Starting phenix.real_space_refine on Wed Jul 1 21:45:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wl6_66047/07_2026/9wl6_66047.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wl6_66047/07_2026/9wl6_66047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wl6_66047/07_2026/9wl6_66047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wl6_66047/07_2026/9wl6_66047.map" model { file = "/net/cci-nas-00/data/ceres_data/9wl6_66047/07_2026/9wl6_66047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wl6_66047/07_2026/9wl6_66047.cif" } resolution = 1.95 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: 0.85, per 1000 atoms: 0.28 Number of scatterers: 3066 At special positions: 0 Unit cell: (89.28, 82.77, 37.2, 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=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 42 " distance=2.03 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: 0.24 Conformation dependent library (CDL) restraints added in 115.5 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 13 sheets defined 0.0% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 13 through 19 removed outlier: 6.862A pdb=" N ASP B 19 " --> pdb=" O CYS A 18 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ASN A 13 " --> pdb=" O GLU C 14 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ARG C 16 " --> pdb=" O ASN A 13 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE A 15 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N CYS C 18 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N THR A 17 " --> pdb=" O CYS C 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 26 through 29 removed outlier: 6.365A pdb=" N TYR A 26 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLN C 29 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ALA A 28 " --> pdb=" O GLN C 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 35 through 41 removed outlier: 6.825A pdb=" N GLN A 36 " --> pdb=" O HIS B 35 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY B 37 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 38 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP B 39 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N HIS A 35 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N VAL C 38 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N GLY A 37 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 9.866A pdb=" N VAL C 40 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASP A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 49 removed outlier: 6.524A pdb=" N VAL A 48 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 52 through 60 removed outlier: 6.946A pdb=" N THR A 53 " --> pdb=" O PHE B 52 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY B 54 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N MET A 55 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE B 56 " --> pdb=" O MET A 55 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLN A 59 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLU B 60 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N PHE A 52 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N MET C 55 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N GLY A 54 " --> pdb=" O MET C 55 " (cutoff:3.500A) removed outlier: 9.779A pdb=" N VAL C 57 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE A 56 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLN C 59 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLY A 58 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 66 through 75 removed outlier: 6.845A pdb=" N VAL B 73 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG A 74 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN A 67 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ASN C 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE A 69 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLY C 72 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ASN A 71 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ARG C 74 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL A 73 " --> pdb=" O ARG C 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 78 through 79 removed outlier: 6.237A pdb=" N ARG A 78 " --> pdb=" O GLY B 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 83 through 87 removed outlier: 6.025A pdb=" N MET A 84 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE C 87 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR A 86 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.071A pdb=" N ILE A 96 " --> pdb=" O LYS B 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.490A pdb=" N THR A 104 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 108 through 111 removed outlier: 5.952A pdb=" N LEU A 108 " --> pdb=" O GLN B 109 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL B 111 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LYS A 110 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 111 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 114 through 123 removed outlier: 6.957A pdb=" N GLN B 116 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER A 117 " --> pdb=" O GLN B 116 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLY A 114 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N SER C 117 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLN A 116 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N VAL C 119 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N HIS A 118 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE C 121 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N HIS A 120 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ASN C 123 " --> pdb=" O HIS A 120 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLU A 122 " --> pdb=" O ASN C 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 130 through 132 removed outlier: 6.556A pdb=" N THR A 130 " --> pdb=" O ALA B 131 " (cutoff:3.500A) 40 hydrogen bonds defined for protein. 120 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: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 863 1.33 - 1.45: 502 1.45 - 1.57: 1743 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 3138 Sorted by residual: bond pdb=" C TYR B 132 " pdb=" O TYR B 132 " ideal model delta sigma weight residual 1.234 1.211 0.023 1.26e-02 6.30e+03 3.38e+00 bond pdb=" C TYR C 132 " pdb=" O TYR C 132 " ideal model delta sigma weight residual 1.234 1.211 0.022 1.26e-02 6.30e+03 3.12e+00 bond pdb=" C TYR A 132 " pdb=" O TYR A 132 " ideal model delta sigma weight residual 1.234 1.212 0.022 1.26e-02 6.30e+03 3.07e+00 bond pdb=" CB PRO C 34 " pdb=" CG PRO C 34 " ideal model delta sigma weight residual 1.492 1.433 0.059 5.00e-02 4.00e+02 1.38e+00 bond pdb=" CB PRO B 34 " pdb=" CG PRO B 34 " ideal model delta sigma weight residual 1.492 1.433 0.059 5.00e-02 4.00e+02 1.38e+00 ... (remaining 3133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 3878 1.58 - 3.17: 275 3.17 - 4.75: 59 4.75 - 6.34: 18 6.34 - 7.92: 6 Bond angle restraints: 4236 Sorted by residual: angle pdb=" C TYR C 49 " pdb=" N ALA C 50 " pdb=" CA ALA C 50 " ideal model delta sigma weight residual 122.85 119.32 3.53 1.10e+00 8.26e-01 1.03e+01 angle pdb=" C TYR B 49 " pdb=" N ALA B 50 " pdb=" CA ALA B 50 " ideal model delta sigma weight residual 122.85 119.32 3.53 1.10e+00 8.26e-01 1.03e+01 angle pdb=" C TYR A 49 " pdb=" N ALA A 50 " pdb=" CA ALA A 50 " ideal model delta sigma weight residual 122.85 119.34 3.51 1.10e+00 8.26e-01 1.02e+01 angle pdb=" N GLY C 54 " pdb=" CA GLY C 54 " pdb=" C GLY C 54 " ideal model delta sigma weight residual 110.80 115.99 -5.19 1.71e+00 3.42e-01 9.21e+00 angle pdb=" N GLY A 54 " pdb=" CA GLY A 54 " pdb=" C GLY A 54 " ideal model delta sigma weight residual 110.80 115.97 -5.17 1.71e+00 3.42e-01 9.16e+00 ... (remaining 4231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.14: 1635 13.14 - 26.28: 165 26.28 - 39.42: 69 39.42 - 52.56: 45 52.56 - 65.69: 9 Dihedral angle restraints: 1923 sinusoidal: 798 harmonic: 1125 Sorted by residual: dihedral pdb=" CA SER C 46 " pdb=" C SER C 46 " pdb=" N THR C 47 " pdb=" CA THR C 47 " ideal model delta harmonic sigma weight residual -180.00 -162.95 -17.05 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA SER A 46 " pdb=" C SER A 46 " pdb=" N THR A 47 " pdb=" CA THR A 47 " ideal model delta harmonic sigma weight residual -180.00 -162.99 -17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA SER B 46 " pdb=" C SER B 46 " pdb=" N THR B 47 " pdb=" CA THR B 47 " ideal model delta harmonic sigma weight residual -180.00 -162.99 -17.01 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 1920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 225 0.035 - 0.070: 106 0.070 - 0.105: 53 0.105 - 0.141: 42 0.141 - 0.176: 15 Chirality restraints: 441 Sorted by residual: chirality pdb=" CA ARG A 33 " pdb=" N ARG A 33 " pdb=" C ARG A 33 " pdb=" CB ARG A 33 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CA ARG B 33 " pdb=" N ARG B 33 " pdb=" C ARG B 33 " pdb=" CB ARG B 33 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CA ARG C 33 " pdb=" N ARG C 33 " pdb=" C ARG C 33 " pdb=" CB ARG C 33 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 438 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 35 " -0.019 2.00e-02 2.50e+03 1.77e-02 4.71e+00 pdb=" CG HIS A 35 " 0.037 2.00e-02 2.50e+03 pdb=" ND1 HIS A 35 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS A 35 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS A 35 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 35 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 35 " 0.018 2.00e-02 2.50e+03 1.77e-02 4.70e+00 pdb=" CG HIS C 35 " -0.037 2.00e-02 2.50e+03 pdb=" ND1 HIS C 35 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS C 35 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS C 35 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS C 35 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 35 " -0.018 2.00e-02 2.50e+03 1.74e-02 4.55e+00 pdb=" CG HIS B 35 " 0.037 2.00e-02 2.50e+03 pdb=" ND1 HIS B 35 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS B 35 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS B 35 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS B 35 " -0.009 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 836 2.84 - 3.35: 2522 3.35 - 3.87: 5449 3.87 - 4.38: 5931 4.38 - 4.90: 11084 Nonbonded interactions: 25822 Sorted by model distance: nonbonded pdb=" O CYS C 7 " pdb=" ND2 ASN C 13 " model vdw 2.320 3.120 nonbonded pdb=" O CYS B 7 " pdb=" ND2 ASN B 13 " model vdw 2.320 3.120 nonbonded pdb=" O CYS A 7 " pdb=" ND2 ASN A 13 " model vdw 2.320 3.120 nonbonded pdb=" O LEU A 133 " pdb=" NZ LYS B 97 " model vdw 2.364 3.120 nonbonded pdb=" NZ LYS A 97 " pdb=" O LEU C 133 " model vdw 2.371 3.120 ... (remaining 25817 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: 1.380 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.830 Find NCS groups from input model: 0.010 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:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 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 : 0.005 0.059 3147 Z= 0.245 Angle : 1.006 7.920 4254 Z= 0.551 Chirality : 0.063 0.176 441 Planarity : 0.005 0.037 558 Dihedral : 15.495 65.694 1188 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % 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: -3.78 (0.30), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.23), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 74 TYR 0.024 0.004 TYR C 63 PHE 0.024 0.004 PHE B 85 TRP 0.013 0.003 TRP B 3 HIS 0.017 0.005 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.24 ( 3138) covalent geometry : angle 1.00243 / 0.55 ( 4236) SS BOND : bond 0.00625 / 0.45 ( 9) SS BOND : angle 1.68086 / 1.17 ( 18) hydrogen bonds : bond 0.16809 / 9.64 ( 40) hydrogen bonds : angle 8.93082 / 6.27 ( 120) *********************** 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 119 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.126 Fit side-chains REVERT: B 20 ARG cc_start: 0.8951 (mtm180) cc_final: 0.8698 (mtm180) REVERT: B 55 MET cc_start: 0.9290 (ttp) cc_final: 0.8955 (ttp) REVERT: C 10 LYS cc_start: 0.8420 (mttt) cc_final: 0.8138 (mmmt) REVERT: C 74 ARG cc_start: 0.8719 (mtm180) cc_final: 0.8488 (mtp180) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.8440 time to fit residues: 102.0895 Evaluate side-chains 97 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.076 ------------------------------------------------------------------------------- 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: 0.9990 chunk 2 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 29 GLN A 120 HIS A 123 ASN B 120 HIS B 123 ASN C 123 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.110526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.096651 restraints weight = 3119.547| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.34 r_work: 0.3329 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 3147 Z= 0.198 Angle : 0.772 6.713 4254 Z= 0.406 Chirality : 0.055 0.164 441 Planarity : 0.003 0.018 558 Dihedral : 5.855 42.231 438 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.10 % Allowed : 15.32 % Favored : 82.58 % 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: -3.50 (0.31), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.24), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 16 TYR 0.021 0.003 TYR B 86 PHE 0.013 0.003 PHE C 85 TRP 0.014 0.003 TRP A 3 HIS 0.010 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 ( 3138) covalent geometry : angle 0.76867 / 0.40 ( 4236) SS BOND : bond 0.00687 / 0.50 ( 9) SS BOND : angle 1.33649 / 1.02 ( 18) hydrogen bonds : bond 0.04472 / 2.69 ( 40) hydrogen bonds : angle 7.41252 / 5.25 ( 120) *********************** 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 107 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.151 Fit side-chains REVERT: B 20 ARG cc_start: 0.8887 (mtm180) cc_final: 0.8684 (mtm180) REVERT: B 55 MET cc_start: 0.9343 (ttp) cc_final: 0.9069 (ttp) REVERT: C 10 LYS cc_start: 0.8422 (mttt) cc_final: 0.8093 (mmtt) REVERT: C 74 ARG cc_start: 0.8695 (mtm180) cc_final: 0.8458 (mtp180) outliers start: 7 outliers final: 3 residues processed: 102 average time/residue: 0.8186 time to fit residues: 84.9166 Evaluate side-chains 102 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 100 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 38 optimal weight: 0.0770 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.113882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.100096 restraints weight = 3064.272| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.34 r_work: 0.3393 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.2066 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= 0.124 Angle : 0.671 6.115 4254 Z= 0.352 Chirality : 0.052 0.149 441 Planarity : 0.003 0.016 558 Dihedral : 5.539 42.205 438 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.20 % Allowed : 16.22 % Favored : 82.58 % 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: -3.41 (0.32), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.24), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 16 TYR 0.019 0.002 TYR B 86 PHE 0.013 0.002 PHE B 85 TRP 0.010 0.002 TRP A 3 HIS 0.009 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 3138) covalent geometry : angle 0.66788 / 0.35 ( 4236) SS BOND : bond 0.00513 / 0.37 ( 9) SS BOND : angle 1.18927 / 0.91 ( 18) hydrogen bonds : bond 0.03601 / 2.15 ( 40) hydrogen bonds : angle 6.86590 / 4.89 ( 120) *********************** 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 104 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.138 Fit side-chains REVERT: B 20 ARG cc_start: 0.8852 (mtm180) cc_final: 0.8486 (mtm180) REVERT: B 55 MET cc_start: 0.9280 (ttp) cc_final: 0.9074 (ttp) REVERT: B 98 LYS cc_start: 0.8756 (mtpm) cc_final: 0.8318 (mttt) REVERT: C 10 LYS cc_start: 0.8408 (mttt) cc_final: 0.8207 (mmmm) REVERT: C 74 ARG cc_start: 0.8704 (mtm180) cc_final: 0.8472 (mtp180) outliers start: 4 outliers final: 2 residues processed: 101 average time/residue: 0.8235 time to fit residues: 84.5965 Evaluate side-chains 100 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 100 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 17 optimal weight: 0.0980 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN B 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.110929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.096883 restraints weight = 3071.541| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.34 r_work: 0.3333 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3147 Z= 0.185 Angle : 0.731 5.942 4254 Z= 0.387 Chirality : 0.054 0.163 441 Planarity : 0.003 0.017 558 Dihedral : 5.661 37.896 438 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 1.80 % Allowed : 15.62 % Favored : 82.58 % 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: -3.36 (0.32), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.24), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.019 0.003 TYR C 86 PHE 0.021 0.002 PHE B 85 TRP 0.009 0.002 TRP A 3 HIS 0.010 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 3138) covalent geometry : angle 0.72799 / 0.39 ( 4236) SS BOND : bond 0.00635 / 0.46 ( 9) SS BOND : angle 1.24045 / 0.96 ( 18) hydrogen bonds : bond 0.03977 / 2.39 ( 40) hydrogen bonds : angle 7.07729 / 5.08 ( 120) *********************** 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 104 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.126 Fit side-chains REVERT: B 55 MET cc_start: 0.9375 (ttp) cc_final: 0.9087 (ttp) REVERT: B 98 LYS cc_start: 0.8806 (mtpm) cc_final: 0.8354 (mttt) REVERT: C 74 ARG cc_start: 0.8720 (mtm180) cc_final: 0.8468 (mtp180) outliers start: 6 outliers final: 6 residues processed: 99 average time/residue: 0.8279 time to fit residues: 83.3481 Evaluate side-chains 103 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 100 GLU 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: 9.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.108037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.094156 restraints weight = 3124.035| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.33 r_work: 0.3290 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9096 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 3147 Z= 0.340 Angle : 0.861 6.803 4254 Z= 0.460 Chirality : 0.059 0.171 441 Planarity : 0.004 0.021 558 Dihedral : 6.039 38.241 438 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.40 % Allowed : 14.71 % Favored : 82.88 % 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: -3.39 (0.32), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.24), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 16 TYR 0.024 0.003 TYR A 86 PHE 0.023 0.003 PHE B 85 TRP 0.011 0.003 TRP A 3 HIS 0.011 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00793 / 0.34 ( 3138) covalent geometry : angle 0.85852 / 0.46 ( 4236) SS BOND : bond 0.00798 / 0.55 ( 9) SS BOND : angle 1.26645 / 1.00 ( 18) hydrogen bonds : bond 0.05006 / 2.97 ( 40) hydrogen bonds : angle 7.77846 / 5.58 ( 120) *********************** 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 106 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.125 Fit side-chains REVERT: B 55 MET cc_start: 0.9422 (ttp) cc_final: 0.9078 (ttp) REVERT: C 74 ARG cc_start: 0.8680 (mtm180) cc_final: 0.8417 (mtp180) outliers start: 8 outliers final: 5 residues processed: 101 average time/residue: 0.7732 time to fit residues: 79.4821 Evaluate side-chains 103 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 100 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 29 GLN B 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.110239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.096352 restraints weight = 3060.059| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.35 r_work: 0.3338 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3147 Z= 0.194 Angle : 0.744 5.751 4254 Z= 0.394 Chirality : 0.055 0.161 441 Planarity : 0.003 0.020 558 Dihedral : 5.902 39.150 438 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.80 % Allowed : 14.11 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.32), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.25), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 16 TYR 0.018 0.003 TYR A 86 PHE 0.020 0.003 PHE B 85 TRP 0.010 0.002 TRP A 3 HIS 0.010 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 ( 3138) covalent geometry : angle 0.74115 / 0.39 ( 4236) SS BOND : bond 0.00660 / 0.47 ( 9) SS BOND : angle 1.27108 / 0.99 ( 18) hydrogen bonds : bond 0.04122 / 2.47 ( 40) hydrogen bonds : angle 7.24005 / 5.22 ( 120) *********************** 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 105 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.122 Fit side-chains REVERT: B 55 MET cc_start: 0.9406 (ttp) cc_final: 0.9091 (ttp) REVERT: B 98 LYS cc_start: 0.8812 (mtpm) cc_final: 0.8348 (mttt) REVERT: C 74 ARG cc_start: 0.8692 (mtm180) cc_final: 0.8428 (mtp180) outliers start: 6 outliers final: 4 residues processed: 102 average time/residue: 0.6973 time to fit residues: 72.4465 Evaluate side-chains 103 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain B residue 100 GLU 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: 7.9990 chunk 23 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN B 13 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.108758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.094827 restraints weight = 3158.379| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.36 r_work: 0.3301 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 3147 Z= 0.283 Angle : 0.816 6.124 4254 Z= 0.435 Chirality : 0.057 0.166 441 Planarity : 0.004 0.023 558 Dihedral : 6.071 38.899 438 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 1.80 % Allowed : 15.02 % Favored : 83.18 % 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: -3.43 (0.32), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.24), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 16 TYR 0.022 0.003 TYR A 86 PHE 0.021 0.003 PHE B 85 TRP 0.010 0.002 TRP A 3 HIS 0.011 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.28 ( 3138) covalent geometry : angle 0.81399 / 0.43 ( 4236) SS BOND : bond 0.00738 / 0.51 ( 9) SS BOND : angle 1.27169 / 0.99 ( 18) hydrogen bonds : bond 0.04828 / 2.88 ( 40) hydrogen bonds : angle 7.62264 / 5.49 ( 120) *********************** 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 104 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.075 Fit side-chains REVERT: B 55 MET cc_start: 0.9428 (ttp) cc_final: 0.9087 (ttp) REVERT: B 98 LYS cc_start: 0.8827 (mtpm) cc_final: 0.8493 (mttp) REVERT: C 74 ARG cc_start: 0.8681 (mtm180) cc_final: 0.8415 (mtp180) outliers start: 6 outliers final: 5 residues processed: 100 average time/residue: 0.5540 time to fit residues: 56.3377 Evaluate side-chains 102 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 102 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 29 GLN B 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.111405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.097483 restraints weight = 3118.991| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.37 r_work: 0.3346 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.2254 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 : 0.725 5.637 4254 Z= 0.384 Chirality : 0.054 0.158 441 Planarity : 0.003 0.020 558 Dihedral : 5.885 39.965 438 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.20 % Allowed : 16.22 % Favored : 82.58 % 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: -3.40 (0.32), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.25), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 16 TYR 0.016 0.003 TYR B 86 PHE 0.019 0.002 PHE B 85 TRP 0.009 0.002 TRP A 3 HIS 0.010 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 3138) covalent geometry : angle 0.72136 / 0.38 ( 4236) SS BOND : bond 0.00632 / 0.45 ( 9) SS BOND : angle 1.28467 / 0.99 ( 18) hydrogen bonds : bond 0.04018 / 2.41 ( 40) hydrogen bonds : angle 7.12023 / 5.14 ( 120) *********************** 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 101 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.122 Fit side-chains REVERT: B 55 MET cc_start: 0.9411 (ttp) cc_final: 0.9101 (ttp) REVERT: B 98 LYS cc_start: 0.8825 (mtpm) cc_final: 0.8525 (mttp) REVERT: C 74 ARG cc_start: 0.8698 (mtm180) cc_final: 0.8432 (mtp180) outliers start: 4 outliers final: 3 residues processed: 99 average time/residue: 0.7267 time to fit residues: 73.2118 Evaluate side-chains 100 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 100 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN B 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.110195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.096291 restraints weight = 3126.660| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.37 r_work: 0.3326 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3147 Z= 0.224 Angle : 0.768 5.813 4254 Z= 0.408 Chirality : 0.056 0.159 441 Planarity : 0.004 0.021 558 Dihedral : 5.971 40.528 438 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 1.50 % Allowed : 15.32 % Favored : 83.18 % 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: -3.42 (0.32), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.25), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 16 TYR 0.019 0.003 TYR A 86 PHE 0.020 0.002 PHE B 85 TRP 0.010 0.002 TRP A 3 HIS 0.010 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.22 ( 3138) covalent geometry : angle 0.76530 / 0.41 ( 4236) SS BOND : bond 0.00685 / 0.48 ( 9) SS BOND : angle 1.27542 / 0.99 ( 18) hydrogen bonds : bond 0.04359 / 2.61 ( 40) hydrogen bonds : angle 7.32651 / 5.30 ( 120) *********************** 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 103 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.125 Fit side-chains REVERT: B 55 MET cc_start: 0.9424 (ttp) cc_final: 0.9087 (ttp) REVERT: B 98 LYS cc_start: 0.8857 (mtpm) cc_final: 0.8555 (mttp) REVERT: C 74 ARG cc_start: 0.8704 (mtm180) cc_final: 0.8437 (mtp180) REVERT: C 84 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8425 (tpt) outliers start: 5 outliers final: 4 residues processed: 100 average time/residue: 0.7668 time to fit residues: 78.0462 Evaluate side-chains 103 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 102 LEU 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: 6.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 20 optimal weight: 0.0970 chunk 2 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 GLN A 29 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.114203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.100352 restraints weight = 3052.914| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.35 r_work: 0.3403 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3147 Z= 0.127 Angle : 0.670 5.425 4254 Z= 0.354 Chirality : 0.052 0.150 441 Planarity : 0.003 0.019 558 Dihedral : 5.684 40.273 438 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 1.50 % Allowed : 15.92 % Favored : 82.58 % 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: -3.36 (0.33), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.25), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 74 TYR 0.015 0.002 TYR C 132 PHE 0.017 0.002 PHE B 85 TRP 0.008 0.002 TRP A 3 HIS 0.009 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 3138) covalent geometry : angle 0.66663 / 0.35 ( 4236) SS BOND : bond 0.00533 / 0.38 ( 9) SS BOND : angle 1.20572 / 0.93 ( 18) hydrogen bonds : bond 0.03470 / 2.09 ( 40) hydrogen bonds : angle 6.78234 / 4.90 ( 120) ********************** 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 100 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.131 Fit side-chains REVERT: B 98 LYS cc_start: 0.8827 (mtpm) cc_final: 0.8529 (mttp) REVERT: C 74 ARG cc_start: 0.8704 (mtm180) cc_final: 0.8439 (mtp180) REVERT: C 84 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8284 (tpt) outliers start: 5 outliers final: 3 residues processed: 97 average time/residue: 0.7924 time to fit residues: 78.1693 Evaluate side-chains 99 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 102 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.113468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.099557 restraints weight = 3049.042| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.35 r_work: 0.3378 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3147 Z= 0.139 Angle : 0.679 5.453 4254 Z= 0.359 Chirality : 0.052 0.151 441 Planarity : 0.003 0.022 558 Dihedral : 5.661 40.577 438 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.50 % Allowed : 15.92 % Favored : 82.58 % 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: -3.34 (0.33), residues: 393 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.25), 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 0.018 0.002 PHE C 85 TRP 0.009 0.002 TRP A 3 HIS 0.009 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 3138) covalent geometry : angle 0.67558 / 0.36 ( 4236) SS BOND : bond 0.00543 / 0.39 ( 9) SS BOND : angle 1.20029 / 0.92 ( 18) hydrogen bonds : bond 0.03567 / 2.17 ( 40) hydrogen bonds : angle 6.76169 / 4.88 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1978.27 seconds wall clock time: 34 minutes 23.91 seconds (2063.91 seconds total)