Starting phenix.real_space_refine on Thu Oct 22 19:35:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/34ad_59706/10_2026/34ad_59706.cif Found real_map, /net/cci-nas-00/data/ceres_data/34ad_59706/10_2026/34ad_59706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/34ad_59706/10_2026/34ad_59706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/34ad_59706/10_2026/34ad_59706.map" model { file = "/net/cci-nas-00/data/ceres_data/34ad_59706/10_2026/34ad_59706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/34ad_59706/10_2026/34ad_59706.cif" } resolution = 2.6 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: 5 Type Number sf(0) Gaussians S 3 5.16 5 C 1398 2.51 5 N 354 2.21 5 O 402 1.98 5 H 2163 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4320 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1440 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "B" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1440 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "C" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1440 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Time building chain proxies: 1.00, per 1000 atoms: 0.23 Number of scatterers: 4320 At special positions: 0 Unit cell: (82.611, 77.679, 32.058, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 O 402 8.00 N 354 7.00 C 1398 6.00 H 2163 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 78.3 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 522 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 52.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 6.557A pdb=" N MET A 13 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL B 16 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LYS A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.654A pdb=" N ALA A 19 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 34 removed outlier: 6.494A pdb=" N ALA A 25 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL B 28 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASN A 27 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL B 30 " --> pdb=" O ASN A 27 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA A 29 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL B 32 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N HIS A 31 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ARG B 34 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE A 33 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA B 25 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL C 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN B 27 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N VAL C 30 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA B 29 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL C 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N HIS B 31 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ARG C 34 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE B 33 " --> pdb=" O ARG C 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 66 removed outlier: 6.799A pdb=" N PHE A 64 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL B 65 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU A 66 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE B 64 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL C 65 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU B 66 " --> pdb=" O VAL C 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 73 Processing sheet with id=AA6, first strand: chain 'A' and resid 76 through 80 removed outlier: 6.897A pdb=" N SER A 77 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR B 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER B 77 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR C 78 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.262A pdb=" N GLY A 83 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLY B 83 " --> pdb=" O ILE C 84 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 99 removed outlier: 6.493A pdb=" N VAL B 93 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR C 96 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE B 95 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ASN C 98 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA B 97 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 103 through 110 removed outlier: 6.946A pdb=" N ARG A 104 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR B 105 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A 106 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE B 107 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA A 108 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ARG B 104 " --> pdb=" O ARG C 103 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR C 105 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR B 106 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE C 107 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA B 108 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'A' and resid 118 through 121 removed outlier: 6.317A pdb=" N THR A 118 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL B 121 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA A 120 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THR B 118 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL C 121 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA B 120 " --> pdb=" O VAL C 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 38 hydrogen bonds defined for protein. 111 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: 0.83 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 2163 1.12 - 1.30: 351 1.30 - 1.47: 828 1.47 - 1.64: 1023 1.64 - 1.81: 6 Bond restraints: 4371 Sorted by residual: bond pdb=" NE2 HIS B 90 " pdb=" HE2 HIS B 90 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N SER C 77 " pdb=" H SER C 77 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE1 TRP B 79 " pdb=" HE1 TRP B 79 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N VAL B 71 " pdb=" H VAL B 71 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CD2 TYR A 105 " pdb=" HD2 TYR A 105 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 4366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 5530 1.77 - 3.53: 1647 3.53 - 5.30: 490 5.30 - 7.06: 229 7.06 - 8.83: 9 Bond angle restraints: 7905 Sorted by residual: angle pdb=" CA ASP C 18 " pdb=" CB ASP C 18 " pdb=" CG ASP C 18 " ideal model delta sigma weight residual 112.60 119.16 -6.56 1.00e+00 1.00e+00 4.30e+01 angle pdb=" CA ASP B 18 " pdb=" CB ASP B 18 " pdb=" CG ASP B 18 " ideal model delta sigma weight residual 112.60 118.78 -6.18 1.00e+00 1.00e+00 3.82e+01 angle pdb=" CA ASP A 18 " pdb=" CB ASP A 18 " pdb=" CG ASP A 18 " ideal model delta sigma weight residual 112.60 118.55 -5.95 1.00e+00 1.00e+00 3.54e+01 angle pdb=" CA PHE A 33 " pdb=" CB PHE A 33 " pdb=" CG PHE A 33 " ideal model delta sigma weight residual 113.80 119.02 -5.22 1.00e+00 1.00e+00 2.73e+01 angle pdb=" CB HIS C 88 " pdb=" CG HIS C 88 " pdb=" CD2 HIS C 88 " ideal model delta sigma weight residual 131.20 124.87 6.33 1.30e+00 5.92e-01 2.37e+01 ... (remaining 7900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 1833 15.88 - 31.77: 120 31.77 - 47.65: 51 47.65 - 63.53: 59 63.53 - 79.41: 10 Dihedral angle restraints: 2073 sinusoidal: 1101 harmonic: 972 Sorted by residual: dihedral pdb=" CA ILE A 26 " pdb=" C ILE A 26 " pdb=" N ASN A 27 " pdb=" CA ASN A 27 " ideal model delta harmonic sigma weight residual 180.00 151.17 28.83 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ILE B 26 " pdb=" C ILE B 26 " pdb=" N ASN B 27 " pdb=" CA ASN B 27 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ILE C 26 " pdb=" C ILE C 26 " pdb=" N ASN C 27 " pdb=" CA ASN C 27 " ideal model delta harmonic sigma weight residual 180.00 151.68 28.32 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 2070 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.070: 181 0.070 - 0.140: 119 0.140 - 0.210: 37 0.210 - 0.280: 9 0.280 - 0.350: 8 Chirality restraints: 354 Sorted by residual: chirality pdb=" CA TYR B 114 " pdb=" N TYR B 114 " pdb=" C TYR B 114 " pdb=" CB TYR B 114 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA ILE A 68 " pdb=" N ILE A 68 " pdb=" C ILE A 68 " pdb=" CB ILE A 68 " both_signs ideal model delta sigma weight residual False 2.43 2.11 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA SER C 85 " pdb=" N SER C 85 " pdb=" C SER C 85 " pdb=" CB SER C 85 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 351 not shown) Planarity restraints: 627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 79 " -0.130 2.00e-02 2.50e+03 7.12e-02 2.03e+02 pdb=" CG TRP C 79 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP C 79 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 79 " 0.055 2.00e-02 2.50e+03 pdb=" NE1 TRP C 79 " 0.082 2.00e-02 2.50e+03 pdb=" CE2 TRP C 79 " 0.050 2.00e-02 2.50e+03 pdb=" CE3 TRP C 79 " 0.077 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 79 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 79 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP C 79 " -0.043 2.00e-02 2.50e+03 pdb=" HD1 TRP C 79 " -0.097 2.00e-02 2.50e+03 pdb=" HE1 TRP C 79 " 0.085 2.00e-02 2.50e+03 pdb=" HE3 TRP C 79 " 0.097 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 79 " -0.026 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 79 " -0.012 2.00e-02 2.50e+03 pdb=" HH2 TRP C 79 " -0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 103 " -0.283 9.50e-02 1.11e+02 1.19e-01 1.28e+02 pdb=" NE ARG C 103 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG C 103 " -0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG C 103 " -0.079 2.00e-02 2.50e+03 pdb=" NH2 ARG C 103 " -0.011 2.00e-02 2.50e+03 pdb="HH11 ARG C 103 " 0.161 2.00e-02 2.50e+03 pdb="HH12 ARG C 103 " -0.057 2.00e-02 2.50e+03 pdb="HH21 ARG C 103 " 0.088 2.00e-02 2.50e+03 pdb="HH22 ARG C 103 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 79 " -0.116 2.00e-02 2.50e+03 5.60e-02 1.26e+02 pdb=" CG TRP B 79 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP B 79 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP B 79 " 0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP B 79 " 0.065 2.00e-02 2.50e+03 pdb=" CE2 TRP B 79 " 0.037 2.00e-02 2.50e+03 pdb=" CE3 TRP B 79 " 0.056 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 79 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 79 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 79 " -0.032 2.00e-02 2.50e+03 pdb=" HD1 TRP B 79 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 TRP B 79 " 0.058 2.00e-02 2.50e+03 pdb=" HE3 TRP B 79 " 0.080 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 79 " -0.020 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 79 " -0.003 2.00e-02 2.50e+03 pdb=" HH2 TRP B 79 " -0.102 2.00e-02 2.50e+03 ... (remaining 624 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 484 2.23 - 2.82: 8231 2.82 - 3.42: 11558 3.42 - 4.01: 16070 4.01 - 4.60: 22358 Nonbonded interactions: 58701 Sorted by model distance: nonbonded pdb=" HG SER B 117 " pdb=" O SER C 117 " model vdw 1.641 2.450 nonbonded pdb=" HG SER A 117 " pdb=" O SER B 117 " model vdw 1.645 2.450 nonbonded pdb=" OD2 ASP A 74 " pdb=" HH TYR B 105 " model vdw 1.687 2.450 nonbonded pdb=" HZ1 LYS C 76 " pdb=" OD2 ASP C 99 " model vdw 1.723 2.450 nonbonded pdb=" OE1 GLU C 72 " pdb=" HG1 THR C 75 " model vdw 1.726 2.450 ... (remaining 58696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.660 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:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 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 : 0.012 0.041 2208 Z= 0.718 Angle : 1.884 6.714 3003 Z= 1.244 Chirality : 0.105 0.350 354 Planarity : 0.014 0.129 369 Dihedral : 12.715 57.598 780 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.56 % Allowed : 4.27 % Favored : 93.16 % Cbeta Deviations : 0.38 % 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: -1.57 (0.46), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 103 TYR 0.052 0.014 TYR A 105 PHE 0.037 0.009 PHE A 33 TRP 0.087 0.037 TRP C 79 HIS 0.007 0.002 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.01179 / 0.72 ( 2208) covalent geometry : angle 1.88394 / 1.24 ( 3003) hydrogen bonds : bond 0.12305 / 6.15 ( 38) hydrogen bonds : angle 8.39188 / 5.52 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7218 (tpt-90) cc_final: 0.6433 (tpm170) REVERT: A 34 ARG cc_start: 0.7830 (ttt-90) cc_final: 0.7589 (ttt90) REVERT: A 72 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8056 (mt-10) REVERT: A 89 GLU cc_start: 0.8571 (mt-10) cc_final: 0.7405 (pp20) REVERT: A 104 ARG cc_start: 0.8063 (mtt180) cc_final: 0.6684 (ptt-90) REVERT: B 16 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8439 (t) REVERT: B 21 ARG cc_start: 0.7650 (tpt-90) cc_final: 0.7122 (mtt-85) REVERT: B 34 ARG cc_start: 0.7279 (ttt-90) cc_final: 0.6764 (tpp80) REVERT: B 89 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7890 (mt-10) REVERT: C 18 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7433 (p0) REVERT: C 21 ARG cc_start: 0.7830 (tpt-90) cc_final: 0.5573 (pmt-80) REVERT: C 34 ARG cc_start: 0.7524 (ttt-90) cc_final: 0.5739 (tpp-160) REVERT: C 35 LYS cc_start: 0.7728 (tttt) cc_final: 0.7017 (tttt) REVERT: C 63 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7158 (mt-10) REVERT: C 89 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7393 (tp30) REVERT: C 104 ARG cc_start: 0.7655 (mtt180) cc_final: 0.6446 (mmp-170) outliers start: 6 outliers final: 1 residues processed: 74 average time/residue: 1.0578 time to fit residues: 79.7635 Evaluate side-chains 55 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain C residue 18 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [12, 24, 13, 1, 8, 16, 15, 25, 26, 9, 11] chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.168058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.148818 restraints weight = 6961.765| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 2.06 r_work: 0.4050 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3948 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2208 Z= 0.129 Angle : 0.587 4.134 3003 Z= 0.322 Chirality : 0.053 0.131 354 Planarity : 0.003 0.022 369 Dihedral : 6.909 25.228 301 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.99 % Allowed : 12.82 % Favored : 84.19 % 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: -1.60 (0.47), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 103 TYR 0.010 0.002 TYR B 78 PHE 0.009 0.001 PHE A 33 TRP 0.008 0.002 TRP A 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 2208) covalent geometry : angle 0.58749 / 0.32 ( 3003) hydrogen bonds : bond 0.03636 / 1.88 ( 38) hydrogen bonds : angle 5.91515 / 3.87 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7627 (tpt-90) cc_final: 0.6957 (tpm170) REVERT: A 89 GLU cc_start: 0.8563 (mt-10) cc_final: 0.7636 (pp20) REVERT: A 104 ARG cc_start: 0.8522 (mtt180) cc_final: 0.7645 (ptt-90) REVERT: B 21 ARG cc_start: 0.8081 (tpt-90) cc_final: 0.7689 (mtt-85) REVERT: B 89 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8067 (mt-10) REVERT: C 21 ARG cc_start: 0.8093 (tpt-90) cc_final: 0.5995 (pmt-80) REVERT: C 34 ARG cc_start: 0.8137 (ttt-90) cc_final: 0.6739 (mmt-90) REVERT: C 89 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7826 (tp30) REVERT: C 104 ARG cc_start: 0.8434 (mtt180) cc_final: 0.8012 (mmp80) outliers start: 7 outliers final: 1 residues processed: 56 average time/residue: 1.4059 time to fit residues: 80.0191 Evaluate side-chains 47 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [8, 23, 2, 10, 20, 13, 0, 24, 21, 7, 26] chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.4249 r_free = 0.4249 target = 0.159778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.140931 restraints weight = 7179.971| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.08 r_work: 0.3977 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3871 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2208 Z= 0.179 Angle : 0.583 4.269 3003 Z= 0.320 Chirality : 0.052 0.133 354 Planarity : 0.006 0.073 369 Dihedral : 6.436 24.847 298 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.28 % Allowed : 17.52 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.48), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.012 0.002 TYR A 114 PHE 0.008 0.001 PHE B 95 TRP 0.003 0.001 TRP C 79 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 ( 2208) covalent geometry : angle 0.58302 / 0.32 ( 3003) hydrogen bonds : bond 0.03870 / 2.05 ( 38) hydrogen bonds : angle 5.38024 / 3.54 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7923 (tpt-90) cc_final: 0.7231 (tpm170) REVERT: A 63 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8001 (tt0) REVERT: A 89 GLU cc_start: 0.8636 (mt-10) cc_final: 0.7735 (pp20) REVERT: A 104 ARG cc_start: 0.8538 (mtt180) cc_final: 0.7354 (ptt-90) REVERT: B 21 ARG cc_start: 0.8279 (tpt-90) cc_final: 0.7814 (mtt-85) REVERT: B 80 LYS cc_start: 0.8716 (tttt) cc_final: 0.8509 (tttt) REVERT: B 89 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8072 (mt-10) REVERT: C 21 ARG cc_start: 0.8502 (tpt-90) cc_final: 0.6502 (pmt-80) REVERT: C 34 ARG cc_start: 0.8366 (ttt-90) cc_final: 0.6903 (mmt-90) REVERT: C 63 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8155 (tt0) REVERT: C 65 VAL cc_start: 0.9135 (m) cc_final: 0.8865 (t) REVERT: C 89 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7945 (tp30) REVERT: C 99 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7703 (t0) REVERT: C 104 ARG cc_start: 0.8574 (mtt180) cc_final: 0.7948 (mmp80) outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 1.4076 time to fit residues: 72.8469 Evaluate side-chains 45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 99 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [22, 6, 11, 23, 5, 9, 25, 1, 17, 13, 10] chunk 22 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.160838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.142266 restraints weight = 7094.103| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 1.99 r_work: 0.3988 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3892 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2208 Z= 0.138 Angle : 0.519 4.551 3003 Z= 0.282 Chirality : 0.050 0.129 354 Planarity : 0.005 0.063 369 Dihedral : 6.082 24.700 298 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.14 % Allowed : 20.09 % Favored : 77.78 % 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: -1.65 (0.50), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 34 TYR 0.008 0.001 TYR B 114 PHE 0.007 0.001 PHE A 33 TRP 0.001 0.000 TRP C 79 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 2208) covalent geometry : angle 0.51868 / 0.28 ( 3003) hydrogen bonds : bond 0.03317 / 1.80 ( 38) hydrogen bonds : angle 5.12597 / 3.40 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.120 Fit side-chains REVERT: A 21 ARG cc_start: 0.7894 (tpt-90) cc_final: 0.7228 (tpm170) REVERT: A 89 GLU cc_start: 0.8576 (mt-10) cc_final: 0.7772 (pp20) REVERT: A 92 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: A 104 ARG cc_start: 0.8533 (mtt180) cc_final: 0.7362 (ptt-90) REVERT: B 21 ARG cc_start: 0.8300 (tpt-90) cc_final: 0.7857 (mtt-85) REVERT: B 72 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7911 (tt0) REVERT: B 89 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8051 (mt-10) REVERT: C 21 ARG cc_start: 0.8518 (tpt-90) cc_final: 0.6473 (pmt-80) REVERT: C 34 ARG cc_start: 0.8402 (ttt-90) cc_final: 0.6961 (mmt-90) REVERT: C 35 LYS cc_start: 0.8193 (tttt) cc_final: 0.7784 (tttt) REVERT: C 65 VAL cc_start: 0.9108 (m) cc_final: 0.8867 (p) REVERT: C 89 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7915 (tp30) REVERT: C 99 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7621 (t0) REVERT: C 104 ARG cc_start: 0.8574 (mtt180) cc_final: 0.8058 (mmp80) outliers start: 5 outliers final: 2 residues processed: 47 average time/residue: 1.5799 time to fit residues: 75.3038 Evaluate side-chains 45 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 99 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [2, 17, 5, 21, 0, 15, 19, 7, 13, 9, 25] chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 19 optimal weight: 0.3980 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 = 0.4259 r_free = 0.4259 target = 0.160738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.141932 restraints weight = 6968.693| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 1.99 r_work: 0.3995 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2208 Z= 0.149 Angle : 0.521 4.452 3003 Z= 0.284 Chirality : 0.050 0.130 354 Planarity : 0.005 0.043 369 Dihedral : 5.966 24.554 298 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.71 % Allowed : 19.23 % Favored : 79.06 % 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: -1.74 (0.50), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 34 TYR 0.009 0.001 TYR A 114 PHE 0.008 0.001 PHE B 33 TRP 0.001 0.000 TRP C 79 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 2208) covalent geometry : angle 0.52122 / 0.28 ( 3003) hydrogen bonds : bond 0.03466 / 1.87 ( 38) hydrogen bonds : angle 5.03153 / 3.33 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.103 Fit side-chains REVERT: A 21 ARG cc_start: 0.7981 (tpt-90) cc_final: 0.7328 (tpm170) REVERT: A 89 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7788 (pp20) REVERT: A 92 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: A 104 ARG cc_start: 0.8438 (mtt180) cc_final: 0.7406 (ptt-90) REVERT: B 21 ARG cc_start: 0.8234 (tpt-90) cc_final: 0.7863 (mtt-85) REVERT: B 34 ARG cc_start: 0.8134 (ttt-90) cc_final: 0.7709 (tpp80) REVERT: B 89 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8067 (mt-10) REVERT: C 21 ARG cc_start: 0.8509 (tpt-90) cc_final: 0.6512 (pmt-80) REVERT: C 34 ARG cc_start: 0.8393 (ttt-90) cc_final: 0.6976 (mmt-90) REVERT: C 63 GLU cc_start: 0.8447 (tt0) cc_final: 0.8233 (tt0) REVERT: C 89 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7817 (mm-30) REVERT: C 99 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7656 (t0) REVERT: C 104 ARG cc_start: 0.8478 (mtt180) cc_final: 0.8076 (mmp80) outliers start: 4 outliers final: 2 residues processed: 42 average time/residue: 1.7132 time to fit residues: 72.8801 Evaluate side-chains 44 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 99 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [9, 20, 22, 3, 10, 18, 11, 2, 25, 6, 26] chunk 9 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 0.0970 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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 = 0.4318 r_free = 0.4318 target = 0.165637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.147490 restraints weight = 7252.843| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 2.05 r_work: 0.4060 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3964 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2208 Z= 0.085 Angle : 0.477 4.446 3003 Z= 0.257 Chirality : 0.050 0.128 354 Planarity : 0.005 0.048 369 Dihedral : 5.602 23.090 298 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.43 % Allowed : 20.94 % Favored : 78.63 % 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: -1.72 (0.50), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.30 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 34 TYR 0.010 0.001 TYR B 114 PHE 0.009 0.001 PHE A 33 TRP 0.001 0.000 TRP C 79 HIS 0.001 0.001 HIS C 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 ( 2208) covalent geometry : angle 0.47727 / 0.26 ( 3003) hydrogen bonds : bond 0.02761 / 1.55 ( 38) hydrogen bonds : angle 4.78875 / 3.20 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.120 Fit side-chains REVERT: A 21 ARG cc_start: 0.7935 (tpt-90) cc_final: 0.7204 (tpm170) REVERT: A 89 GLU cc_start: 0.8562 (mt-10) cc_final: 0.7836 (pp20) REVERT: A 104 ARG cc_start: 0.8364 (mtt180) cc_final: 0.7336 (ptt-90) REVERT: B 21 ARG cc_start: 0.8026 (tpt-90) cc_final: 0.7670 (mtp-110) REVERT: B 34 ARG cc_start: 0.8303 (ttt-90) cc_final: 0.7878 (tpp80) REVERT: B 89 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8113 (mt-10) REVERT: C 21 ARG cc_start: 0.8470 (tpt-90) cc_final: 0.6440 (pmt-80) REVERT: C 34 ARG cc_start: 0.8327 (ttt-90) cc_final: 0.6874 (mmt-90) REVERT: C 104 ARG cc_start: 0.8454 (mtt180) cc_final: 0.8056 (mmp80) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 1.5922 time to fit residues: 69.3991 Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [19, 7, 1, 13, 20, 12, 18, 6, 0, 4, 21] chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.163396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.145064 restraints weight = 7205.139| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.05 r_work: 0.4036 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3939 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2208 Z= 0.120 Angle : 0.500 4.471 3003 Z= 0.270 Chirality : 0.050 0.128 354 Planarity : 0.004 0.046 369 Dihedral : 5.546 23.467 297 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.43 % Allowed : 23.93 % Favored : 75.64 % 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: -1.76 (0.50), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 34 TYR 0.008 0.001 TYR A 114 PHE 0.008 0.001 PHE A 33 TRP 0.001 0.000 TRP A 79 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 2208) covalent geometry : angle 0.49968 / 0.27 ( 3003) hydrogen bonds : bond 0.03010 / 1.62 ( 38) hydrogen bonds : angle 4.77571 / 3.18 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.094 Fit side-chains REVERT: A 21 ARG cc_start: 0.8014 (tpt-90) cc_final: 0.7313 (tpm170) REVERT: A 89 GLU cc_start: 0.8586 (mt-10) cc_final: 0.7842 (pp20) REVERT: A 104 ARG cc_start: 0.8380 (mtt180) cc_final: 0.7402 (ptt-90) REVERT: B 21 ARG cc_start: 0.8064 (tpt-90) cc_final: 0.7702 (mtp-110) REVERT: B 89 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8082 (mt-10) REVERT: C 21 ARG cc_start: 0.8500 (tpt-90) cc_final: 0.6475 (pmt-80) REVERT: C 34 ARG cc_start: 0.8372 (ttt-90) cc_final: 0.7014 (mmt-90) REVERT: C 89 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7888 (mm-30) REVERT: C 104 ARG cc_start: 0.8463 (mtt180) cc_final: 0.8094 (mmp80) outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 1.6575 time to fit residues: 67.1840 Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [15, 12, 19, 22, 18, 21, 8, 0, 1, 6, 3] chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4290 r_free = 0.4290 target = 0.163166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.145354 restraints weight = 7176.638| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 2.00 r_work: 0.4042 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3946 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2208 Z= 0.113 Angle : 0.492 4.473 3003 Z= 0.265 Chirality : 0.050 0.128 354 Planarity : 0.005 0.064 369 Dihedral : 5.518 23.330 297 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.85 % Allowed : 22.65 % Favored : 76.50 % 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: -1.78 (0.50), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 34 TYR 0.009 0.001 TYR B 114 PHE 0.009 0.001 PHE A 33 TRP 0.001 0.000 TRP C 79 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 2208) covalent geometry : angle 0.49244 / 0.27 ( 3003) hydrogen bonds : bond 0.02953 / 1.59 ( 38) hydrogen bonds : angle 4.75501 / 3.18 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.113 Fit side-chains REVERT: A 21 ARG cc_start: 0.7973 (tpt-90) cc_final: 0.7307 (tpm170) REVERT: A 89 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7836 (pp20) REVERT: A 104 ARG cc_start: 0.8387 (mtt180) cc_final: 0.7379 (ptt-90) REVERT: B 21 ARG cc_start: 0.8051 (tpt-90) cc_final: 0.7690 (mtp-110) REVERT: B 89 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8068 (mt-10) REVERT: C 13 MET cc_start: 0.8333 (ttp) cc_final: 0.7659 (mtm) REVERT: C 21 ARG cc_start: 0.8485 (tpt-90) cc_final: 0.6476 (pmt-80) REVERT: C 34 ARG cc_start: 0.8345 (ttt-90) cc_final: 0.8033 (tpp80) REVERT: C 89 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7864 (mm-30) REVERT: C 99 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7719 (t0) REVERT: C 104 ARG cc_start: 0.8446 (mtt180) cc_final: 0.8065 (mmp80) outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 1.6845 time to fit residues: 66.6465 Evaluate side-chains 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 99 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [21, 18, 26, 12, 23, 25, 1, 10, 19, 4, 2] chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.164538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.147571 restraints weight = 7314.400| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 1.96 r_work: 0.4073 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3981 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2208 Z= 0.088 Angle : 0.479 4.562 3003 Z= 0.256 Chirality : 0.050 0.126 354 Planarity : 0.005 0.058 369 Dihedral : 5.334 22.727 297 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.85 % Allowed : 23.50 % Favored : 75.64 % 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: -1.76 (0.50), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 34 TYR 0.010 0.001 TYR B 114 PHE 0.010 0.001 PHE A 33 TRP 0.001 0.000 TRP C 79 HIS 0.001 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 ( 2208) covalent geometry : angle 0.47939 / 0.26 ( 3003) hydrogen bonds : bond 0.02719 / 1.49 ( 38) hydrogen bonds : angle 4.67588 / 3.14 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.121 Fit side-chains REVERT: A 21 ARG cc_start: 0.7915 (tpt-90) cc_final: 0.7169 (tpm170) REVERT: A 89 GLU cc_start: 0.8535 (mt-10) cc_final: 0.7846 (pp20) REVERT: A 104 ARG cc_start: 0.8359 (mtt180) cc_final: 0.7324 (ptt-90) REVERT: B 21 ARG cc_start: 0.8010 (tpt-90) cc_final: 0.7655 (mtp-110) REVERT: B 89 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8140 (mt-10) REVERT: C 13 MET cc_start: 0.8311 (ttp) cc_final: 0.7633 (mtm) REVERT: C 21 ARG cc_start: 0.8457 (tpt-90) cc_final: 0.6488 (pmt-80) REVERT: C 34 ARG cc_start: 0.8338 (ttt-90) cc_final: 0.8043 (tpp80) REVERT: C 35 LYS cc_start: 0.8199 (tttt) cc_final: 0.6683 (pttm) REVERT: C 89 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7822 (mm-30) REVERT: C 104 ARG cc_start: 0.8416 (mtt180) cc_final: 0.8090 (mmp80) outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 1.7163 time to fit residues: 67.8525 Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [24, 8, 19, 26, 4, 25, 5, 3, 22, 10, 11] chunk 24 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4310 r_free = 0.4310 target = 0.163583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.146869 restraints weight = 7211.131| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 1.91 r_work: 0.4073 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3983 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2208 Z= 0.095 Angle : 0.485 4.509 3003 Z= 0.260 Chirality : 0.050 0.127 354 Planarity : 0.005 0.063 369 Dihedral : 5.333 22.378 297 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.43 % Allowed : 24.36 % 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: -1.79 (0.50), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 34 TYR 0.009 0.001 TYR B 114 PHE 0.011 0.001 PHE A 33 TRP 0.001 0.000 TRP A 79 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.09 ( 2208) covalent geometry : angle 0.48471 / 0.26 ( 3003) hydrogen bonds : bond 0.02720 / 1.46 ( 38) hydrogen bonds : angle 4.67369 / 3.15 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.082 Fit side-chains REVERT: A 21 ARG cc_start: 0.7898 (tpt-90) cc_final: 0.7188 (tpm170) REVERT: A 89 GLU cc_start: 0.8540 (mt-10) cc_final: 0.7855 (pp20) REVERT: A 104 ARG cc_start: 0.8320 (mtt180) cc_final: 0.7335 (ptt-90) REVERT: B 21 ARG cc_start: 0.8003 (tpt-90) cc_final: 0.7649 (mtp-110) REVERT: C 13 MET cc_start: 0.8328 (ttp) cc_final: 0.7658 (mtm) REVERT: C 21 ARG cc_start: 0.8454 (tpt-90) cc_final: 0.6499 (pmt-80) REVERT: C 34 ARG cc_start: 0.8358 (ttt-90) cc_final: 0.8065 (tpp80) REVERT: C 89 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7820 (mm-30) REVERT: C 104 ARG cc_start: 0.8408 (mtt180) cc_final: 0.8109 (mmp80) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 1.7183 time to fit residues: 66.1464 Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: [6, 26, 16, 9, 3, 18, 23, 7, 11, 1, 22] chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 chunk 23 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 1 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 overall best weight: 1.2342 ------------------------------------------------------------------------------- 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 = 0.4302 r_free = 0.4302 target = 0.163543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.147024 restraints weight = 7320.184| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.89 r_work: 0.4063 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3973 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2208 Z= 0.107 Angle : 0.483 4.499 3003 Z= 0.261 Chirality : 0.050 0.127 354 Planarity : 0.005 0.062 369 Dihedral : 5.356 22.454 297 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.85 % Allowed : 23.50 % Favored : 75.64 % 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: -1.80 (0.50), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 34 TYR 0.009 0.001 TYR B 114 PHE 0.011 0.001 PHE A 33 TRP 0.001 0.000 TRP C 79 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 2208) covalent geometry : angle 0.48318 / 0.26 ( 3003) hydrogen bonds : bond 0.02856 / 1.52 ( 38) hydrogen bonds : angle 4.67515 / 3.15 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2496.55 seconds wall clock time: 42 minutes 57.13 seconds (2577.13 seconds total)