Starting phenix.real_space_refine on Fri Jul 25 01:18:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gd6_51248/07_2025/9gd6_51248.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gd6_51248/07_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_51248/07_2025/9gd6_51248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gd6_51248/07_2025/9gd6_51248.map" model { file = "/net/cci-nas-00/data/ceres_data/9gd6_51248/07_2025/9gd6_51248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gd6_51248/07_2025/9gd6_51248.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.60, per 1000 atoms: 0.65 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: 1.78 Conformation dependent library (CDL) restraints added in 975.3 milliseconds 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: 0.89 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: 1.88 Time building geometry restraints manager: 2.10 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: 0.01 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: 0.690 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.590 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.410 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP C 149 HIS 0.001 0.000 HIS D 118 PHE 0.009 0.001 PHE E 40 TYR 0.008 0.001 TYR E 67 ARG 0.002 0.000 ARG F 114 Details of bonding type rmsd hydrogen bonds : bond 0.15190 ( 320) hydrogen bonds : angle 5.54050 ( 894) covalent geometry : bond 0.00286 ( 7278) covalent geometry : angle 0.65823 ( 9822) *********************** 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 : 0.622 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: 1.7499 time to fit residues: 181.3219 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 : 0.747 ------------------------------------------------------------------------------- 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 70 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.190557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.149105 restraints weight = 8799.718| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.79 r_work: 0.3557 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7278 Z= 0.228 Angle : 0.633 9.835 9822 Z= 0.321 Chirality : 0.046 0.157 1038 Planarity : 0.004 0.036 1266 Dihedral : 5.887 59.973 991 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.69 % Allowed : 1.62 % Favored : 97.69 % Rotamer: Outliers : 5.95 % Allowed : 18.78 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.28), residues: 864 helix: 0.20 (0.24), residues: 456 sheet: 0.29 (0.47), residues: 132 loop : -1.04 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 133 HIS 0.003 0.001 HIS A 118 PHE 0.025 0.002 PHE A 40 TYR 0.006 0.001 TYR A 142 ARG 0.003 0.000 ARG E 34 Details of bonding type rmsd hydrogen bonds : bond 0.04893 ( 320) hydrogen bonds : angle 4.56703 ( 894) covalent geometry : bond 0.00526 ( 7278) covalent geometry : angle 0.63294 ( 9822) *********************** 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 140 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 0.746 Fit side-chains REVERT: A 83 VAL cc_start: 0.8722 (p) cc_final: 0.8479 (t) REVERT: A 111 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: B 16 VAL cc_start: 0.8364 (t) cc_final: 0.8072 (p) REVERT: C 79 GLU cc_start: 0.7861 (tt0) cc_final: 0.7611 (tt0) REVERT: E 16 VAL cc_start: 0.8268 (t) cc_final: 0.8030 (p) REVERT: E 120 SER cc_start: 0.8712 (p) cc_final: 0.8353 (m) REVERT: F 115 ASN cc_start: 0.5949 (OUTLIER) cc_final: 0.5409 (m110) REVERT: F 127 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6976 (mm-30) REVERT: F 129 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7204 (mp0) outliers start: 45 outliers final: 21 residues processed: 124 average time/residue: 1.2335 time to fit residues: 162.2159 Evaluate side-chains 117 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.760 ------------------------------------------------------------------------------- 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 111 GLN Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 123 VAL 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 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 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 123 VAL Chi-restraints excluded: chain E residue 36 VAL 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 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 20 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 HIS A 111 GLN B 42 GLN D 51 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.192085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.150479 restraints weight = 8897.480| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.85 r_work: 0.3583 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7278 Z= 0.109 Angle : 0.542 9.385 9822 Z= 0.268 Chirality : 0.041 0.142 1038 Planarity : 0.003 0.034 1266 Dihedral : 5.043 36.917 989 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.69 % Allowed : 1.27 % Favored : 98.03 % Rotamer: Outliers : 3.31 % Allowed : 20.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.28), residues: 864 helix: 0.59 (0.25), residues: 456 sheet: 0.56 (0.48), residues: 132 loop : -1.01 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 133 HIS 0.002 0.000 HIS F 118 PHE 0.014 0.001 PHE A 40 TYR 0.004 0.001 TYR D 142 ARG 0.006 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 320) hydrogen bonds : angle 4.22044 ( 894) covalent geometry : bond 0.00236 ( 7278) covalent geometry : angle 0.54160 ( 9822) *********************** 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 112 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.833 Fit side-chains REVERT: A 83 VAL cc_start: 0.8605 (p) cc_final: 0.8401 (t) REVERT: B 41 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7618 (pmm) REVERT: C 79 GLU cc_start: 0.7872 (tt0) cc_final: 0.7615 (tt0) REVERT: E 120 SER cc_start: 0.8669 (p) cc_final: 0.8317 (m) outliers start: 25 outliers final: 12 residues processed: 102 average time/residue: 0.9968 time to fit residues: 109.8491 Evaluate side-chains 98 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET 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 3 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 51 optimal weight: 5.9990 chunk 66 optimal weight: 0.0000 chunk 80 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS C 51 HIS D 69 HIS F 3 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.190585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.149080 restraints weight = 8932.151| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.86 r_work: 0.3554 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2450 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= 0.162 Angle : 0.537 9.287 9822 Z= 0.276 Chirality : 0.043 0.180 1038 Planarity : 0.003 0.035 1266 Dihedral : 4.941 45.076 984 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.69 % Allowed : 1.50 % Favored : 97.80 % Rotamer: Outliers : 4.76 % Allowed : 20.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.28), residues: 864 helix: 0.68 (0.25), residues: 456 sheet: 0.50 (0.48), residues: 132 loop : -1.18 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 133 HIS 0.002 0.001 HIS A 118 PHE 0.017 0.002 PHE A 40 TYR 0.007 0.001 TYR D 142 ARG 0.004 0.000 ARG F 34 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 320) hydrogen bonds : angle 4.31577 ( 894) covalent geometry : bond 0.00371 ( 7278) covalent geometry : angle 0.53741 ( 9822) *********************** 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 106 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 70 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8832 (mtm110) cc_final: 0.8558 (mtp180) REVERT: A 45 GLU cc_start: 0.5598 (OUTLIER) cc_final: 0.5230 (mt-10) REVERT: B 41 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7635 (pmm) REVERT: C 45 GLU cc_start: 0.5542 (OUTLIER) cc_final: 0.5330 (mt-10) REVERT: C 79 GLU cc_start: 0.7872 (tt0) cc_final: 0.7620 (tt0) REVERT: D 45 GLU cc_start: 0.5909 (OUTLIER) cc_final: 0.5439 (mt-10) REVERT: D 115 ASN cc_start: 0.6494 (OUTLIER) cc_final: 0.6228 (m-40) REVERT: E 45 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5769 (mt-10) REVERT: E 120 SER cc_start: 0.8699 (p) cc_final: 0.8402 (m) REVERT: F 41 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7536 (pmm) outliers start: 36 outliers final: 18 residues processed: 91 average time/residue: 1.0235 time to fit residues: 99.4407 Evaluate side-chains 97 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 D residue 115 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 3 ASN Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 112 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.191358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.149645 restraints weight = 8823.995| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.87 r_work: 0.3565 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7278 Z= 0.114 Angle : 0.525 10.651 9822 Z= 0.260 Chirality : 0.041 0.149 1038 Planarity : 0.003 0.035 1266 Dihedral : 4.827 44.788 984 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.69 % Allowed : 1.50 % Favored : 97.80 % Rotamer: Outliers : 4.23 % Allowed : 20.11 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.28), residues: 864 helix: 0.89 (0.25), residues: 456 sheet: 0.49 (0.48), residues: 132 loop : -1.19 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 133 HIS 0.002 0.000 HIS F 118 PHE 0.014 0.001 PHE B 40 TYR 0.005 0.001 TYR D 142 ARG 0.003 0.000 ARG F 34 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 320) hydrogen bonds : angle 4.17624 ( 894) covalent geometry : bond 0.00253 ( 7278) covalent geometry : angle 0.52500 ( 9822) *********************** 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 115 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8825 (mtm110) cc_final: 0.8541 (mtp180) REVERT: A 45 GLU cc_start: 0.5615 (OUTLIER) cc_final: 0.5242 (mt-10) REVERT: B 41 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7647 (pmm) REVERT: B 120 SER cc_start: 0.8697 (p) cc_final: 0.8339 (m) REVERT: C 45 GLU cc_start: 0.5486 (OUTLIER) cc_final: 0.5258 (mt-10) REVERT: C 79 GLU cc_start: 0.7875 (tt0) cc_final: 0.7625 (tt0) REVERT: D 45 GLU cc_start: 0.5958 (OUTLIER) cc_final: 0.5473 (mt-10) REVERT: E 16 VAL cc_start: 0.8173 (t) cc_final: 0.7947 (p) REVERT: E 45 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5857 (mt-10) REVERT: E 120 SER cc_start: 0.8703 (p) cc_final: 0.8391 (m) REVERT: F 41 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7511 (pmm) outliers start: 32 outliers final: 20 residues processed: 99 average time/residue: 1.0667 time to fit residues: 112.5860 Evaluate side-chains 107 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 45 GLU Chi-restraints excluded: chain C residue 68 MET 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 115 ASN Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 41 MET Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 112 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 79 optimal weight: 0.0270 chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.191769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.150175 restraints weight = 8770.239| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.86 r_work: 0.3573 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7278 Z= 0.099 Angle : 0.497 8.989 9822 Z= 0.250 Chirality : 0.041 0.130 1038 Planarity : 0.003 0.034 1266 Dihedral : 4.669 43.879 984 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.69 % Allowed : 1.62 % Favored : 97.69 % Rotamer: Outliers : 4.37 % Allowed : 19.44 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.28), residues: 864 helix: 1.13 (0.25), residues: 456 sheet: 0.44 (0.48), residues: 132 loop : -1.13 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 133 HIS 0.001 0.000 HIS D 118 PHE 0.012 0.001 PHE B 40 TYR 0.004 0.000 TYR E 67 ARG 0.003 0.000 ARG F 34 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 320) hydrogen bonds : angle 4.05983 ( 894) covalent geometry : bond 0.00216 ( 7278) covalent geometry : angle 0.49739 ( 9822) *********************** 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 110 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8802 (mtm110) cc_final: 0.8494 (mtp180) REVERT: A 45 GLU cc_start: 0.5580 (OUTLIER) cc_final: 0.5192 (mt-10) REVERT: B 41 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7641 (pmm) REVERT: B 120 SER cc_start: 0.8702 (p) cc_final: 0.8341 (m) REVERT: C 45 GLU cc_start: 0.5447 (OUTLIER) cc_final: 0.5227 (mt-10) REVERT: C 79 GLU cc_start: 0.7898 (tt0) cc_final: 0.7649 (tt0) REVERT: D 45 GLU cc_start: 0.5963 (OUTLIER) cc_final: 0.5460 (mt-10) REVERT: D 111 GLN cc_start: 0.7985 (tt0) cc_final: 0.7752 (tt0) REVERT: E 45 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.5947 (mt-10) REVERT: E 120 SER cc_start: 0.8705 (p) cc_final: 0.8392 (m) REVERT: F 41 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7439 (pmm) outliers start: 33 outliers final: 21 residues processed: 95 average time/residue: 1.2939 time to fit residues: 129.9285 Evaluate side-chains 105 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 3 ASN Chi-restraints excluded: chain C residue 41 MET Chi-restraints excluded: chain C residue 45 GLU 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 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 112 VAL 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 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.0050 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.189658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.148405 restraints weight = 8753.446| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.84 r_work: 0.3551 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7278 Z= 0.182 Angle : 0.547 11.233 9822 Z= 0.279 Chirality : 0.043 0.146 1038 Planarity : 0.004 0.040 1266 Dihedral : 5.163 51.749 984 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.69 % Allowed : 2.08 % Favored : 97.22 % Rotamer: Outliers : 4.89 % Allowed : 19.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.28), residues: 864 helix: 1.06 (0.25), residues: 456 sheet: 0.39 (0.47), residues: 132 loop : -1.25 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 78 HIS 0.003 0.001 HIS E 69 PHE 0.017 0.002 PHE A 40 TYR 0.007 0.001 TYR D 142 ARG 0.003 0.000 ARG F 34 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 320) hydrogen bonds : angle 4.30871 ( 894) covalent geometry : bond 0.00422 ( 7278) covalent geometry : angle 0.54659 ( 9822) *********************** 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 109 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8808 (mtm110) cc_final: 0.8500 (mtp180) REVERT: A 45 GLU cc_start: 0.5908 (OUTLIER) cc_final: 0.5476 (mt-10) REVERT: B 41 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7623 (pmm) REVERT: B 45 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6171 (mt-10) REVERT: B 120 SER cc_start: 0.8728 (p) cc_final: 0.8359 (m) REVERT: C 45 GLU cc_start: 0.5591 (OUTLIER) cc_final: 0.5313 (mt-10) REVERT: C 79 GLU cc_start: 0.7900 (tt0) cc_final: 0.7645 (tt0) REVERT: D 111 GLN cc_start: 0.7979 (tt0) cc_final: 0.7727 (tt0) REVERT: E 16 VAL cc_start: 0.8286 (t) cc_final: 0.8051 (p) REVERT: E 45 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6325 (mt-10) REVERT: E 120 SER cc_start: 0.8770 (p) cc_final: 0.8456 (m) REVERT: F 41 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7453 (pmm) outliers start: 37 outliers final: 23 residues processed: 92 average time/residue: 1.0110 time to fit residues: 99.4273 Evaluate side-chains 101 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 116 ILE 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 68 MET Chi-restraints excluded: chain D residue 112 VAL 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 112 VAL 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 38 optimal weight: 0.8980 chunk 57 optimal weight: 0.2980 chunk 68 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.191850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.149457 restraints weight = 8671.640| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.84 r_work: 0.3581 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7278 Z= 0.092 Angle : 0.527 11.824 9822 Z= 0.253 Chirality : 0.040 0.121 1038 Planarity : 0.003 0.034 1266 Dihedral : 4.947 59.727 984 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.69 % Allowed : 1.16 % Favored : 98.15 % Rotamer: Outliers : 3.70 % Allowed : 20.63 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.28), residues: 864 helix: 1.27 (0.25), residues: 456 sheet: 0.35 (0.47), residues: 132 loop : -1.10 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 133 HIS 0.001 0.000 HIS D 118 PHE 0.012 0.001 PHE B 40 TYR 0.004 0.000 TYR E 67 ARG 0.002 0.000 ARG F 34 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 320) hydrogen bonds : angle 4.05211 ( 894) covalent geometry : bond 0.00196 ( 7278) covalent geometry : angle 0.52706 ( 9822) *********************** 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 107 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8822 (mtm110) cc_final: 0.8510 (mtp180) REVERT: A 45 GLU cc_start: 0.5780 (OUTLIER) cc_final: 0.5354 (mt-10) REVERT: B 41 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7623 (pmm) REVERT: B 45 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.6078 (mt-10) REVERT: B 120 SER cc_start: 0.8672 (p) cc_final: 0.8338 (m) REVERT: C 45 GLU cc_start: 0.5525 (OUTLIER) cc_final: 0.5256 (mt-10) REVERT: C 79 GLU cc_start: 0.7854 (tt0) cc_final: 0.7589 (tt0) REVERT: C 115 ASN cc_start: 0.5705 (OUTLIER) cc_final: 0.5225 (m110) REVERT: D 111 GLN cc_start: 0.7978 (tt0) cc_final: 0.7736 (tt0) REVERT: E 45 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6248 (mt-10) REVERT: E 120 SER cc_start: 0.8719 (p) cc_final: 0.8417 (m) REVERT: F 41 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7436 (pmm) outliers start: 28 outliers final: 16 residues processed: 95 average time/residue: 1.0891 time to fit residues: 110.1237 Evaluate side-chains 100 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 45 GLU 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 115 ASN Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 68 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 3 ASN 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 13 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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** F 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.189282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146581 restraints weight = 8712.860| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.87 r_work: 0.3552 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7278 Z= 0.172 Angle : 0.571 11.297 9822 Z= 0.282 Chirality : 0.043 0.139 1038 Planarity : 0.003 0.036 1266 Dihedral : 4.950 43.011 984 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.69 % Allowed : 2.20 % Favored : 97.11 % Rotamer: Outliers : 4.23 % Allowed : 20.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.28), residues: 864 helix: 1.20 (0.25), residues: 456 sheet: 0.44 (0.46), residues: 132 loop : -1.21 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 78 HIS 0.003 0.001 HIS E 69 PHE 0.016 0.002 PHE A 40 TYR 0.007 0.001 TYR D 142 ARG 0.002 0.000 ARG F 34 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 320) hydrogen bonds : angle 4.23409 ( 894) covalent geometry : bond 0.00397 ( 7278) covalent geometry : angle 0.57106 ( 9822) *********************** 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 107 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.984 Fit side-chains REVERT: A 18 ARG cc_start: 0.8806 (mtm110) cc_final: 0.8477 (mtp180) REVERT: B 41 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7619 (pmm) REVERT: B 45 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6169 (mt-10) REVERT: B 120 SER cc_start: 0.8710 (p) cc_final: 0.8362 (m) REVERT: C 45 GLU cc_start: 0.5647 (OUTLIER) cc_final: 0.5354 (mt-10) REVERT: C 79 GLU cc_start: 0.7863 (tt0) cc_final: 0.7600 (tt0) REVERT: C 115 ASN cc_start: 0.5984 (OUTLIER) cc_final: 0.5505 (m-40) REVERT: D 111 GLN cc_start: 0.7978 (tt0) cc_final: 0.7732 (tt0) REVERT: E 16 VAL cc_start: 0.8295 (t) cc_final: 0.8081 (p) REVERT: E 45 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6380 (mt-10) REVERT: E 120 SER cc_start: 0.8755 (p) cc_final: 0.8455 (m) REVERT: F 41 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7462 (pmm) REVERT: F 120 SER cc_start: 0.8673 (p) cc_final: 0.8455 (m) outliers start: 32 outliers final: 20 residues processed: 90 average time/residue: 1.2430 time to fit residues: 118.8460 Evaluate side-chains 101 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 45 GLU 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 68 MET Chi-restraints excluded: chain D residue 112 VAL 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 E residue 123 VAL 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 112 VAL 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 51 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 41 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.190916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.148253 restraints weight = 8889.924| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.90 r_work: 0.3568 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7278 Z= 0.111 Angle : 0.550 11.654 9822 Z= 0.264 Chirality : 0.041 0.130 1038 Planarity : 0.003 0.034 1266 Dihedral : 4.769 47.911 984 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.69 % Allowed : 1.50 % Favored : 97.80 % Rotamer: Outliers : 3.70 % Allowed : 21.43 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.28), residues: 864 helix: 1.30 (0.25), residues: 456 sheet: 0.44 (0.46), residues: 132 loop : -1.12 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 133 HIS 0.002 0.000 HIS E 69 PHE 0.012 0.001 PHE A 40 TYR 0.004 0.001 TYR D 142 ARG 0.002 0.000 ARG F 34 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 320) hydrogen bonds : angle 4.13370 ( 894) covalent geometry : bond 0.00246 ( 7278) covalent geometry : angle 0.55043 ( 9822) ********************** 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 103 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8821 (mtm110) cc_final: 0.8499 (mtp180) REVERT: B 41 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7634 (pmm) REVERT: B 45 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6157 (mt-10) REVERT: B 120 SER cc_start: 0.8664 (p) cc_final: 0.8403 (m) REVERT: C 45 GLU cc_start: 0.5640 (OUTLIER) cc_final: 0.5310 (mt-10) REVERT: C 79 GLU cc_start: 0.7886 (tt0) cc_final: 0.7619 (tt0) REVERT: D 111 GLN cc_start: 0.7955 (tt0) cc_final: 0.7706 (tt0) REVERT: E 16 VAL cc_start: 0.8237 (t) cc_final: 0.8014 (p) REVERT: E 45 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6331 (mt-10) REVERT: E 120 SER cc_start: 0.8724 (p) cc_final: 0.8427 (m) REVERT: F 41 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7424 (pmm) REVERT: F 45 GLU cc_start: 0.6246 (OUTLIER) cc_final: 0.5943 (mt-10) outliers start: 28 outliers final: 21 residues processed: 88 average time/residue: 1.1984 time to fit residues: 111.7360 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 : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 114 ARG Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 45 GLU 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 116 ILE Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 68 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 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 45 GLU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 112 VAL 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 40 optimal weight: 2.9990 chunk 23 optimal weight: 0.0270 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 overall best weight: 0.7638 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.190875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.148425 restraints weight = 8668.368| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.86 r_work: 0.3572 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3129 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= 0.109 Angle : 0.556 11.653 9822 Z= 0.265 Chirality : 0.041 0.134 1038 Planarity : 0.003 0.035 1266 Dihedral : 4.702 48.977 982 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.69 % Allowed : 1.85 % Favored : 97.45 % Rotamer: Outliers : 3.97 % Allowed : 20.77 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.28), residues: 864 helix: 1.32 (0.25), residues: 456 sheet: 0.42 (0.46), residues: 132 loop : -1.09 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 133 HIS 0.002 0.000 HIS E 69 PHE 0.012 0.001 PHE B 40 TYR 0.004 0.001 TYR D 142 ARG 0.002 0.000 ARG F 34 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 320) hydrogen bonds : angle 4.12045 ( 894) covalent geometry : bond 0.00239 ( 7278) covalent geometry : angle 0.55614 ( 9822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5260.12 seconds wall clock time: 95 minutes 50.66 seconds (5750.66 seconds total)