A 16 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 19 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N CYS A 18 " --> pdb=" O ASP B 19 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP A 19 " --> pdb=" O CYS C 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 26 through 29 removed outlier: 6.346A pdb=" N TYR A 26 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N GLN C 29 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA A 28 " --> pdb=" O GLN C 29 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 35 through 41 removed outlier: 6.846A pdb=" N GLN A 36 " --> pdb=" O HIS B 35 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLY B 37 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL A 38 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP B 39 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N HIS A 35 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N VAL C 38 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N GLY A 37 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N VAL C 40 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASP A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 49 removed outlier: 6.601A pdb=" N VAL A 48 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 60 removed outlier: 6.981A pdb=" N VAL B 57 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY A 58 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR A 53 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ILE C 56 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N MET A 55 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLY C 58 " --> pdb=" O MET A 55 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 57 " --> pdb=" O GLY C 58 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N GLU C 60 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLN A 59 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 75 removed outlier: 6.813A pdb=" N VAL B 73 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ARG A 74 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASN A 67 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ASN C 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE A 69 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLY C 72 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ASN A 71 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ARG C 74 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL A 73 " --> pdb=" O ARG C 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 78 through 79 removed outlier: 6.316A pdb=" N ARG A 78 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 83 through 87 removed outlier: 6.082A pdb=" N MET A 84 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ILE C 87 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TYR A 86 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.123A pdb=" N ILE A 96 " --> pdb=" O LYS B 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.588A pdb=" N THR A 104 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.048A pdb=" N LEU A 108 " --> pdb=" O GLN B 109 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL B 111 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LYS A 110 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL A 111 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 114 through 115 removed outlier: 6.622A pdb=" N GLY A 114 " --> pdb=" O ILE C 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 119 through 123 removed outlier: 6.459A pdb=" N HIS A 120 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ASN C 123 " --> pdb=" O HIS A 120 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU A 122 " --> pdb=" O ASN C 123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 130 through 132 removed outlier: 6.553A pdb=" N THR A 130 " --> pdb=" O ALA B 131 " (cutoff:3.500A) 44 hydrogen bonds defined for protein. 132 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: 0.31 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1012 1.34 - 1.46: 434 1.46 - 1.58: 1662 1.58 - 1.70: 0 1.70 - 1.82: 30 Bond restraints: 3138 Sorted by residual: bond pdb=" CA ARG C 20 " pdb=" C ARG C 20 " ideal model delta sigma weight residual 1.530 1.508 0.023 1.17e-02 7.31e+03 3.70e+00 bond pdb=" CA ARG A 20 " pdb=" C ARG A 20 " ideal model delta sigma weight residual 1.530 1.508 0.022 1.17e-02 7.31e+03 3.66e+00 bond pdb=" CA ARG B 20 " pdb=" C ARG B 20 " ideal model delta sigma weight residual 1.530 1.508 0.022 1.17e-02 7.31e+03 3.64e+00 bond pdb=" N TYR B 132 " pdb=" CA TYR B 132 " ideal model delta sigma weight residual 1.455 1.435 0.020 1.29e-02 6.01e+03 2.42e+00 bond pdb=" C ALA A 131 " pdb=" N TYR A 132 " ideal model delta sigma weight residual 1.331 1.311 0.020 1.30e-02 5.92e+03 2.41e+00 ... (remaining 3133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 4009 1.45 - 2.90: 172 2.90 - 4.35: 46 4.35 - 5.80: 6 5.80 - 7.25: 3 Bond angle restraints: 4236 Sorted by residual: angle pdb=" C PRO B 34 " pdb=" N HIS B 35 " pdb=" CA HIS B 35 " ideal model delta sigma weight residual 121.85 117.86 3.99 1.77e+00 3.19e-01 5.08e+00 angle pdb=" C PRO C 34 " pdb=" N HIS C 35 " pdb=" CA HIS C 35 " ideal model delta sigma weight residual 121.85 117.87 3.98 1.77e+00 3.19e-01 5.05e+00 angle pdb=" C PRO A 34 " pdb=" N HIS A 35 " pdb=" CA HIS A 35 " ideal model delta sigma weight residual 121.85 117.88 3.97 1.77e+00 3.19e-01 5.03e+00 angle pdb=" N TYR C 132 " pdb=" CA TYR C 132 " pdb=" C TYR C 132 " ideal model delta sigma weight residual 109.24 112.49 -3.25 1.51e+00 4.39e-01 4.64e+00 angle pdb=" N TYR B 132 " pdb=" CA TYR B 132 " pdb=" C TYR B 132 " ideal model delta sigma weight residual 109.24 112.45 -3.21 1.51e+00 4.39e-01 4.53e+00 ... (remaining 4231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 1692 17.35 - 34.69: 150 34.69 - 52.04: 63 52.04 - 69.38: 12 69.38 - 86.73: 6 Dihedral angle restraints: 1923 sinusoidal: 798 harmonic: 1125 Sorted by residual: dihedral pdb=" CA HIS A 118 " pdb=" C HIS A 118 " pdb=" N VAL A 119 " pdb=" CA VAL A 119 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA HIS C 118 " pdb=" C HIS C 118 " pdb=" N VAL C 119 " pdb=" CA VAL C 119 " ideal model delta harmonic sigma weight residual 180.00 156.47 23.53 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA HIS B 118 " pdb=" C HIS B 118 " pdb=" N VAL B 119 " pdb=" CA VAL B 119 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 1920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 201 0.028 - 0.056: 121 0.056 - 0.084: 44 0.084 - 0.111: 39 0.111 - 0.139: 36 Chirality restraints: 441 Sorted by residual: chirality pdb=" CA PHE B 85 " pdb=" N PHE B 85 " pdb=" C PHE B 85 " pdb=" CB PHE B 85 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ARG A 20 " pdb=" N ARG A 20 " pdb=" C ARG A 20 " pdb=" CB ARG A 20 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA PHE C 85 " pdb=" N PHE C 85 " pdb=" C PHE C 85 " pdb=" CB PHE C 85 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 438 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 85 " 0.013 2.00e-02 2.50e+03 1.59e-02 4.43e+00 pdb=" CG PHE B 85 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 85 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 85 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 85 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 85 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 85 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 85 " 0.013 2.00e-02 2.50e+03 1.58e-02 4.39e+00 pdb=" CG PHE A 85 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 85 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 85 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 85 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 85 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 85 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 85 " 0.013 2.00e-02 2.50e+03 1.58e-02 4.35e+00 pdb=" CG PHE C 85 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE C 85 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE C 85 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 85 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 85 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 85 " -0.000 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 451 2.78 - 3.31: 2799 3.31 - 3.84: 5333 3.84 - 4.37: 6211 4.37 - 4.90: 11174 Nonbonded interactions: 25968 Sorted by model distance: nonbonded pdb=" OD2 ASP A 19 " pdb=" NH2 ARG C 20 " model vdw 2.247 3.120 nonbonded pdb=" NH2 ARG A 20 " pdb=" OD2 ASP B 19 " model vdw 2.261 3.120 nonbonded pdb=" O SER A 46 " pdb=" N SER B 46 " model vdw 2.492 3.120 nonbonded pdb=" N SER A 46 " pdb=" O SER C 46 " model vdw 2.493 3.120 nonbonded pdb=" OE2 GLU A 100 " pdb=" CD2 LEU A 133 " model vdw 2.502 3.460 ... (remaining 25963 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.360 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 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 : 0.004 0.023 3147 Z= 0.207 Angle : 0.752 7.254 4254 Z= 0.398 Chirality : 0.057 0.139 441 Planarity : 0.004 0.021 558 Dihedral : 16.530 86.729 1188 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 11.71 % Favored : 88.29 % 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: -4.02 (0.29), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.22), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 78 TYR 0.014 0.003 TYR C 86 PHE 0.036 0.005 PHE B 85 TRP 0.003 0.001 TRP C 3 HIS 0.012 0.004 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.21 ( 3138) covalent geometry : angle 0.74927 / 0.40 ( 4236) SS BOND : bond 0.00496 / 0.36 ( 9) SS BOND : angle 1.20375 / 0.86 ( 18) hydrogen bonds : bond 0.17326 / 11.69 ( 44) hydrogen bonds : angle 9.09509 / 6.12 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.122 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.6800 time to fit residues: 96.3422 Evaluate side-chains 90 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.0270 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 0.0050 chunk 30 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 overall best weight: 3.2058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 67 ASN A 123 ASN B 67 ASN B 123 ASN C 13 ASN C 59 GLN C 123 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.141230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.127554 restraints weight = 3011.824| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.22 r_work: 0.3753 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3147 Z= 0.174 Angle : 0.768 6.573 4254 Z= 0.396 Chirality : 0.057 0.178 441 Planarity : 0.004 0.025 558 Dihedral : 8.462 71.595 438 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.40 % Allowed : 19.22 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.31), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.24), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 74 TYR 0.018 0.002 TYR B 86 PHE 0.007 0.002 PHE C 80 TRP 0.004 0.001 TRP B 3 HIS 0.009 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 ( 3138) covalent geometry : angle 0.76504 / 0.39 ( 4236) SS BOND : bond 0.00587 / 0.42 ( 9) SS BOND : angle 1.26331 / 0.95 ( 18) hydrogen bonds : bond 0.03331 / 2.20 ( 44) hydrogen bonds : angle 6.91527 / 4.58 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.074 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 95 average time/residue: 0.7003 time to fit residues: 67.8598 Evaluate side-chains 89 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain C residue 102 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN B 25 GLN B 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.139234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.125452 restraints weight = 2963.903| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.20 r_work: 0.3728 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3147 Z= 0.200 Angle : 0.785 6.766 4254 Z= 0.407 Chirality : 0.058 0.183 441 Planarity : 0.004 0.029 558 Dihedral : 8.707 75.742 438 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 3.00 % Allowed : 17.72 % Favored : 79.28 % 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: -3.57 (0.32), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.24), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.016 0.002 TYR A 86 PHE 0.010 0.002 PHE A 85 TRP 0.003 0.001 TRP B 3 HIS 0.009 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 ( 3138) covalent geometry : angle 0.78226 / 0.41 ( 4236) SS BOND : bond 0.00550 / 0.40 ( 9) SS BOND : angle 1.22397 / 0.90 ( 18) hydrogen bonds : bond 0.03546 / 2.36 ( 44) hydrogen bonds : angle 6.84440 / 4.48 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.126 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 91 average time/residue: 0.7014 time to fit residues: 65.1184 Evaluate side-chains 89 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain C residue 102 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 33 optimal weight: 0.0030 chunk 17 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 6 optimal weight: 5.9990 overall best weight: 3.0174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 29 GLN B 25 GLN C 120 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.140572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.126873 restraints weight = 2961.020| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.21 r_work: 0.3745 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3147 Z= 0.162 Angle : 0.744 6.403 4254 Z= 0.386 Chirality : 0.056 0.173 441 Planarity : 0.004 0.028 558 Dihedral : 8.676 78.273 438 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.40 % Allowed : 17.72 % Favored : 79.88 % 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: -3.60 (0.32), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.24), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 16 TYR 0.015 0.002 TYR B 86 PHE 0.006 0.002 PHE A 85 TRP 0.003 0.001 TRP A 3 HIS 0.008 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 3138) covalent geometry : angle 0.74131 / 0.38 ( 4236) SS BOND : bond 0.00515 / 0.38 ( 9) SS BOND : angle 1.21989 / 0.89 ( 18) hydrogen bonds : bond 0.03006 / 2.00 ( 44) hydrogen bonds : angle 6.65131 / 4.35 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.123 Fit side-chains REVERT: C 14 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7731 (tp30) outliers start: 8 outliers final: 5 residues processed: 94 average time/residue: 0.6988 time to fit residues: 67.0190 Evaluate side-chains 92 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain C residue 102 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN B 25 GLN C 120 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.137110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.123308 restraints weight = 2995.975| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.21 r_work: 0.3694 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 3147 Z= 0.275 Angle : 0.852 8.024 4254 Z= 0.445 Chirality : 0.061 0.192 441 Planarity : 0.005 0.029 558 Dihedral : 9.210 84.999 438 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 3.00 % Allowed : 16.82 % Favored : 80.18 % 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: -3.57 (0.31), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.24), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 33 TYR 0.017 0.003 TYR A 86 PHE 0.009 0.002 PHE B 85 TRP 0.003 0.002 TRP C 3 HIS 0.009 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.27 ( 3138) covalent geometry : angle 0.84932 / 0.44 ( 4236) SS BOND : bond 0.00632 / 0.45 ( 9) SS BOND : angle 1.31471 / 0.97 ( 18) hydrogen bonds : bond 0.03896 / 2.57 ( 44) hydrogen bonds : angle 6.96791 / 4.59 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.128 Fit side-chains REVERT: C 83 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8146 (ttmm) REVERT: C 91 LYS cc_start: 0.8875 (mttt) cc_final: 0.8645 (mttp) outliers start: 10 outliers final: 6 residues processed: 93 average time/residue: 0.7121 time to fit residues: 67.5481 Evaluate side-chains 93 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 102 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN B 25 GLN C 120 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.138450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.124696 restraints weight = 2950.668| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.20 r_work: 0.3716 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3147 Z= 0.208 Angle : 0.792 7.087 4254 Z= 0.413 Chirality : 0.058 0.186 441 Planarity : 0.004 0.031 558 Dihedral : 9.289 86.928 438 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 3.00 % Allowed : 17.42 % Favored : 79.58 % 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: -3.59 (0.31), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.24), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 33 TYR 0.015 0.002 TYR A 86 PHE 0.006 0.002 PHE A 52 TRP 0.004 0.001 TRP C 3 HIS 0.009 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 ( 3138) covalent geometry : angle 0.78895 / 0.41 ( 4236) SS BOND : bond 0.00594 / 0.42 ( 9) SS BOND : angle 1.30085 / 0.95 ( 18) hydrogen bonds : bond 0.03460 / 2.29 ( 44) hydrogen bonds : angle 6.85128 / 4.48 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.124 Fit side-chains REVERT: C 14 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7727 (tp30) REVERT: C 100 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7666 (mt-10) outliers start: 10 outliers final: 5 residues processed: 91 average time/residue: 0.6558 time to fit residues: 60.8773 Evaluate side-chains 91 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 102 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 27 optimal weight: 0.0970 chunk 28 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN B 25 GLN C 25 GLN C 120 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.137820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.123981 restraints weight = 3018.236| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.21 r_work: 0.3708 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3147 Z= 0.241 Angle : 0.818 7.217 4254 Z= 0.429 Chirality : 0.060 0.190 441 Planarity : 0.005 0.031 558 Dihedral : 9.415 87.070 438 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 3.60 % Allowed : 17.12 % Favored : 79.28 % 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: -3.57 (0.31), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.24), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 33 TYR 0.017 0.003 TYR A 86 PHE 0.020 0.003 PHE A 85 TRP 0.004 0.002 TRP C 3 HIS 0.009 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 ( 3138) covalent geometry : angle 0.81549 / 0.43 ( 4236) SS BOND : bond 0.00614 / 0.44 ( 9) SS BOND : angle 1.31626 / 0.96 ( 18) hydrogen bonds : bond 0.03734 / 2.47 ( 44) hydrogen bonds : angle 6.93796 / 4.56 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.073 Fit side-chains REVERT: C 14 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7724 (tp30) REVERT: C 83 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8184 (ttmm) REVERT: C 100 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7713 (mt-10) outliers start: 12 outliers final: 6 residues processed: 91 average time/residue: 0.5358 time to fit residues: 49.7004 Evaluate side-chains 93 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 128 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN B 25 GLN C 120 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.140080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.126317 restraints weight = 3011.997| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 1.22 r_work: 0.3742 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3147 Z= 0.162 Angle : 0.753 6.712 4254 Z= 0.391 Chirality : 0.056 0.177 441 Planarity : 0.004 0.029 558 Dihedral : 9.158 86.022 438 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 1.80 % Allowed : 18.92 % Favored : 79.28 % 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: -3.61 (0.31), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.24), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 33 TYR 0.015 0.002 TYR B 86 PHE 0.010 0.002 PHE A 85 TRP 0.004 0.001 TRP C 3 HIS 0.008 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 3138) covalent geometry : angle 0.75007 / 0.39 ( 4236) SS BOND : bond 0.00550 / 0.39 ( 9) SS BOND : angle 1.27922 / 0.93 ( 18) hydrogen bonds : bond 0.03137 / 2.09 ( 44) hydrogen bonds : angle 6.70424 / 4.37 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.157 Fit side-chains REVERT: C 14 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7677 (tp30) REVERT: C 100 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7628 (mt-10) outliers start: 6 outliers final: 4 residues processed: 91 average time/residue: 0.6918 time to fit residues: 64.2250 Evaluate side-chains 91 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 128 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN B 25 GLN C 25 GLN C 120 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.137782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.123988 restraints weight = 3025.677| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.21 r_work: 0.3711 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3147 Z= 0.247 Angle : 0.824 7.094 4254 Z= 0.432 Chirality : 0.059 0.191 441 Planarity : 0.005 0.030 558 Dihedral : 9.308 86.277 438 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 2.40 % Allowed : 18.62 % Favored : 78.98 % 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: -3.55 (0.31), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.24), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 33 TYR 0.023 0.003 TYR C 63 PHE 0.024 0.003 PHE A 85 TRP 0.004 0.002 TRP C 3 HIS 0.009 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.25 ( 3138) covalent geometry : angle 0.82096 / 0.43 ( 4236) SS BOND : bond 0.00604 / 0.43 ( 9) SS BOND : angle 1.32089 / 0.97 ( 18) hydrogen bonds : bond 0.03792 / 2.52 ( 44) hydrogen bonds : angle 6.92316 / 4.55 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.130 Fit side-chains REVERT: C 100 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7695 (mt-10) outliers start: 8 outliers final: 6 residues processed: 89 average time/residue: 0.7051 time to fit residues: 64.0332 Evaluate side-chains 92 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 128 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN B 25 GLN C 25 GLN C 120 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.139495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.125775 restraints weight = 2963.020| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.21 r_work: 0.3734 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3147 Z= 0.177 Angle : 0.769 6.900 4254 Z= 0.401 Chirality : 0.057 0.180 441 Planarity : 0.004 0.030 558 Dihedral : 9.141 84.843 438 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 2.40 % Allowed : 18.62 % Favored : 78.98 % 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: -3.58 (0.32), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.24), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 74 TYR 0.023 0.003 TYR C 63 PHE 0.017 0.003 PHE A 85 TRP 0.004 0.001 TRP C 3 HIS 0.008 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 ( 3138) covalent geometry : angle 0.76578 / 0.40 ( 4236) SS BOND : bond 0.00566 / 0.40 ( 9) SS BOND : angle 1.30071 / 0.95 ( 18) hydrogen bonds : bond 0.03349 / 2.24 ( 44) hydrogen bonds : angle 6.74470 / 4.41 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 786 Ramachandran restraints generated. 393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.119 Fit side-chains REVERT: B 26 TYR cc_start: 0.9043 (t80) cc_final: 0.8837 (t80) REVERT: C 14 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7704 (tp30) REVERT: C 100 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7682 (mt-10) outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 0.6848 time to fit residues: 62.8895 Evaluate side-chains 91 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 128 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN B 25 GLN C 25 GLN C 120 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.143346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.129823 restraints weight = 2962.513| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 1.20 r_work: 0.3791 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3147 Z= 0.125 Angle : 0.707 6.151 4254 Z= 0.368 Chirality : 0.054 0.166 441 Planarity : 0.004 0.026 558 Dihedral : 8.787 81.127 438 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 1.20 % Allowed : 19.52 % Favored : 79.28 % 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: -3.60 (0.32), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.24), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 33 TYR 0.017 0.002 TYR C 63 PHE 0.021 0.002 PHE B 85 TRP 0.004 0.001 TRP C 3 HIS 0.008 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 3138) covalent geometry : angle 0.70448 / 0.37 ( 4236) SS BOND : bond 0.00481 / 0.35 ( 9) SS BOND : angle 1.22447 / 0.89 ( 18) hydrogen bonds : bond 0.02956 / 1.98 ( 44) hydrogen bonds : angle 6.49182 / 4.25 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1876.22 seconds wall clock time: 32 minutes 43.91 seconds (1963.91 seconds total)