Starting phenix.real_space_refine on Fri Aug 22 18:35:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gd6_51248/08_2025/9gd6_51248.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gd6_51248/08_2025/9gd6_51248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gd6_51248/08_2025/9gd6_51248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gd6_51248/08_2025/9gd6_51248.map" model { file = "/net/cci-nas-00/data/ceres_data/9gd6_51248/08_2025/9gd6_51248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gd6_51248/08_2025/9gd6_51248.cif" } resolution = 2.8 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= 0.003 sd= 0.043 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 P 6 5.49 5 S 42 5.16 5 C 4536 2.51 5 N 1224 2.21 5 O 1308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7116 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1186 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain: "B" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1186 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain: "C" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1186 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain: "D" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1186 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain: "E" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1186 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain: "F" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1186 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Time building chain proxies: 2.00, per 1000 atoms: 0.28 Number of scatterers: 7116 At special positions: 0 Unit cell: (90.47, 85.49, 70.55, 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 42 16.00 P 6 15.00 O 1308 8.00 N 1224 7.00 C 4536 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: 0.58 Conformation dependent library (CDL) restraints added in 397.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1608 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 6 sheets defined 55.0% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 20 through 32 removed outlier: 3.507A pdb=" N ILE A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 53 through 56 Processing helix chain 'A' and resid 60 through 69 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.794A pdb=" N GLU A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.802A pdb=" N LEU A 139 " --> pdb=" O PRO A 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 20 through 32 removed outlier: 3.568A pdb=" N ILE B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 53 through 56 Processing helix chain 'B' and resid 60 through 69 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 122 through 134 removed outlier: 3.679A pdb=" N GLU B 127 " --> pdb=" O VAL B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.877A pdb=" N LEU B 139 " --> pdb=" O PRO B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'C' and resid 20 through 32 removed outlier: 3.518A pdb=" N ILE C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 52 Processing helix chain 'C' and resid 53 through 56 Processing helix chain 'C' and resid 60 through 69 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.664A pdb=" N GLU C 127 " --> pdb=" O VAL C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.847A pdb=" N LEU C 139 " --> pdb=" O PRO C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'D' and resid 12 through 18 Processing helix chain 'D' and resid 20 through 32 removed outlier: 3.514A pdb=" N ILE D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 52 Processing helix chain 'D' and resid 53 through 56 Processing helix chain 'D' and resid 60 through 69 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 122 through 134 removed outlier: 3.779A pdb=" N GLU D 127 " --> pdb=" O VAL D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 139 removed outlier: 3.831A pdb=" N LEU D 139 " --> pdb=" O PRO D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'E' and resid 12 through 17 Processing helix chain 'E' and resid 20 through 32 removed outlier: 3.548A pdb=" N ILE E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 52 Processing helix chain 'E' and resid 53 through 56 Processing helix chain 'E' and resid 60 through 69 Processing helix chain 'E' and resid 82 through 92 Processing helix chain 'E' and resid 104 through 109 Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.678A pdb=" N GLU E 127 " --> pdb=" O VAL E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 139 removed outlier: 3.863A pdb=" N LEU E 139 " --> pdb=" O PRO E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 151 Processing helix chain 'F' and resid 12 through 18 Processing helix chain 'F' and resid 20 through 32 Processing helix chain 'F' and resid 44 through 52 Processing helix chain 'F' and resid 53 through 56 Processing helix chain 'F' and resid 60 through 69 Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'F' and resid 104 through 109 Processing helix chain 'F' and resid 122 through 134 removed outlier: 3.637A pdb=" N GLU F 127 " --> pdb=" O VAL F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 139 removed outlier: 3.857A pdb=" N LEU F 139 " --> pdb=" O PRO F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 151 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 42 removed outlier: 6.433A pdb=" N VAL A 77 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 38 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ALA A 75 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE A 40 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 73 " --> pdb=" O PHE A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 34 through 41 removed outlier: 6.351A pdb=" N VAL B 77 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU B 38 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA B 75 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE B 40 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 73 " --> pdb=" O PHE B 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 41 removed outlier: 6.340A pdb=" N VAL C 77 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU C 38 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA C 75 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE C 40 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 73 " --> pdb=" O PHE C 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 34 through 41 removed outlier: 6.372A pdb=" N VAL D 77 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU D 38 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA D 75 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE D 40 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL D 73 " --> pdb=" O PHE D 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 34 through 41 removed outlier: 6.329A pdb=" N VAL E 77 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU E 38 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ALA E 75 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N PHE E 40 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL E 73 " --> pdb=" O PHE E 40 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU E 5 " --> pdb=" O GLY E 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 34 through 41 removed outlier: 6.328A pdb=" N VAL F 77 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU F 38 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA F 75 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE F 40 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL F 73 " --> pdb=" O PHE F 40 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 894 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: 1.08 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2334 1.35 - 1.46: 1651 1.46 - 1.58: 3203 1.58 - 1.70: 24 1.70 - 1.81: 66 Bond restraints: 7278 Sorted by residual: bond pdb=" CA ARG F 114 " pdb=" CB ARG F 114 " ideal model delta sigma weight residual 1.532 1.566 -0.035 1.58e-02 4.01e+03 4.79e+00 bond pdb=" CA ARG D 114 " pdb=" CB ARG D 114 " ideal model delta sigma weight residual 1.532 1.558 -0.026 1.58e-02 4.01e+03 2.78e+00 bond pdb=" CB ARG F 114 " pdb=" CG ARG F 114 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" CB ARG D 114 " pdb=" CG ARG D 114 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CA ARG F 114 " pdb=" C ARG F 114 " ideal model delta sigma weight residual 1.520 1.533 -0.013 1.17e-02 7.31e+03 1.18e+00 ... (remaining 7273 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 9685 2.24 - 4.48: 115 4.48 - 6.72: 13 6.72 - 8.96: 4 8.96 - 11.20: 5 Bond angle restraints: 9822 Sorted by residual: angle pdb=" CA ARG F 114 " pdb=" CB ARG F 114 " pdb=" CG ARG F 114 " ideal model delta sigma weight residual 114.10 123.25 -9.15 2.00e+00 2.50e-01 2.09e+01 angle pdb=" CA ARG D 114 " pdb=" CB ARG D 114 " pdb=" CG ARG D 114 " ideal model delta sigma weight residual 114.10 121.58 -7.48 2.00e+00 2.50e-01 1.40e+01 angle pdb=" C ARG F 114 " pdb=" CA ARG F 114 " pdb=" CB ARG F 114 " ideal model delta sigma weight residual 110.14 115.45 -5.31 1.60e+00 3.91e-01 1.10e+01 angle pdb=" C ASN C 115 " pdb=" N ILE C 116 " pdb=" CA ILE C 116 " ideal model delta sigma weight residual 121.97 127.81 -5.84 1.80e+00 3.09e-01 1.05e+01 angle pdb=" CA LEU A 132 " pdb=" CB LEU A 132 " pdb=" CG LEU A 132 " ideal model delta sigma weight residual 116.30 127.50 -11.20 3.50e+00 8.16e-02 1.02e+01 ... (remaining 9817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 3644 17.05 - 34.10: 457 34.10 - 51.15: 141 51.15 - 68.20: 49 68.20 - 85.25: 17 Dihedral angle restraints: 4308 sinusoidal: 1788 harmonic: 2520 Sorted by residual: dihedral pdb=" CA MET A 41 " pdb=" C MET A 41 " pdb=" N GLN A 42 " pdb=" CA GLN A 42 " ideal model delta harmonic sigma weight residual 180.00 161.67 18.33 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA MET E 41 " pdb=" C MET E 41 " pdb=" N GLN E 42 " pdb=" CA GLN E 42 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA MET D 41 " pdb=" C MET D 41 " pdb=" N GLN D 42 " pdb=" CA GLN D 42 " ideal model delta harmonic sigma weight residual 180.00 163.02 16.98 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 4305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 503 0.024 - 0.049: 311 0.049 - 0.073: 143 0.073 - 0.097: 50 0.097 - 0.122: 31 Chirality restraints: 1038 Sorted by residual: chirality pdb=" CA VAL C 74 " pdb=" N VAL C 74 " pdb=" C VAL C 74 " pdb=" CB VAL C 74 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA VAL A 74 " pdb=" N VAL A 74 " pdb=" C VAL A 74 " pdb=" CB VAL A 74 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.57e-01 chirality pdb=" CA VAL B 74 " pdb=" N VAL B 74 " pdb=" C VAL B 74 " pdb=" CB VAL B 74 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.53e-01 ... (remaining 1035 not shown) Planarity restraints: 1266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 114 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.64e+00 pdb=" C ARG F 114 " 0.041 2.00e-02 2.50e+03 pdb=" O ARG F 114 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN F 115 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 114 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.94e+00 pdb=" C ARG D 114 " 0.034 2.00e-02 2.50e+03 pdb=" O ARG D 114 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN D 115 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 115 " 0.005 2.00e-02 2.50e+03 1.06e-02 1.12e+00 pdb=" C ASN C 115 " -0.018 2.00e-02 2.50e+03 pdb=" O ASN C 115 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE C 116 " 0.006 2.00e-02 2.50e+03 ... (remaining 1263 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1611 2.79 - 3.32: 6201 3.32 - 3.84: 11760 3.84 - 4.37: 14208 4.37 - 4.90: 25097 Nonbonded interactions: 58877 Sorted by model distance: nonbonded pdb=" O ASN F 115 " pdb=" N ILE F 117 " model vdw 2.260 3.120 nonbonded pdb=" O CYS A 109 " pdb=" NZ LYS C 31 " model vdw 2.271 3.120 nonbonded pdb=" O ASN D 115 " pdb=" N ILE D 117 " model vdw 2.295 3.120 nonbonded pdb=" O ASN C 115 " pdb=" N ILE C 117 " model vdw 2.304 3.120 nonbonded pdb=" NZ LYS E 12 " pdb=" OD1 ASN E 115 " model vdw 2.309 3.120 ... (remaining 58872 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' selection = chain 'D' selection = chain 'E' 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: 0.590 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.690 Find NCS groups from input model: 0.120 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:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7278 Z= 0.138 Angle : 0.658 11.196 9822 Z= 0.348 Chirality : 0.041 0.122 1038 Planarity : 0.003 0.025 1266 Dihedral : 17.886 85.248 2700 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.69 % Allowed : 1.16 % Favored : 98.15 % Rotamer: Outliers : 2.12 % Allowed : 22.75 % Favored : 75.13 % 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 aren not related in a simple way. whole: -0.73 (0.27), residues: 864 helix: -0.18 (0.24), residues: 456 sheet: -0.05 (0.45), residues: 132 loop : -0.97 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 114 TYR 0.008 0.001 TYR E 67 PHE 0.009 0.001 PHE E 40 TRP 0.008 0.001 TRP C 149 HIS 0.001 0.000 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7278) covalent geometry : angle 0.65823 ( 9822) hydrogen bonds : bond 0.15190 ( 320) hydrogen bonds : angle 5.54050 ( 894) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.280 Fit side-chains REVERT: A 83 VAL cc_start: 0.8474 (p) cc_final: 0.8266 (t) REVERT: A 123 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8206 (t) REVERT: B 16 VAL cc_start: 0.8376 (t) cc_final: 0.8167 (p) REVERT: C 79 GLU cc_start: 0.7483 (tt0) cc_final: 0.7280 (tt0) REVERT: C 91 LEU cc_start: 0.8828 (mp) cc_final: 0.8610 (mp) REVERT: C 123 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8211 (t) REVERT: E 68 MET cc_start: 0.7507 (ttt) cc_final: 0.7198 (ttp) REVERT: F 123 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.7693 (t) REVERT: F 127 GLU cc_start: 0.6754 (mm-30) cc_final: 0.6411 (mm-30) outliers start: 16 outliers final: 5 residues processed: 99 average time/residue: 0.6412 time to fit residues: 66.7534 Evaluate side-chains 93 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 123 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN B 51 HIS ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS F 51 HIS ** F 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.190248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.148707 restraints weight = 8931.247| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.82 r_work: 0.3551 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 7278 Z= 0.248 Angle : 0.645 9.747 9822 Z= 0.329 Chirality : 0.046 0.151 1038 Planarity : 0.004 0.036 1266 Dihedral : 5.834 56.514 991 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.69 % Allowed : 1.62 % Favored : 97.69 % Rotamer: Outliers : 6.08 % Allowed : 18.52 % Favored : 75.40 % 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 aren not related in a simple way. whole: -0.17 (0.28), residues: 864 helix: 0.25 (0.25), residues: 444 sheet: 0.34 (0.47), residues: 132 loop : -0.69 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 34 TYR 0.007 0.001 TYR A 142 PHE 0.027 0.002 PHE A 40 TRP 0.011 0.001 TRP F 133 HIS 0.004 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 7278) covalent geometry : angle 0.64477 ( 9822) hydrogen bonds : bond 0.05027 ( 320) hydrogen bonds : angle 4.62089 ( 894) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 95 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 83 VAL cc_start: 0.8716 (p) cc_final: 0.8477 (t) REVERT: B 16 VAL cc_start: 0.8376 (t) cc_final: 0.8078 (p) REVERT: B 73 VAL cc_start: 0.8631 (m) cc_final: 0.8419 (p) REVERT: C 79 GLU cc_start: 0.7839 (tt0) cc_final: 0.7570 (tt0) REVERT: E 16 VAL cc_start: 0.8276 (t) cc_final: 0.8037 (p) REVERT: E 120 SER cc_start: 0.8707 (p) cc_final: 0.8345 (m) REVERT: F 115 ASN cc_start: 0.6098 (OUTLIER) cc_final: 0.5870 (m-40) REVERT: F 127 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7003 (mm-30) REVERT: F 129 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7190 (mp0) outliers start: 46 outliers final: 20 residues processed: 123 average time/residue: 0.5190 time to fit residues: 67.8312 Evaluate side-chains 112 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 115 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 46 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 6 optimal weight: 0.0870 chunk 12 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS B 42 GLN D 51 HIS D 115 ASN F 3 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.191636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.149881 restraints weight = 8802.165| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.83 r_work: 0.3572 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7278 Z= 0.115 Angle : 0.552 11.253 9822 Z= 0.272 Chirality : 0.041 0.148 1038 Planarity : 0.003 0.035 1266 Dihedral : 5.113 39.487 989 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.69 % Allowed : 1.27 % Favored : 98.03 % Rotamer: Outliers : 3.97 % Allowed : 20.50 % Favored : 75.53 % 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 aren not related in a simple way. whole: 0.01 (0.28), residues: 864 helix: 0.55 (0.25), residues: 456 sheet: 0.57 (0.48), residues: 132 loop : -1.07 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 34 TYR 0.004 0.001 TYR D 142 PHE 0.017 0.001 PHE A 40 TRP 0.007 0.001 TRP D 133 HIS 0.001 0.000 HIS F 118 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7278) covalent geometry : angle 0.55183 ( 9822) hydrogen bonds : bond 0.03679 ( 320) hydrogen bonds : angle 4.26343 ( 894) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.324 Fit side-chains REVERT: B 41 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7599 (pmm) REVERT: C 79 GLU cc_start: 0.7857 (tt0) cc_final: 0.7603 (tt0) REVERT: D 26 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8040 (ttmp) REVERT: E 68 MET cc_start: 0.7575 (ttt) cc_final: 0.7354 (ttp) REVERT: E 120 SER cc_start: 0.8697 (p) cc_final: 0.8357 (m) outliers start: 30 outliers final: 12 residues processed: 105 average time/residue: 0.5108 time to fit residues: 57.1565 Evaluate side-chains 100 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 68 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 83 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 0.0170 chunk 20 optimal weight: 5.9990 overall best weight: 1.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN B 69 HIS C 51 HIS F 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.190291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.148568 restraints weight = 8890.222| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.86 r_work: 0.3559 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7278 Z= 0.155 Angle : 0.539 9.391 9822 Z= 0.275 Chirality : 0.043 0.187 1038 Planarity : 0.003 0.035 1266 Dihedral : 4.989 46.152 984 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.69 % Allowed : 1.50 % Favored : 97.80 % Rotamer: Outliers : 5.16 % Allowed : 18.78 % Favored : 76.06 % 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 aren not related in a simple way. whole: 0.08 (0.28), residues: 864 helix: 0.69 (0.25), residues: 456 sheet: 0.56 (0.48), residues: 132 loop : -1.17 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 34 TYR 0.006 0.001 TYR D 142 PHE 0.018 0.002 PHE A 40 TRP 0.006 0.001 TRP D 133 HIS 0.002 0.001 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 7278) covalent geometry : angle 0.53892 ( 9822) hydrogen bonds : bond 0.04102 ( 320) hydrogen bonds : angle 4.29726 ( 894) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 74 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.5697 (OUTLIER) cc_final: 0.5309 (mt-10) REVERT: B 41 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7594 (pmm) REVERT: B 73 VAL cc_start: 0.8652 (m) cc_final: 0.8427 (p) REVERT: C 79 GLU cc_start: 0.7842 (tt0) cc_final: 0.7597 (tt0) REVERT: D 115 ASN cc_start: 0.6498 (OUTLIER) cc_final: 0.6233 (m-40) REVERT: E 45 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.5805 (mt-10) REVERT: E 120 SER cc_start: 0.8732 (p) cc_final: 0.8410 (m) outliers start: 39 outliers final: 19 residues processed: 95 average time/residue: 0.4571 time to fit residues: 46.5624 Evaluate side-chains 97 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 68 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 51 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN D 69 HIS ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.190523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.148919 restraints weight = 8852.588| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.84 r_work: 0.3559 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7278 Z= 0.141 Angle : 0.537 10.941 9822 Z= 0.268 Chirality : 0.042 0.151 1038 Planarity : 0.003 0.038 1266 Dihedral : 5.005 48.543 984 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.69 % Allowed : 2.08 % Favored : 97.22 % Rotamer: Outliers : 4.63 % Allowed : 19.58 % Favored : 75.79 % 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 aren not related in a simple way. whole: 0.22 (0.28), residues: 864 helix: 0.88 (0.25), residues: 456 sheet: 0.56 (0.48), residues: 132 loop : -1.22 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 34 TYR 0.006 0.001 TYR D 142 PHE 0.016 0.002 PHE A 40 TRP 0.005 0.001 TRP A 133 HIS 0.002 0.000 HIS F 118 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7278) covalent geometry : angle 0.53687 ( 9822) hydrogen bonds : bond 0.03874 ( 320) hydrogen bonds : angle 4.21922 ( 894) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 77 time to evaluate : 0.271 Fit side-chains REVERT: A 45 GLU cc_start: 0.5815 (OUTLIER) cc_final: 0.5400 (mt-10) REVERT: B 41 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7602 (pmm) REVERT: B 73 VAL cc_start: 0.8600 (m) cc_final: 0.8374 (p) REVERT: B 120 SER cc_start: 0.8709 (p) cc_final: 0.8338 (m) REVERT: C 45 GLU cc_start: 0.5523 (OUTLIER) cc_final: 0.5292 (mt-10) REVERT: C 79 GLU cc_start: 0.7839 (tt0) cc_final: 0.7592 (tt0) REVERT: D 45 GLU cc_start: 0.6064 (OUTLIER) cc_final: 0.5560 (mt-10) REVERT: E 45 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5959 (mt-10) REVERT: E 120 SER cc_start: 0.8727 (p) cc_final: 0.8444 (m) outliers start: 35 outliers final: 18 residues processed: 93 average time/residue: 0.5187 time to fit residues: 51.3074 Evaluate side-chains 104 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 68 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 11 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.0370 chunk 57 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.191599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.150002 restraints weight = 8891.902| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.87 r_work: 0.3572 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7278 Z= 0.096 Angle : 0.504 10.931 9822 Z= 0.249 Chirality : 0.041 0.133 1038 Planarity : 0.003 0.034 1266 Dihedral : 4.851 47.816 984 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.69 % Allowed : 1.16 % Favored : 98.15 % Rotamer: Outliers : 4.37 % Allowed : 19.84 % Favored : 75.79 % 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 aren not related in a simple way. whole: 0.53 (0.28), residues: 864 helix: 1.17 (0.25), residues: 456 sheet: 0.63 (0.48), residues: 132 loop : -1.12 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 114 TYR 0.004 0.000 TYR E 67 PHE 0.013 0.001 PHE B 40 TRP 0.004 0.000 TRP A 133 HIS 0.002 0.000 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 7278) covalent geometry : angle 0.50409 ( 9822) hydrogen bonds : bond 0.03237 ( 320) hydrogen bonds : angle 4.02598 ( 894) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.5715 (OUTLIER) cc_final: 0.5300 (mt-10) REVERT: B 41 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7610 (pmm) REVERT: B 120 SER cc_start: 0.8697 (p) cc_final: 0.8343 (m) REVERT: C 45 GLU cc_start: 0.5499 (OUTLIER) cc_final: 0.5265 (mt-10) REVERT: C 79 GLU cc_start: 0.7845 (tt0) cc_final: 0.7595 (tt0) REVERT: D 45 GLU cc_start: 0.6076 (OUTLIER) cc_final: 0.5562 (mt-10) REVERT: E 45 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.5978 (mt-10) REVERT: E 120 SER cc_start: 0.8699 (p) cc_final: 0.8390 (m) outliers start: 33 outliers final: 22 residues processed: 94 average time/residue: 0.5334 time to fit residues: 53.2841 Evaluate side-chains 102 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 3 ASN Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 116 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 52 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN D 111 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.189558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148280 restraints weight = 8803.810| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.84 r_work: 0.3551 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7278 Z= 0.168 Angle : 0.536 9.961 9822 Z= 0.272 Chirality : 0.043 0.128 1038 Planarity : 0.004 0.036 1266 Dihedral : 5.104 52.811 984 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.69 % Allowed : 2.08 % Favored : 97.22 % Rotamer: Outliers : 4.23 % Allowed : 19.97 % Favored : 75.79 % 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 aren not related in a simple way. whole: 0.45 (0.28), residues: 864 helix: 1.14 (0.25), residues: 456 sheet: 0.61 (0.48), residues: 132 loop : -1.24 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 114 TYR 0.006 0.001 TYR D 142 PHE 0.017 0.002 PHE D 40 TRP 0.005 0.001 TRP A 133 HIS 0.002 0.001 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 7278) covalent geometry : angle 0.53585 ( 9822) hydrogen bonds : bond 0.04080 ( 320) hydrogen bonds : angle 4.20087 ( 894) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.280 Fit side-chains REVERT: B 41 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7599 (pmm) REVERT: B 120 SER cc_start: 0.8713 (p) cc_final: 0.8352 (m) REVERT: C 45 GLU cc_start: 0.5615 (OUTLIER) cc_final: 0.5342 (mt-10) REVERT: C 79 GLU cc_start: 0.7834 (tt0) cc_final: 0.7582 (tt0) REVERT: D 45 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5729 (mt-10) REVERT: D 111 GLN cc_start: 0.8013 (tt0) cc_final: 0.7768 (tt0) REVERT: E 16 VAL cc_start: 0.8268 (t) cc_final: 0.8040 (p) REVERT: E 45 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6104 (mt-10) REVERT: E 120 SER cc_start: 0.8755 (p) cc_final: 0.8447 (m) REVERT: F 41 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7510 (pmm) outliers start: 32 outliers final: 23 residues processed: 90 average time/residue: 0.5229 time to fit residues: 50.1020 Evaluate side-chains 103 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain E residue 3 ASN Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 116 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.189501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.147483 restraints weight = 8811.450| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.88 r_work: 0.3568 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7278 Z= 0.113 Angle : 0.524 11.306 9822 Z= 0.258 Chirality : 0.041 0.120 1038 Planarity : 0.003 0.035 1266 Dihedral : 5.007 57.337 984 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.69 % Allowed : 1.39 % Favored : 97.92 % Rotamer: Outliers : 4.23 % Allowed : 19.84 % Favored : 75.93 % 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 aren not related in a simple way. whole: 0.56 (0.28), residues: 864 helix: 1.23 (0.25), residues: 456 sheet: 0.63 (0.47), residues: 132 loop : -1.17 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 114 TYR 0.006 0.001 TYR E 67 PHE 0.013 0.001 PHE A 40 TRP 0.004 0.000 TRP A 133 HIS 0.002 0.000 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7278) covalent geometry : angle 0.52410 ( 9822) hydrogen bonds : bond 0.03469 ( 320) hydrogen bonds : angle 4.08896 ( 894) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.287 Fit side-chains REVERT: B 41 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7613 (pmm) REVERT: B 45 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.6083 (mt-10) REVERT: B 120 SER cc_start: 0.8683 (p) cc_final: 0.8404 (m) REVERT: C 45 GLU cc_start: 0.5621 (OUTLIER) cc_final: 0.5309 (mt-10) REVERT: C 79 GLU cc_start: 0.7842 (tt0) cc_final: 0.7589 (tt0) REVERT: C 115 ASN cc_start: 0.5740 (OUTLIER) cc_final: 0.5345 (m110) REVERT: D 45 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5725 (mt-10) REVERT: D 111 GLN cc_start: 0.7980 (tt0) cc_final: 0.7725 (tt0) REVERT: E 16 VAL cc_start: 0.8194 (t) cc_final: 0.7975 (p) REVERT: E 45 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.6203 (mt-10) REVERT: E 120 SER cc_start: 0.8728 (p) cc_final: 0.8417 (m) REVERT: F 41 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7436 (pmm) outliers start: 32 outliers final: 20 residues processed: 96 average time/residue: 0.5289 time to fit residues: 54.0601 Evaluate side-chains 106 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 3 ASN Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 116 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 45 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 63 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.192284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.150885 restraints weight = 8759.419| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.81 r_work: 0.3575 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7278 Z= 0.101 Angle : 0.526 11.131 9822 Z= 0.256 Chirality : 0.041 0.143 1038 Planarity : 0.003 0.035 1266 Dihedral : 4.673 48.964 984 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.69 % Allowed : 1.50 % Favored : 97.80 % Rotamer: Outliers : 4.10 % Allowed : 20.50 % Favored : 75.40 % 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 aren not related in a simple way. whole: 0.64 (0.28), residues: 864 helix: 1.30 (0.25), residues: 456 sheet: 0.63 (0.47), residues: 132 loop : -1.12 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 114 TYR 0.011 0.001 TYR E 67 PHE 0.012 0.001 PHE D 40 TRP 0.004 0.000 TRP A 133 HIS 0.002 0.000 HIS E 69 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 7278) covalent geometry : angle 0.52585 ( 9822) hydrogen bonds : bond 0.03255 ( 320) hydrogen bonds : angle 4.03986 ( 894) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 78 time to evaluate : 0.295 Fit side-chains REVERT: B 41 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7623 (pmm) REVERT: B 45 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.6012 (mt-10) REVERT: B 120 SER cc_start: 0.8673 (p) cc_final: 0.8400 (m) REVERT: C 45 GLU cc_start: 0.5641 (OUTLIER) cc_final: 0.5332 (mt-10) REVERT: C 79 GLU cc_start: 0.7831 (tt0) cc_final: 0.7583 (tt0) REVERT: C 115 ASN cc_start: 0.6060 (OUTLIER) cc_final: 0.5787 (m-40) REVERT: D 45 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5725 (mt-10) REVERT: D 111 GLN cc_start: 0.7967 (tt0) cc_final: 0.7737 (tt0) REVERT: E 45 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6411 (mt-10) REVERT: E 120 SER cc_start: 0.8708 (p) cc_final: 0.8397 (m) REVERT: F 41 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7440 (pmm) outliers start: 31 outliers final: 21 residues processed: 93 average time/residue: 0.5525 time to fit residues: 54.5130 Evaluate side-chains 106 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 3 ASN Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 116 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 0.0570 chunk 9 optimal weight: 0.4980 chunk 33 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.192510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.152313 restraints weight = 8686.057| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.70 r_work: 0.3590 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7278 Z= 0.101 Angle : 0.546 10.890 9822 Z= 0.262 Chirality : 0.041 0.139 1038 Planarity : 0.003 0.034 1266 Dihedral : 4.667 49.377 984 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.69 % Allowed : 1.39 % Favored : 97.92 % Rotamer: Outliers : 3.97 % Allowed : 20.63 % Favored : 75.40 % 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 aren not related in a simple way. whole: 0.67 (0.28), residues: 864 helix: 1.34 (0.25), residues: 456 sheet: 0.59 (0.47), residues: 132 loop : -1.10 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 114 TYR 0.004 0.000 TYR E 52 PHE 0.014 0.001 PHE A 40 TRP 0.004 0.000 TRP A 133 HIS 0.002 0.000 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 7278) covalent geometry : angle 0.54647 ( 9822) hydrogen bonds : bond 0.03247 ( 320) hydrogen bonds : angle 4.05587 ( 894) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1728 Ramachandran restraints generated. 864 Oldfield, 0 Emsley, 864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.284 Fit side-chains REVERT: B 41 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7643 (pmm) REVERT: B 45 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.6017 (mt-10) REVERT: B 120 SER cc_start: 0.8656 (p) cc_final: 0.8392 (m) REVERT: C 79 GLU cc_start: 0.7817 (tt0) cc_final: 0.7569 (tt0) REVERT: D 45 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.5709 (mt-10) REVERT: D 111 GLN cc_start: 0.7923 (tt0) cc_final: 0.7686 (tt0) REVERT: E 45 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6360 (mt-10) REVERT: E 120 SER cc_start: 0.8711 (p) cc_final: 0.8399 (m) REVERT: F 41 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7446 (pmm) outliers start: 30 outliers final: 21 residues processed: 91 average time/residue: 0.5353 time to fit residues: 51.8747 Evaluate side-chains 102 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LYS Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 3 ASN Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 116 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 22 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.191684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.150641 restraints weight = 8766.674| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.76 r_work: 0.3568 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7278 Z= 0.125 Angle : 0.566 10.795 9822 Z= 0.274 Chirality : 0.042 0.140 1038 Planarity : 0.003 0.035 1266 Dihedral : 4.661 48.544 982 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.69 % Allowed : 1.62 % Favored : 97.69 % Rotamer: Outliers : 3.70 % Allowed : 21.16 % Favored : 75.13 % 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 aren not related in a simple way. whole: 0.62 (0.28), residues: 864 helix: 1.28 (0.25), residues: 456 sheet: 0.61 (0.47), residues: 132 loop : -1.12 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 114 TYR 0.005 0.001 TYR E 67 PHE 0.017 0.001 PHE E 40 TRP 0.004 0.001 TRP B 78 HIS 0.002 0.000 HIS E 69 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7278) covalent geometry : angle 0.56588 ( 9822) hydrogen bonds : bond 0.03628 ( 320) hydrogen bonds : angle 4.16041 ( 894) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2236.29 seconds wall clock time: 39 minutes 7.26 seconds (2347.26 seconds total)