Starting phenix.real_space_refine on Tue Aug 4 15:34:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9w_65791/08_2026/9w9w_65791.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9w_65791/08_2026/9w9w_65791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w9w_65791/08_2026/9w9w_65791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9w_65791/08_2026/9w9w_65791.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w9w_65791/08_2026/9w9w_65791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9w_65791/08_2026/9w9w_65791.map" } resolution = 2.27 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= 0.002 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 6 5.16 5 C 2832 2.51 5 N 735 2.21 5 O 813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4386 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 729 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "C" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 733 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain breaks: 1 Restraints were copied for chains: A, E, D, F Time building chain proxies: 0.84, per 1000 atoms: 0.19 Number of scatterers: 4386 At special positions: 0 Unit cell: (128.34, 128.34, 34.41, 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 6 16.00 O 813 8.00 N 735 7.00 C 2832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 144.0 milliseconds 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1068 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 23 sheets defined 0.0% alpha, 44.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 6.432A pdb=" N MET B 13 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N VAL A 16 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LYS B 15 " --> pdb=" O VAL A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 removed outlier: 6.298A pdb=" N ALA B 19 " --> pdb=" O VAL A 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 27 removed outlier: 6.717A pdb=" N ILE B 26 " --> pdb=" O ASN E 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 31 through 34 removed outlier: 6.076A pdb=" N HIS B 31 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ARG A 34 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N PHE B 33 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 62 through 65 removed outlier: 6.464A pdb=" N GLU B 63 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.163A pdb=" N VAL B 71 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 80 removed outlier: 6.971A pdb=" N SER B 77 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TYR A 78 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N LYS B 76 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 9.618A pdb=" N TRP E 79 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N TYR B 78 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 83 through 84 removed outlier: 6.717A pdb=" N ARG B 83 " --> pdb=" O ILE E 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 93 through 99 removed outlier: 6.366A pdb=" N VAL B 94 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ALA E 97 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR B 96 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ASP E 99 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASN B 98 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 103 through 110 removed outlier: 6.669A pdb=" N ARG B 103 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N THR A 106 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR B 105 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA A 108 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 107 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU A 110 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA B 109 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU B 110 " --> pdb=" O ALA E 109 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.883A pdb=" N TYR B 114 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 118 through 122 removed outlier: 5.937A pdb=" N THR B 118 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL A 121 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA B 120 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 13 through 16 removed outlier: 6.565A pdb=" N VAL C 14 " --> pdb=" O LYS F 15 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 21 removed outlier: 6.734A pdb=" N VAL C 20 " --> pdb=" O ARG F 21 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 25 through 34 removed outlier: 6.983A pdb=" N ILE C 26 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ALA F 29 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL C 28 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N HIS F 31 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL C 30 " --> pdb=" O HIS F 31 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N PHE F 33 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL C 32 " --> pdb=" O PHE F 33 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 63 through 65 removed outlier: 6.501A pdb=" N PHE C 64 " --> pdb=" O VAL F 65 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 69 through 73 removed outlier: 6.497A pdb=" N TYR C 69 " --> pdb=" O LYS D 70 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N GLU D 72 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL C 71 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 76 through 80 removed outlier: 6.962A pdb=" N SER C 77 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR D 78 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 9.454A pdb=" N LYS C 76 " --> pdb=" O SER F 77 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N TRP F 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N TYR C 78 " --> pdb=" O TRP F 79 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 83 through 84 removed outlier: 6.649A pdb=" N ARG C 83 " --> pdb=" O ILE F 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 91 through 99 removed outlier: 6.322A pdb=" N ALA C 91 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL D 94 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL C 93 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N THR D 96 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE C 95 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ASN D 98 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA C 97 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 103 through 110 removed outlier: 6.997A pdb=" N ALA C 109 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU D 110 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG C 104 " --> pdb=" O TYR F 105 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE F 107 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR C 106 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ALA F 109 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N ALA C 108 " --> pdb=" O ALA F 109 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 114 through 115 removed outlier: 6.926A pdb=" N TYR C 114 " --> pdb=" O SER F 115 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 118 through 122 removed outlier: 5.857A pdb=" N THR C 118 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL D 121 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA C 120 " --> pdb=" O VAL D 121 " (cutoff:3.500A) 75 hydrogen bonds defined for protein. 225 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: 0.50 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1380 1.34 - 1.46: 891 1.46 - 1.57: 2205 1.57 - 1.69: 0 1.69 - 1.80: 12 Bond restraints: 4488 Sorted by residual: bond pdb=" CG LEU C 12 " pdb=" CD1 LEU C 12 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.63e+00 bond pdb=" CG LEU F 12 " pdb=" CD1 LEU F 12 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.62e+00 bond pdb=" CG LEU D 12 " pdb=" CD1 LEU D 12 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.62e+00 bond pdb=" C SER D 23 " pdb=" N PRO D 24 " ideal model delta sigma weight residual 1.326 1.339 -0.012 1.44e-02 4.82e+03 7.34e-01 bond pdb=" C SER F 23 " pdb=" N PRO F 24 " ideal model delta sigma weight residual 1.326 1.338 -0.012 1.44e-02 4.82e+03 6.39e-01 ... (remaining 4483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 5834 1.06 - 2.12: 201 2.12 - 3.18: 55 3.18 - 4.24: 6 4.24 - 5.29: 9 Bond angle restraints: 6105 Sorted by residual: angle pdb=" CB ARG F 34 " pdb=" CG ARG F 34 " pdb=" CD ARG F 34 " ideal model delta sigma weight residual 111.30 115.67 -4.37 2.30e+00 1.89e-01 3.61e+00 angle pdb=" CB ARG D 34 " pdb=" CG ARG D 34 " pdb=" CD ARG D 34 " ideal model delta sigma weight residual 111.30 115.63 -4.33 2.30e+00 1.89e-01 3.55e+00 angle pdb=" CB ARG C 34 " pdb=" CG ARG C 34 " pdb=" CD ARG C 34 " ideal model delta sigma weight residual 111.30 115.63 -4.33 2.30e+00 1.89e-01 3.54e+00 angle pdb=" CA MET C 13 " pdb=" CB MET C 13 " pdb=" CG MET C 13 " ideal model delta sigma weight residual 114.10 117.80 -3.70 2.00e+00 2.50e-01 3.43e+00 angle pdb=" CA MET D 13 " pdb=" CB MET D 13 " pdb=" CG MET D 13 " ideal model delta sigma weight residual 114.10 117.80 -3.70 2.00e+00 2.50e-01 3.42e+00 ... (remaining 6100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.48: 2251 14.48 - 28.95: 236 28.95 - 43.43: 126 43.43 - 57.91: 33 57.91 - 72.38: 21 Dihedral angle restraints: 2667 sinusoidal: 1026 harmonic: 1641 Sorted by residual: dihedral pdb=" CA GLU B 63 " pdb=" CB GLU B 63 " pdb=" CG GLU B 63 " pdb=" CD GLU B 63 " ideal model delta sinusoidal sigma weight residual 60.00 118.58 -58.58 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA GLU A 63 " pdb=" CB GLU A 63 " pdb=" CG GLU A 63 " pdb=" CD GLU A 63 " ideal model delta sinusoidal sigma weight residual 60.00 118.57 -58.57 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA GLU E 63 " pdb=" CB GLU E 63 " pdb=" CG GLU E 63 " pdb=" CD GLU E 63 " ideal model delta sinusoidal sigma weight residual 60.00 118.55 -58.55 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 2664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 368 0.025 - 0.051: 193 0.051 - 0.076: 47 0.076 - 0.101: 41 0.101 - 0.126: 71 Chirality restraints: 720 Sorted by residual: chirality pdb=" CA VAL D 65 " pdb=" N VAL D 65 " pdb=" C VAL D 65 " pdb=" CB VAL D 65 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA VAL F 65 " pdb=" N VAL F 65 " pdb=" C VAL F 65 " pdb=" CB VAL F 65 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA VAL C 71 " pdb=" N VAL C 71 " pdb=" C VAL C 71 " pdb=" CB VAL C 71 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 717 not shown) Planarity restraints: 753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 66 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" CD GLU C 66 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU C 66 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU C 66 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 66 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" CD GLU D 66 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU D 66 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU D 66 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 66 " 0.009 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" CD GLU F 66 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU F 66 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU F 66 " 0.012 2.00e-02 2.50e+03 ... (remaining 750 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 415 2.76 - 3.29: 3844 3.29 - 3.83: 7432 3.83 - 4.36: 8131 4.36 - 4.90: 15934 Nonbonded interactions: 35756 Sorted by model distance: nonbonded pdb=" OD2 ASP C 74 " pdb=" OH TYR C 105 " model vdw 2.225 3.040 nonbonded pdb=" OD2 ASP F 74 " pdb=" OH TYR F 105 " model vdw 2.225 3.040 nonbonded pdb=" OD2 ASP D 74 " pdb=" OH TYR D 105 " model vdw 2.226 3.040 nonbonded pdb=" NZ LYS B 15 " pdb=" OE2 GLU F 89 " model vdw 2.251 3.120 nonbonded pdb=" OE2 GLU C 89 " pdb=" NZ LYS A 15 " model vdw 2.252 3.120 ... (remaining 35751 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 'B' selection = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'F' } 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: 2.430 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.920 Find NCS groups from input model: 0.040 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:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 4488 Z= 0.118 Angle : 0.518 5.295 6105 Z= 0.278 Chirality : 0.049 0.126 720 Planarity : 0.003 0.021 753 Dihedral : 17.107 72.382 1599 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 15.62 % Favored : 84.38 % 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: -3.02 (0.31), residues: 531 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 34 TYR 0.012 0.001 TYR E 114 PHE 0.008 0.001 PHE F 33 TRP 0.003 0.001 TRP E 79 HIS 0.002 0.001 HIS F 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 4488) covalent geometry : angle 0.51839 / 0.28 ( 6105) hydrogen bonds : bond 0.17876 / 12.30 ( 75) hydrogen bonds : angle 9.47591 / 6.62 ( 225) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.166 Fit side-chains REVERT: A 74 ASP cc_start: 0.8560 (t0) cc_final: 0.8294 (t0) REVERT: A 83 ARG cc_start: 0.7415 (mtm-85) cc_final: 0.6709 (mmp-170) REVERT: A 98 ASN cc_start: 0.8660 (m110) cc_final: 0.8416 (m-40) REVERT: A 104 ARG cc_start: 0.7838 (mtt90) cc_final: 0.6941 (mmt180) REVERT: D 34 ARG cc_start: 0.7857 (tpp-160) cc_final: 0.7540 (tpm170) REVERT: E 77 SER cc_start: 0.8573 (t) cc_final: 0.8321 (t) REVERT: E 83 ARG cc_start: 0.7398 (mtm-85) cc_final: 0.6941 (ppt90) REVERT: E 98 ASN cc_start: 0.8643 (m110) cc_final: 0.8328 (m-40) REVERT: F 103 ARG cc_start: 0.8501 (mtm180) cc_final: 0.6338 (mmt180) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.6487 time to fit residues: 80.4704 Evaluate side-chains 105 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 90 HIS C 124 ASN D 31 HIS D 90 HIS D 124 ASN F 124 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.162014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.134480 restraints weight = 5093.160| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.91 r_work: 0.3902 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4488 Z= 0.197 Angle : 0.597 5.449 6105 Z= 0.329 Chirality : 0.051 0.136 720 Planarity : 0.005 0.055 753 Dihedral : 5.512 19.870 603 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 6.04 % Allowed : 17.29 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.32), residues: 531 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 104 TYR 0.013 0.002 TYR C 114 PHE 0.014 0.002 PHE B 33 TRP 0.004 0.001 TRP B 79 HIS 0.005 0.001 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 ( 4488) covalent geometry : angle 0.59688 / 0.33 ( 6105) hydrogen bonds : bond 0.03384 / 2.33 ( 75) hydrogen bonds : angle 6.44966 / 4.44 ( 225) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.103 Fit side-chains REVERT: B 83 ARG cc_start: 0.7421 (mtt180) cc_final: 0.7071 (mtt180) REVERT: C 63 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8085 (mt-10) REVERT: A 74 ASP cc_start: 0.8537 (t0) cc_final: 0.8249 (t0) REVERT: A 83 ARG cc_start: 0.7566 (mtm-85) cc_final: 0.6944 (mmp-170) REVERT: A 104 ARG cc_start: 0.7753 (mtt90) cc_final: 0.6531 (mmt180) REVERT: D 104 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7784 (ttm170) REVERT: E 98 ASN cc_start: 0.8794 (m110) cc_final: 0.8469 (m-40) REVERT: F 63 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8101 (mt-10) REVERT: F 103 ARG cc_start: 0.8687 (mtm180) cc_final: 0.6099 (mmt180) outliers start: 29 outliers final: 12 residues processed: 111 average time/residue: 0.6231 time to fit residues: 70.7725 Evaluate side-chains 109 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 88 HIS Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 46 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 38 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 ASN C 31 HIS A 98 ASN E 31 HIS E 98 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.159471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.132779 restraints weight = 5036.705| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 1.81 r_work: 0.3872 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3793 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4488 Z= 0.270 Angle : 0.649 5.145 6105 Z= 0.363 Chirality : 0.053 0.151 720 Planarity : 0.005 0.070 753 Dihedral : 5.778 20.261 603 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 7.08 % Allowed : 17.71 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.33), residues: 531 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 83 TYR 0.014 0.002 TYR C 105 PHE 0.016 0.002 PHE C 33 TRP 0.005 0.001 TRP E 79 HIS 0.007 0.001 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.27 ( 4488) covalent geometry : angle 0.64916 / 0.36 ( 6105) hydrogen bonds : bond 0.03225 / 2.20 ( 75) hydrogen bonds : angle 6.41421 / 4.42 ( 225) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.103 Fit side-chains REVERT: B 83 ARG cc_start: 0.7484 (mtt180) cc_final: 0.7259 (mtt180) REVERT: C 13 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7686 (tmt) REVERT: C 34 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8190 (ttm-80) REVERT: C 66 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7828 (mp0) REVERT: A 13 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.7639 (tmt) REVERT: A 74 ASP cc_start: 0.8594 (t0) cc_final: 0.8280 (t0) REVERT: A 83 ARG cc_start: 0.7584 (mtm-85) cc_final: 0.7037 (mmp-170) REVERT: D 104 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7857 (ttm170) REVERT: F 103 ARG cc_start: 0.8701 (mtm180) cc_final: 0.6156 (mmt180) outliers start: 34 outliers final: 17 residues processed: 117 average time/residue: 0.6071 time to fit residues: 72.7635 Evaluate side-chains 120 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 ASN A 124 ASN F 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.158281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.131837 restraints weight = 4992.028| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 1.83 r_work: 0.3856 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 4488 Z= 0.311 Angle : 0.680 5.265 6105 Z= 0.381 Chirality : 0.054 0.144 720 Planarity : 0.004 0.026 753 Dihedral : 6.037 21.568 603 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 5.42 % Allowed : 19.38 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.32), residues: 531 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 34 TYR 0.014 0.003 TYR C 105 PHE 0.016 0.002 PHE C 33 TRP 0.005 0.001 TRP E 79 HIS 0.008 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00737 / 0.31 ( 4488) covalent geometry : angle 0.68043 / 0.38 ( 6105) hydrogen bonds : bond 0.03089 / 2.10 ( 75) hydrogen bonds : angle 6.24819 / 4.29 ( 225) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.102 Fit side-chains REVERT: C 13 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7791 (tmt) REVERT: C 15 LYS cc_start: 0.8506 (mttm) cc_final: 0.8234 (mtmt) REVERT: C 18 ASP cc_start: 0.7881 (t0) cc_final: 0.7619 (t0) REVERT: C 34 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8259 (ttm-80) REVERT: C 66 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7843 (mp0) REVERT: A 13 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7596 (tmt) REVERT: A 74 ASP cc_start: 0.8589 (t0) cc_final: 0.8280 (t0) REVERT: D 34 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.7572 (tpp-160) REVERT: F 34 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.8045 (ttm110) REVERT: F 62 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7335 (mt-10) REVERT: F 83 ARG cc_start: 0.8187 (mtm-85) cc_final: 0.7794 (mtm-85) REVERT: F 103 ARG cc_start: 0.8709 (mtm180) cc_final: 0.6150 (mmt180) outliers start: 26 outliers final: 16 residues processed: 112 average time/residue: 0.6024 time to fit residues: 69.0447 Evaluate side-chains 117 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.162120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.136256 restraints weight = 5004.406| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.77 r_work: 0.3908 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4488 Z= 0.167 Angle : 0.576 5.335 6105 Z= 0.317 Chirality : 0.050 0.136 720 Planarity : 0.003 0.037 753 Dihedral : 5.781 21.032 603 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.62 % Allowed : 19.58 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.33), residues: 531 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 104 TYR 0.013 0.002 TYR C 114 PHE 0.015 0.002 PHE C 33 TRP 0.002 0.001 TRP B 79 HIS 0.004 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 4488) covalent geometry : angle 0.57595 / 0.32 ( 6105) hydrogen bonds : bond 0.02520 / 1.71 ( 75) hydrogen bonds : angle 5.99161 / 4.07 ( 225) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.173 Fit side-chains REVERT: C 13 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7801 (tmt) REVERT: C 34 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8161 (ttm-80) REVERT: C 66 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7828 (mt-10) REVERT: C 123 THR cc_start: 0.9040 (m) cc_final: 0.8704 (m) REVERT: A 13 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7592 (tmt) REVERT: A 74 ASP cc_start: 0.8560 (t0) cc_final: 0.8282 (t0) REVERT: A 83 ARG cc_start: 0.7396 (mtm-85) cc_final: 0.7035 (mmp-170) REVERT: D 34 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.7683 (tpp-160) REVERT: D 35 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7630 (pttm) REVERT: F 34 ARG cc_start: 0.8474 (ttm-80) cc_final: 0.8254 (ttm-80) REVERT: F 62 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: F 66 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6943 (mp0) REVERT: F 83 ARG cc_start: 0.8170 (mtm-85) cc_final: 0.7800 (mtm-85) REVERT: F 103 ARG cc_start: 0.8657 (mtm180) cc_final: 0.6213 (mmt180) outliers start: 27 outliers final: 15 residues processed: 117 average time/residue: 0.6520 time to fit residues: 78.1592 Evaluate side-chains 122 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 88 HIS Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.159636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.134417 restraints weight = 5139.990| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.74 r_work: 0.3867 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 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 : 0.007 0.035 4488 Z= 0.276 Angle : 0.654 5.683 6105 Z= 0.363 Chirality : 0.053 0.142 720 Planarity : 0.004 0.053 753 Dihedral : 6.094 22.011 603 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 6.04 % Allowed : 20.21 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.32), residues: 531 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 83 TYR 0.014 0.002 TYR C 114 PHE 0.017 0.002 PHE C 33 TRP 0.005 0.001 TRP A 79 HIS 0.005 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.28 ( 4488) covalent geometry : angle 0.65439 / 0.36 ( 6105) hydrogen bonds : bond 0.02913 / 1.98 ( 75) hydrogen bonds : angle 6.09152 / 4.16 ( 225) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.104 Fit side-chains REVERT: C 15 LYS cc_start: 0.8499 (mttm) cc_final: 0.8286 (mtmt) REVERT: C 34 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8274 (ttm-80) REVERT: C 66 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7796 (mt-10) REVERT: A 13 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7570 (tmt) REVERT: A 74 ASP cc_start: 0.8596 (t0) cc_final: 0.8288 (t0) REVERT: A 83 ARG cc_start: 0.7446 (mtm-85) cc_final: 0.7010 (mmp-170) REVERT: D 34 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.7629 (tpp-160) REVERT: D 35 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7636 (pttm) REVERT: F 34 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8160 (ttm110) REVERT: F 62 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: F 66 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6968 (mp0) REVERT: F 83 ARG cc_start: 0.8173 (mtm-85) cc_final: 0.7790 (mtm-85) REVERT: F 103 ARG cc_start: 0.8679 (mtm180) cc_final: 0.6191 (mmt180) outliers start: 29 outliers final: 17 residues processed: 116 average time/residue: 0.6509 time to fit residues: 77.2428 Evaluate side-chains 123 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 9.9990 chunk 52 optimal weight: 0.2980 chunk 44 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 ASN F 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.162583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.137174 restraints weight = 4968.018| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.74 r_work: 0.3920 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3842 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4488 Z= 0.149 Angle : 0.559 5.598 6105 Z= 0.308 Chirality : 0.050 0.135 720 Planarity : 0.003 0.051 753 Dihedral : 5.822 20.902 603 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.38 % Allowed : 21.88 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.33), residues: 531 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 34 TYR 0.012 0.002 TYR C 114 PHE 0.015 0.002 PHE C 33 TRP 0.002 0.000 TRP D 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 4488) covalent geometry : angle 0.55879 / 0.31 ( 6105) hydrogen bonds : bond 0.02407 / 1.64 ( 75) hydrogen bonds : angle 5.86490 / 3.98 ( 225) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.125 Fit side-chains REVERT: B 83 ARG cc_start: 0.7543 (mtt180) cc_final: 0.6960 (ptp90) REVERT: C 34 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8194 (ttm-80) REVERT: C 66 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7782 (mt-10) REVERT: C 123 THR cc_start: 0.9034 (m) cc_final: 0.8706 (m) REVERT: A 13 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7491 (tmt) REVERT: A 74 ASP cc_start: 0.8523 (t0) cc_final: 0.8232 (t0) REVERT: A 83 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.7015 (mmp-170) REVERT: D 34 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.7656 (tpp-160) REVERT: D 35 LYS cc_start: 0.8221 (ttmt) cc_final: 0.7639 (pttm) REVERT: F 62 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: F 83 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7696 (mtm-85) REVERT: F 103 ARG cc_start: 0.8655 (mtm180) cc_final: 0.6234 (mmt180) outliers start: 21 outliers final: 13 residues processed: 112 average time/residue: 0.6725 time to fit residues: 77.1442 Evaluate side-chains 121 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 88 HIS Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 ASN F 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.156039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.129295 restraints weight = 5033.974| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.86 r_work: 0.3845 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 4488 Z= 0.332 Angle : 0.718 6.759 6105 Z= 0.397 Chirality : 0.054 0.144 720 Planarity : 0.004 0.044 753 Dihedral : 6.267 22.297 603 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.58 % Allowed : 22.08 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.32), residues: 531 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 34 TYR 0.015 0.003 TYR C 114 PHE 0.017 0.002 PHE C 33 TRP 0.005 0.001 TRP E 79 HIS 0.006 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00784 / 0.33 ( 4488) covalent geometry : angle 0.71832 / 0.40 ( 6105) hydrogen bonds : bond 0.03076 / 2.07 ( 75) hydrogen bonds : angle 6.07055 / 4.16 ( 225) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.110 Fit side-chains REVERT: B 83 ARG cc_start: 0.7544 (mtt180) cc_final: 0.7324 (mtt180) REVERT: C 13 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7757 (tmt) REVERT: C 66 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7840 (mt-10) REVERT: A 13 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7583 (tmt) REVERT: A 74 ASP cc_start: 0.8618 (t0) cc_final: 0.8293 (t0) REVERT: A 83 ARG cc_start: 0.7420 (mtm-85) cc_final: 0.6988 (mmt-90) REVERT: D 34 ARG cc_start: 0.8447 (ttm-80) cc_final: 0.7528 (tpp-160) REVERT: D 35 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7680 (pttm) REVERT: F 62 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7338 (mt-10) REVERT: F 66 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6993 (mp0) REVERT: F 83 ARG cc_start: 0.8153 (mtm-85) cc_final: 0.7770 (mtm-85) REVERT: F 103 ARG cc_start: 0.8695 (mtm180) cc_final: 0.6117 (mmt180) outliers start: 22 outliers final: 14 residues processed: 113 average time/residue: 0.6108 time to fit residues: 70.6236 Evaluate side-chains 121 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain D residue 35 LYS Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 20 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 ASN F 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.164250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.137396 restraints weight = 5008.663| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.89 r_work: 0.3934 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3852 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4488 Z= 0.122 Angle : 0.559 6.164 6105 Z= 0.301 Chirality : 0.050 0.137 720 Planarity : 0.003 0.034 753 Dihedral : 5.852 20.081 603 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.29 % Allowed : 24.38 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.33), residues: 531 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 104 TYR 0.013 0.001 TYR A 114 PHE 0.013 0.002 PHE B 33 TRP 0.003 0.000 TRP D 79 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 4488) covalent geometry : angle 0.55895 / 0.30 ( 6105) hydrogen bonds : bond 0.02246 / 1.55 ( 75) hydrogen bonds : angle 5.75072 / 3.89 ( 225) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.107 Fit side-chains REVERT: B 83 ARG cc_start: 0.7503 (mtt180) cc_final: 0.6942 (ptp90) REVERT: C 15 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7491 (mtpp) REVERT: C 18 ASP cc_start: 0.7857 (t0) cc_final: 0.7302 (m-30) REVERT: C 34 ARG cc_start: 0.8470 (ttt180) cc_final: 0.8259 (ttm-80) REVERT: C 66 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7765 (mt-10) REVERT: C 123 THR cc_start: 0.9068 (m) cc_final: 0.8536 (p) REVERT: A 13 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7364 (tmt) REVERT: A 74 ASP cc_start: 0.8512 (t0) cc_final: 0.8178 (t0) REVERT: A 83 ARG cc_start: 0.7403 (mtm-85) cc_final: 0.6859 (mmp-170) REVERT: D 34 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.7497 (tpp-160) REVERT: D 35 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7545 (pttm) REVERT: F 62 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: F 83 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.7584 (mtm-85) REVERT: F 103 ARG cc_start: 0.8694 (mtm180) cc_final: 0.6085 (mmt180) outliers start: 11 outliers final: 5 residues processed: 109 average time/residue: 0.6615 time to fit residues: 73.6814 Evaluate side-chains 112 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 ASN A 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.159028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.131673 restraints weight = 5019.345| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.90 r_work: 0.3865 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 4488 Z= 0.236 Angle : 0.673 7.346 6105 Z= 0.365 Chirality : 0.052 0.138 720 Planarity : 0.003 0.034 753 Dihedral : 6.214 22.147 603 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.88 % Allowed : 24.58 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.32), residues: 531 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 83 TYR 0.015 0.002 TYR C 114 PHE 0.016 0.002 PHE C 33 TRP 0.004 0.001 TRP A 79 HIS 0.004 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.24 ( 4488) covalent geometry : angle 0.67256 / 0.37 ( 6105) hydrogen bonds : bond 0.02748 / 1.87 ( 75) hydrogen bonds : angle 5.79317 / 3.95 ( 225) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: B 83 ARG cc_start: 0.7537 (mtt180) cc_final: 0.7313 (mtt180) REVERT: C 34 ARG cc_start: 0.8564 (ttt180) cc_final: 0.8361 (ttm-80) REVERT: C 66 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7809 (mt-10) REVERT: C 123 THR cc_start: 0.9095 (m) cc_final: 0.8793 (m) REVERT: A 13 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7522 (tmt) REVERT: A 74 ASP cc_start: 0.8580 (t0) cc_final: 0.8239 (t0) REVERT: A 83 ARG cc_start: 0.7351 (mtm-85) cc_final: 0.6811 (mmp-170) REVERT: D 34 ARG cc_start: 0.8469 (ttm-80) cc_final: 0.7482 (tpp-160) REVERT: D 35 LYS cc_start: 0.8289 (ttmt) cc_final: 0.7550 (pttm) REVERT: F 62 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7197 (mt-10) REVERT: F 83 ARG cc_start: 0.8107 (mtm-85) cc_final: 0.7699 (mtm-85) REVERT: F 103 ARG cc_start: 0.8706 (mtm180) cc_final: 0.6063 (mmt180) outliers start: 9 outliers final: 6 residues processed: 108 average time/residue: 0.6789 time to fit residues: 74.9544 Evaluate side-chains 111 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.160663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.133778 restraints weight = 4969.498| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 1.82 r_work: 0.3898 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4488 Z= 0.191 Angle : 0.619 6.556 6105 Z= 0.339 Chirality : 0.051 0.135 720 Planarity : 0.003 0.031 753 Dihedral : 6.062 21.578 603 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.29 % Allowed : 24.38 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.32), residues: 531 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 83 TYR 0.014 0.002 TYR C 114 PHE 0.015 0.002 PHE C 33 TRP 0.002 0.001 TRP A 79 HIS 0.004 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 ( 4488) covalent geometry : angle 0.61883 / 0.34 ( 6105) hydrogen bonds : bond 0.02580 / 1.72 ( 75) hydrogen bonds : angle 5.72083 / 3.89 ( 225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2159.49 seconds wall clock time: 37 minutes 19.59 seconds (2239.59 seconds total)