Starting phenix.real_space_refine on Wed Sep 17 09:25:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vvi_43560/09_2025/8vvi_43560.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vvi_43560/09_2025/8vvi_43560.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 { model { file = "/net/cci-nas-00/data/ceres_data/8vvi_43560/09_2025/8vvi_43560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vvi_43560/09_2025/8vvi_43560.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vvi_43560/09_2025/8vvi_43560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vvi_43560/09_2025/8vvi_43560.map" } 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= 0.000 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 5074 2.51 5 N 1263 2.21 5 O 1381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7762 Number of models: 1 Model: "" Number of chains: 7 Chain: "F" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 775 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "A" Number of atoms: 1958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1958 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 5, 'TRANS': 232} Chain: "C" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 775 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "D" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 775 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "E" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 775 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "G" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 775 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "B" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1929 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 5, 'TRANS': 229} Time building chain proxies: 1.99, per 1000 atoms: 0.26 Number of scatterers: 7762 At special positions: 0 Unit cell: (67.962, 73.746, 124.356, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1381 8.00 N 1263 7.00 C 5074 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: 0.59 Conformation dependent library (CDL) restraints added in 418.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1808 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 73.7% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'F' and resid 4 through 23 Processing helix chain 'F' and resid 24 through 27 removed outlier: 3.664A pdb=" N LYS F 27 " --> pdb=" O ARG F 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 24 through 27' Processing helix chain 'F' and resid 32 through 54 Processing helix chain 'F' and resid 61 through 63 No H-bonds generated for 'chain 'F' and resid 61 through 63' Processing helix chain 'F' and resid 64 through 99 Processing helix chain 'A' and resid 14 through 41 removed outlier: 3.668A pdb=" N SER A 18 " --> pdb=" O ASP A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 67 Proline residue: A 48 - end of helix Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 100 through 119 removed outlier: 3.588A pdb=" N LYS A 104 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG A 113 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 116 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 171 removed outlier: 4.123A pdb=" N MET A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.950A pdb=" N TRP A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 246 removed outlier: 3.592A pdb=" N LYS A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 246 " --> pdb=" O TYR A 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 24 removed outlier: 3.624A pdb=" N ASN C 23 " --> pdb=" O ILE C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 55 Proline residue: C 34 - end of helix removed outlier: 3.549A pdb=" N HIS C 55 " --> pdb=" O ILE C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 99 Proline residue: C 66 - end of helix removed outlier: 3.885A pdb=" N THR C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 76 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TRP C 77 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA C 78 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 99 " --> pdb=" O PHE C 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 4 No H-bonds generated for 'chain 'D' and resid 2 through 4' Processing helix chain 'D' and resid 5 through 24 removed outlier: 3.799A pdb=" N ASN D 23 " --> pdb=" O ILE D 19 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D 24 " --> pdb=" O PHE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 53 removed outlier: 3.557A pdb=" N LEU D 32 " --> pdb=" O SER D 28 " (cutoff:3.500A) Proline residue: D 34 - end of helix Processing helix chain 'D' and resid 64 through 99 Processing helix chain 'E' and resid 2 through 24 removed outlier: 3.633A pdb=" N ASN E 23 " --> pdb=" O ILE E 19 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG E 24 " --> pdb=" O PHE E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 53 removed outlier: 3.767A pdb=" N LEU E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Proline residue: E 34 - end of helix removed outlier: 3.592A pdb=" N ILE E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY E 52 " --> pdb=" O GLY E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 98 Proline residue: E 66 - end of helix removed outlier: 4.600A pdb=" N PHE E 76 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N TRP E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA E 78 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 24 removed outlier: 3.652A pdb=" N TYR G 7 " --> pdb=" O HIS G 3 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN G 23 " --> pdb=" O ILE G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 54 removed outlier: 3.749A pdb=" N LEU G 32 " --> pdb=" O SER G 28 " (cutoff:3.500A) Proline residue: G 34 - end of helix Processing helix chain 'G' and resid 60 through 72 Proline residue: G 66 - end of helix Processing helix chain 'G' and resid 75 through 98 removed outlier: 4.315A pdb=" N SER G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 41 removed outlier: 4.212A pdb=" N SER B 18 " --> pdb=" O ASP B 14 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP B 21 " --> pdb=" O ILE B 17 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 67 removed outlier: 3.505A pdb=" N VAL B 47 " --> pdb=" O ASP B 43 " (cutoff:3.500A) Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 100 through 119 removed outlier: 4.073A pdb=" N ILE B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 removed outlier: 4.661A pdb=" N ASN B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 170 removed outlier: 4.120A pdb=" N PHE B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 187 removed outlier: 3.951A pdb=" N TRP B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 246 removed outlier: 3.512A pdb=" N ILE B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 246 " --> pdb=" O TYR B 242 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 77 removed outlier: 3.530A pdb=" N VAL A 220 " --> pdb=" O PHE A 85 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 129 " --> pdb=" O ARG A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 75 through 77 Processing sheet with id=AA3, first strand: chain 'B' and resid 188 through 192 531 hydrogen bonds defined for protein. 1584 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: 1.20 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2424 1.34 - 1.46: 1657 1.46 - 1.58: 3756 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 7925 Sorted by residual: bond pdb=" C LEU D 65 " pdb=" N PRO D 66 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.36e-02 5.41e+03 6.00e-01 bond pdb=" CB PRO A 198 " pdb=" CG PRO A 198 " ideal model delta sigma weight residual 1.492 1.529 -0.037 5.00e-02 4.00e+02 5.37e-01 bond pdb=" CA ASP B 89 " pdb=" CB ASP B 89 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.69e-02 3.50e+03 5.28e-01 bond pdb=" CB ASP A 109 " pdb=" CG ASP A 109 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.05e-01 bond pdb=" N LYS A 79 " pdb=" CA LYS A 79 " ideal model delta sigma weight residual 1.462 1.472 -0.010 1.48e-02 4.57e+03 4.99e-01 ... (remaining 7920 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 10517 1.34 - 2.68: 139 2.68 - 4.02: 25 4.02 - 5.37: 17 5.37 - 6.71: 1 Bond angle restraints: 10699 Sorted by residual: angle pdb=" C PRO B 88 " pdb=" N ASP B 89 " pdb=" CA ASP B 89 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C ASN D 26 " pdb=" N LYS D 27 " pdb=" CA LYS D 27 " ideal model delta sigma weight residual 121.54 126.84 -5.30 1.91e+00 2.74e-01 7.70e+00 angle pdb=" C ASN G 26 " pdb=" N LYS G 27 " pdb=" CA LYS G 27 " ideal model delta sigma weight residual 121.54 126.36 -4.82 1.91e+00 2.74e-01 6.38e+00 angle pdb=" CA LYS A 79 " pdb=" CB LYS A 79 " pdb=" CG LYS A 79 " ideal model delta sigma weight residual 114.10 118.21 -4.11 2.00e+00 2.50e-01 4.23e+00 angle pdb=" C PRO A 88 " pdb=" N ASP A 89 " pdb=" CA ASP A 89 " ideal model delta sigma weight residual 121.54 125.26 -3.72 1.91e+00 2.74e-01 3.80e+00 ... (remaining 10694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 4217 17.88 - 35.77: 369 35.77 - 53.65: 62 53.65 - 71.54: 14 71.54 - 89.42: 4 Dihedral angle restraints: 4666 sinusoidal: 1876 harmonic: 2790 Sorted by residual: dihedral pdb=" CB GLU B 239 " pdb=" CG GLU B 239 " pdb=" CD GLU B 239 " pdb=" OE1 GLU B 239 " ideal model delta sinusoidal sigma weight residual 0.00 89.42 -89.42 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASP A 14 " pdb=" CB ASP A 14 " pdb=" CG ASP A 14 " pdb=" OD1 ASP A 14 " ideal model delta sinusoidal sigma weight residual -30.00 -84.20 54.20 1 2.00e+01 2.50e-03 9.96e+00 dihedral pdb=" CG LYS B 181 " pdb=" CD LYS B 181 " pdb=" CE LYS B 181 " pdb=" NZ LYS B 181 " ideal model delta sinusoidal sigma weight residual 60.00 117.66 -57.66 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 4663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 718 0.026 - 0.052: 309 0.052 - 0.078: 149 0.078 - 0.104: 41 0.104 - 0.130: 19 Chirality restraints: 1236 Sorted by residual: chirality pdb=" CA ILE A 132 " pdb=" N ILE A 132 " pdb=" C ILE A 132 " pdb=" CB ILE A 132 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA ILE B 132 " pdb=" N ILE B 132 " pdb=" C ILE B 132 " pdb=" CB ILE B 132 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE A 130 " pdb=" N ILE A 130 " pdb=" C ILE A 130 " pdb=" CB ILE A 130 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 1233 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 33 " -0.039 5.00e-02 4.00e+02 5.98e-02 5.71e+00 pdb=" N PRO C 34 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 34 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 34 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 100 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A 101 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 87 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO A 88 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " 0.016 5.00e-02 4.00e+02 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 494 2.74 - 3.28: 8140 3.28 - 3.82: 13128 3.82 - 4.36: 16602 4.36 - 4.90: 27998 Nonbonded interactions: 66362 Sorted by model distance: nonbonded pdb=" O GLY F 35 " pdb=" OG1 THR F 39 " model vdw 2.197 3.040 nonbonded pdb=" O ALA B 149 " pdb=" ND2 ASN B 153 " model vdw 2.242 3.120 nonbonded pdb=" OH TYR A 242 " pdb=" OD2 ASP C 63 " model vdw 2.247 3.040 nonbonded pdb=" O ILE B 90 " pdb=" OG1 THR B 100 " model vdw 2.266 3.040 nonbonded pdb=" O PHE C 20 " pdb=" NE2 GLN C 30 " model vdw 2.267 3.120 ... (remaining 66357 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' and resid 13 through 247) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 7.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.420 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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 : 0.002 0.037 7925 Z= 0.088 Angle : 0.445 6.707 10699 Z= 0.239 Chirality : 0.038 0.130 1236 Planarity : 0.003 0.060 1328 Dihedral : 13.855 89.424 2858 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -0.11 (0.27), residues: 954 helix: 0.60 (0.20), residues: 664 sheet: -2.99 (0.61), residues: 46 loop : -1.10 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 230 TYR 0.008 0.001 TYR B 150 PHE 0.009 0.001 PHE B 111 TRP 0.008 0.001 TRP A 183 HIS 0.002 0.000 HIS F 3 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 7925) covalent geometry : angle 0.44493 (10699) hydrogen bonds : bond 0.22544 ( 531) hydrogen bonds : angle 7.41068 ( 1584) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.309 Fit side-chains REVERT: F 25 ARG cc_start: 0.7539 (mmp80) cc_final: 0.6604 (ppt170) REVERT: F 67 THR cc_start: 0.8161 (m) cc_final: 0.7957 (t) REVERT: A 128 GLU cc_start: 0.6401 (mt-10) cc_final: 0.6124 (mt-10) REVERT: D 5 MET cc_start: 0.7507 (tpt) cc_final: 0.7029 (tpt) REVERT: B 21 ASP cc_start: 0.7936 (m-30) cc_final: 0.7675 (m-30) REVERT: B 80 ASP cc_start: 0.5833 (t0) cc_final: 0.5155 (t0) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.6708 time to fit residues: 104.7185 Evaluate side-chains 119 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 HIS F 26 ASN A 246 GLN D 3 HIS E 26 ASN B 218 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.197394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.155593 restraints weight = 7518.816| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.54 r_work: 0.3608 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7925 Z= 0.169 Angle : 0.573 5.774 10699 Z= 0.311 Chirality : 0.043 0.146 1236 Planarity : 0.005 0.049 1328 Dihedral : 4.467 20.499 1021 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.77 % Allowed : 10.97 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.66 (0.27), residues: 954 helix: 1.28 (0.19), residues: 680 sheet: -2.30 (0.70), residues: 38 loop : -1.48 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 225 TYR 0.014 0.001 TYR A 15 PHE 0.013 0.001 PHE A 151 TRP 0.005 0.001 TRP B 183 HIS 0.012 0.001 HIS E 3 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 7925) covalent geometry : angle 0.57306 (10699) hydrogen bonds : bond 0.04905 ( 531) hydrogen bonds : angle 4.40774 ( 1584) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.307 Fit side-chains REVERT: F 1 MET cc_start: 0.5677 (pp-130) cc_final: 0.5409 (pp-130) REVERT: F 24 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.6048 (ttp80) REVERT: F 25 ARG cc_start: 0.7645 (mmp80) cc_final: 0.6458 (ppt170) REVERT: A 128 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6887 (mt-10) REVERT: A 185 MET cc_start: 0.7877 (mpt) cc_final: 0.7675 (mpt) REVERT: A 230 ARG cc_start: 0.6991 (mmp80) cc_final: 0.6773 (mmp-170) REVERT: C 22 MET cc_start: 0.6752 (ptp) cc_final: 0.6492 (ptt) REVERT: D 5 MET cc_start: 0.7946 (tpt) cc_final: 0.7639 (tmm) REVERT: D 73 LYS cc_start: 0.8293 (mttp) cc_final: 0.7610 (mtpt) REVERT: E 73 LYS cc_start: 0.8395 (mtpt) cc_final: 0.8158 (mttp) REVERT: B 21 ASP cc_start: 0.8197 (m-30) cc_final: 0.7967 (m-30) REVERT: B 80 ASP cc_start: 0.6066 (t0) cc_final: 0.5439 (t0) REVERT: B 108 ASP cc_start: 0.8112 (m-30) cc_final: 0.7633 (m-30) REVERT: B 128 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6856 (tp30) outliers start: 15 outliers final: 3 residues processed: 131 average time/residue: 0.6529 time to fit residues: 89.8575 Evaluate side-chains 118 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain B residue 128 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 0.0470 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 60 optimal weight: 0.0870 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN B 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.198861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.159239 restraints weight = 7483.749| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.71 r_work: 0.3635 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7925 Z= 0.134 Angle : 0.508 5.613 10699 Z= 0.274 Chirality : 0.041 0.140 1236 Planarity : 0.004 0.049 1328 Dihedral : 4.401 17.389 1021 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.12 % Allowed : 12.85 % Favored : 85.02 % 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: 1.08 (0.27), residues: 954 helix: 1.61 (0.20), residues: 683 sheet: -1.98 (0.74), residues: 38 loop : -1.47 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 162 TYR 0.010 0.001 TYR A 15 PHE 0.010 0.001 PHE B 111 TRP 0.008 0.001 TRP A 183 HIS 0.010 0.001 HIS E 3 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7925) covalent geometry : angle 0.50758 (10699) hydrogen bonds : bond 0.04012 ( 531) hydrogen bonds : angle 4.08624 ( 1584) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.205 Fit side-chains REVERT: F 24 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.6032 (ttp80) REVERT: F 25 ARG cc_start: 0.7606 (mmp80) cc_final: 0.6464 (ppt170) REVERT: A 128 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6747 (tp30) REVERT: D 5 MET cc_start: 0.7913 (tpt) cc_final: 0.7549 (tmm) REVERT: D 73 LYS cc_start: 0.8323 (mttp) cc_final: 0.7674 (mtpt) REVERT: E 73 LYS cc_start: 0.8395 (mtpt) cc_final: 0.8174 (mttp) REVERT: G 7 TYR cc_start: 0.7594 (m-80) cc_final: 0.7358 (m-80) REVERT: B 159 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7400 (mm-30) REVERT: B 229 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7562 (tt0) outliers start: 18 outliers final: 5 residues processed: 126 average time/residue: 0.6214 time to fit residues: 82.2929 Evaluate side-chains 120 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 237 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.184039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.137023 restraints weight = 7513.193| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.73 r_work: 0.3406 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7925 Z= 0.164 Angle : 0.537 6.471 10699 Z= 0.287 Chirality : 0.042 0.142 1236 Planarity : 0.004 0.051 1328 Dihedral : 4.504 17.555 1021 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.59 % Allowed : 14.03 % Favored : 83.37 % 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: 1.01 (0.27), residues: 954 helix: 1.60 (0.20), residues: 684 sheet: -2.36 (0.64), residues: 51 loop : -1.50 (0.38), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 113 TYR 0.014 0.001 TYR A 15 PHE 0.013 0.001 PHE B 151 TRP 0.011 0.001 TRP A 183 HIS 0.010 0.001 HIS E 3 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 7925) covalent geometry : angle 0.53746 (10699) hydrogen bonds : bond 0.04048 ( 531) hydrogen bonds : angle 4.05626 ( 1584) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.200 Fit side-chains REVERT: F 24 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.5939 (ttp80) REVERT: F 25 ARG cc_start: 0.7381 (mmp80) cc_final: 0.6185 (ppt170) REVERT: A 230 ARG cc_start: 0.6968 (mmp80) cc_final: 0.6651 (mtt90) REVERT: D 5 MET cc_start: 0.7909 (tpt) cc_final: 0.7624 (tmm) REVERT: D 73 LYS cc_start: 0.8257 (mttp) cc_final: 0.7430 (mtpt) REVERT: E 73 LYS cc_start: 0.8317 (mtpt) cc_final: 0.8051 (mttp) REVERT: G 7 TYR cc_start: 0.7491 (m-80) cc_final: 0.7210 (m-80) REVERT: B 21 ASP cc_start: 0.8205 (m-30) cc_final: 0.7994 (m-30) REVERT: B 80 ASP cc_start: 0.6204 (t0) cc_final: 0.5603 (t0) REVERT: B 128 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6810 (tp30) outliers start: 22 outliers final: 6 residues processed: 136 average time/residue: 0.6401 time to fit residues: 91.3009 Evaluate side-chains 123 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 237 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 89 optimal weight: 0.5980 chunk 28 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 37 optimal weight: 0.0980 chunk 73 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 88 optimal weight: 0.4980 chunk 78 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 9 optimal weight: 0.4980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.185795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.139607 restraints weight = 7415.226| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.70 r_work: 0.3429 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7925 Z= 0.129 Angle : 0.507 6.742 10699 Z= 0.272 Chirality : 0.041 0.138 1236 Planarity : 0.004 0.048 1328 Dihedral : 4.418 17.342 1021 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.48 % Allowed : 14.98 % Favored : 82.55 % 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: 1.27 (0.27), residues: 954 helix: 1.78 (0.20), residues: 685 sheet: -2.06 (0.71), residues: 44 loop : -1.48 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 186 TYR 0.010 0.001 TYR A 15 PHE 0.018 0.001 PHE A 111 TRP 0.009 0.001 TRP A 183 HIS 0.008 0.001 HIS E 3 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7925) covalent geometry : angle 0.50717 (10699) hydrogen bonds : bond 0.03658 ( 531) hydrogen bonds : angle 3.91524 ( 1584) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.304 Fit side-chains REVERT: F 24 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.5940 (ttp80) REVERT: A 230 ARG cc_start: 0.6917 (mmp80) cc_final: 0.6647 (mtt90) REVERT: D 5 MET cc_start: 0.7917 (tpt) cc_final: 0.7602 (tmm) REVERT: D 73 LYS cc_start: 0.8229 (mttp) cc_final: 0.7439 (mtpt) REVERT: G 7 TYR cc_start: 0.7455 (m-80) cc_final: 0.7218 (m-80) REVERT: B 128 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6727 (tp30) outliers start: 21 outliers final: 9 residues processed: 127 average time/residue: 0.6197 time to fit residues: 82.8060 Evaluate side-chains 131 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 237 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 0.9980 chunk 15 optimal weight: 0.0030 chunk 79 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 57 ASN E 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.184523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.138845 restraints weight = 7468.458| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.66 r_work: 0.3408 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7925 Z= 0.149 Angle : 0.530 7.015 10699 Z= 0.283 Chirality : 0.041 0.141 1236 Planarity : 0.004 0.048 1328 Dihedral : 4.483 17.456 1021 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.95 % Allowed : 15.21 % Favored : 81.84 % 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: 1.18 (0.27), residues: 954 helix: 1.74 (0.20), residues: 685 sheet: -2.16 (0.66), residues: 49 loop : -1.59 (0.37), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 186 TYR 0.012 0.001 TYR A 15 PHE 0.019 0.001 PHE A 111 TRP 0.011 0.001 TRP A 183 HIS 0.009 0.001 HIS E 3 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 7925) covalent geometry : angle 0.53020 (10699) hydrogen bonds : bond 0.03788 ( 531) hydrogen bonds : angle 3.93796 ( 1584) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.321 Fit side-chains REVERT: F 1 MET cc_start: 0.6169 (OUTLIER) cc_final: 0.5726 (pp-130) REVERT: F 24 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.5997 (ttp80) REVERT: A 113 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7148 (ptm160) REVERT: A 230 ARG cc_start: 0.6877 (mmp80) cc_final: 0.6615 (mtt90) REVERT: D 5 MET cc_start: 0.7954 (tpt) cc_final: 0.7643 (tmm) REVERT: D 70 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8240 (m-40) REVERT: D 73 LYS cc_start: 0.8270 (mttp) cc_final: 0.7453 (mtpt) REVERT: G 7 TYR cc_start: 0.7510 (m-80) cc_final: 0.7272 (m-80) REVERT: B 80 ASP cc_start: 0.6202 (t0) cc_final: 0.5654 (t0) REVERT: B 86 GLN cc_start: 0.6477 (mm-40) cc_final: 0.5984 (mt0) REVERT: B 108 ASP cc_start: 0.7717 (m-30) cc_final: 0.7420 (m-30) REVERT: B 128 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6836 (tp30) outliers start: 25 outliers final: 10 residues processed: 133 average time/residue: 0.6238 time to fit residues: 87.1867 Evaluate side-chains 127 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 237 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 57 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 82 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 57 ASN E 70 ASN B 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.197590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.158632 restraints weight = 7391.090| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.66 r_work: 0.3602 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7925 Z= 0.138 Angle : 0.519 6.871 10699 Z= 0.277 Chirality : 0.041 0.139 1236 Planarity : 0.004 0.048 1328 Dihedral : 4.483 23.519 1021 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.59 % Allowed : 16.27 % Favored : 81.13 % 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: 1.24 (0.27), residues: 954 helix: 1.78 (0.20), residues: 687 sheet: -2.14 (0.66), residues: 49 loop : -1.57 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 162 TYR 0.010 0.001 TYR A 15 PHE 0.017 0.001 PHE A 111 TRP 0.011 0.001 TRP A 183 HIS 0.008 0.001 HIS E 3 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7925) covalent geometry : angle 0.51883 (10699) hydrogen bonds : bond 0.03657 ( 531) hydrogen bonds : angle 3.89165 ( 1584) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.307 Fit side-chains REVERT: F 1 MET cc_start: 0.5893 (OUTLIER) cc_final: 0.5622 (pp-130) REVERT: F 24 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.6184 (ttp80) REVERT: D 5 MET cc_start: 0.7964 (tpt) cc_final: 0.7691 (tmm) REVERT: D 70 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8379 (m-40) REVERT: D 73 LYS cc_start: 0.8411 (mttp) cc_final: 0.7725 (mtpt) REVERT: G 7 TYR cc_start: 0.7623 (m-80) cc_final: 0.7407 (m-80) REVERT: B 86 GLN cc_start: 0.6624 (OUTLIER) cc_final: 0.6181 (mt0) REVERT: B 128 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6870 (tp30) outliers start: 22 outliers final: 9 residues processed: 128 average time/residue: 0.6242 time to fit residues: 83.9531 Evaluate side-chains 130 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 237 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 77 optimal weight: 0.9980 chunk 64 optimal weight: 0.0870 chunk 22 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN D 57 ASN E 70 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.197454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.158459 restraints weight = 7492.809| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.71 r_work: 0.3615 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7925 Z= 0.138 Angle : 0.524 7.242 10699 Z= 0.278 Chirality : 0.041 0.139 1236 Planarity : 0.004 0.047 1328 Dihedral : 4.483 23.252 1021 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.12 % Allowed : 17.81 % Favored : 80.07 % 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: 1.29 (0.27), residues: 954 helix: 1.79 (0.20), residues: 688 sheet: -2.00 (0.72), residues: 44 loop : -1.51 (0.38), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 162 TYR 0.011 0.001 TYR A 15 PHE 0.016 0.001 PHE A 111 TRP 0.012 0.001 TRP A 183 HIS 0.008 0.001 HIS E 3 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 7925) covalent geometry : angle 0.52381 (10699) hydrogen bonds : bond 0.03643 ( 531) hydrogen bonds : angle 3.88789 ( 1584) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.284 Fit side-chains REVERT: F 1 MET cc_start: 0.5905 (OUTLIER) cc_final: 0.5699 (pp-130) REVERT: F 24 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.6171 (ttp80) REVERT: D 5 MET cc_start: 0.7949 (tpt) cc_final: 0.7678 (tmm) REVERT: D 70 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8357 (m-40) REVERT: D 73 LYS cc_start: 0.8407 (mttp) cc_final: 0.7699 (mtpt) REVERT: G 7 TYR cc_start: 0.7572 (m-80) cc_final: 0.7335 (m-80) REVERT: B 80 ASP cc_start: 0.5992 (t0) cc_final: 0.5592 (t0) REVERT: B 86 GLN cc_start: 0.6407 (OUTLIER) cc_final: 0.5869 (mt0) REVERT: B 128 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6840 (tp30) outliers start: 18 outliers final: 11 residues processed: 126 average time/residue: 0.6376 time to fit residues: 84.4069 Evaluate side-chains 128 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 237 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 57 ASN E 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.196830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.159564 restraints weight = 7550.614| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.58 r_work: 0.3597 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7925 Z= 0.153 Angle : 0.537 7.350 10699 Z= 0.285 Chirality : 0.042 0.140 1236 Planarity : 0.004 0.047 1328 Dihedral : 4.541 23.323 1021 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.48 % Allowed : 17.22 % Favored : 80.31 % 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: 1.16 (0.27), residues: 954 helix: 1.71 (0.20), residues: 688 sheet: -2.09 (0.66), residues: 49 loop : -1.56 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 162 TYR 0.013 0.001 TYR A 15 PHE 0.018 0.001 PHE A 111 TRP 0.012 0.001 TRP A 183 HIS 0.008 0.001 HIS E 3 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 7925) covalent geometry : angle 0.53722 (10699) hydrogen bonds : bond 0.03788 ( 531) hydrogen bonds : angle 3.93427 ( 1584) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.319 Fit side-chains REVERT: F 24 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.6208 (ttp80) REVERT: D 5 MET cc_start: 0.7999 (tpt) cc_final: 0.7742 (tmm) REVERT: D 70 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8389 (m-40) REVERT: D 73 LYS cc_start: 0.8453 (mttp) cc_final: 0.7749 (mtpt) REVERT: G 7 TYR cc_start: 0.7622 (m-80) cc_final: 0.7390 (m-80) REVERT: B 86 GLN cc_start: 0.6551 (OUTLIER) cc_final: 0.6115 (mt0) REVERT: B 128 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6957 (tp30) outliers start: 21 outliers final: 12 residues processed: 125 average time/residue: 0.6469 time to fit residues: 85.0280 Evaluate side-chains 130 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 237 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.0000 chunk 3 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 57 ASN E 70 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.197149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.157013 restraints weight = 7505.248| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.50 r_work: 0.3617 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7925 Z= 0.141 Angle : 0.533 7.757 10699 Z= 0.283 Chirality : 0.041 0.138 1236 Planarity : 0.004 0.047 1328 Dihedral : 4.568 32.128 1021 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.24 % Allowed : 17.92 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.23 (0.27), residues: 954 helix: 1.75 (0.20), residues: 688 sheet: -2.06 (0.66), residues: 49 loop : -1.55 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 162 TYR 0.010 0.001 TYR A 15 PHE 0.017 0.001 PHE A 111 TRP 0.012 0.001 TRP A 183 HIS 0.007 0.001 HIS E 3 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7925) covalent geometry : angle 0.53326 (10699) hydrogen bonds : bond 0.03684 ( 531) hydrogen bonds : angle 3.90499 ( 1584) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.280 Fit side-chains REVERT: F 24 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.6213 (ttp80) REVERT: D 5 MET cc_start: 0.7956 (tpt) cc_final: 0.7697 (tmm) REVERT: D 70 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8369 (m-40) REVERT: D 73 LYS cc_start: 0.8405 (mttp) cc_final: 0.7703 (mtpt) REVERT: G 7 TYR cc_start: 0.7589 (m-80) cc_final: 0.7367 (m-80) REVERT: B 80 ASP cc_start: 0.5995 (t0) cc_final: 0.5634 (t0) REVERT: B 86 GLN cc_start: 0.6529 (OUTLIER) cc_final: 0.6138 (mt0) REVERT: B 128 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6841 (tp30) outliers start: 19 outliers final: 12 residues processed: 126 average time/residue: 0.5886 time to fit residues: 78.2680 Evaluate side-chains 127 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain C residue 24 ARG Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 237 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 15 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 3 HIS D 57 ASN E 70 ASN B 86 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.183190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.136952 restraints weight = 7388.608| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.70 r_work: 0.3403 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7925 Z= 0.158 Angle : 0.552 7.715 10699 Z= 0.293 Chirality : 0.042 0.140 1236 Planarity : 0.004 0.047 1328 Dihedral : 4.676 38.324 1021 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.36 % Allowed : 18.16 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.12 (0.27), residues: 954 helix: 1.66 (0.19), residues: 688 sheet: -2.07 (0.66), residues: 49 loop : -1.54 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 162 TYR 0.013 0.001 TYR A 15 PHE 0.017 0.001 PHE A 111 TRP 0.012 0.001 TRP A 183 HIS 0.007 0.001 HIS E 3 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 7925) covalent geometry : angle 0.55201 (10699) hydrogen bonds : bond 0.03838 ( 531) hydrogen bonds : angle 3.96079 ( 1584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3184.53 seconds wall clock time: 55 minutes 7.67 seconds (3307.67 seconds total)