Starting phenix.real_space_refine on Wed Feb 4 09:14:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nz4_49950/02_2026/9nz4_49950.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nz4_49950/02_2026/9nz4_49950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nz4_49950/02_2026/9nz4_49950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nz4_49950/02_2026/9nz4_49950.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nz4_49950/02_2026/9nz4_49950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nz4_49950/02_2026/9nz4_49950.map" } resolution = 3.23 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= 0.034 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 50 5.16 5 C 6178 2.51 5 N 1612 2.21 5 O 1848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9688 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1553 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 5, 'TRANS': 186} Chain: "B" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1553 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 5, 'TRANS': 186} Chain: "C" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1685 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "D" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1606 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 198} Chain: "E" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1685 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Chain: "F" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1606 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 198} Time building chain proxies: 2.36, per 1000 atoms: 0.24 Number of scatterers: 9688 At special positions: 0 Unit cell: (101.01, 145.6, 118.3, 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 50 16.00 O 1848 8.00 N 1612 7.00 C 6178 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: 0.83 Conformation dependent library (CDL) restraints added in 510.3 milliseconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 21 sheets defined 18.9% alpha, 37.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 11 through 14 Processing helix chain 'A' and resid 15 through 36 removed outlier: 3.708A pdb=" N TRP A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.845A pdb=" N ILE A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 72 through 104 removed outlier: 3.727A pdb=" N ARG A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.769A pdb=" N ASN A 111 " --> pdb=" O TRP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'B' and resid 17 through 33 Processing helix chain 'B' and resid 41 through 69 removed outlier: 5.103A pdb=" N TRP B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Proline residue: B 57 - end of helix Processing helix chain 'B' and resid 72 through 104 removed outlier: 3.502A pdb=" N LEU B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.955A pdb=" N SER D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 158 No H-bonds generated for 'chain 'D' and resid 156 through 158' Processing helix chain 'D' and resid 184 through 188 Processing helix chain 'D' and resid 200 through 203 Processing helix chain 'E' and resid 125 through 132 Processing helix chain 'F' and resid 156 through 158 No H-bonds generated for 'chain 'F' and resid 156 through 158' Processing helix chain 'F' and resid 184 through 188 Processing helix chain 'F' and resid 200 through 203 Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 130 removed outlier: 7.596A pdb=" N GLU A 165 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LYS A 178 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ARG A 196 " --> pdb=" O LYS A 178 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY A 180 " --> pdb=" O TYR A 194 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TYR A 194 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER A 182 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA A 192 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG A 184 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLY A 190 " --> pdb=" O ARG A 184 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU A 147 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 125 through 131 removed outlier: 4.169A pdb=" N ILE B 116 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLU B 165 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LYS B 178 " --> pdb=" O ARG B 196 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ARG B 196 " --> pdb=" O LYS B 178 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLY B 180 " --> pdb=" O TYR B 194 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N TYR B 194 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N SER B 182 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA B 192 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ARG B 184 " --> pdb=" O GLY B 190 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY B 190 " --> pdb=" O ARG B 184 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU B 147 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.615A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 118 through 122 removed outlier: 5.914A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 149 through 151 Processing sheet with id=AA7, first strand: chain 'C' and resid 153 through 154 Processing sheet with id=AA8, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.727A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 120 through 124 removed outlier: 5.808A pdb=" N TYR D 175 " --> pdb=" O GLY D 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 120 through 124 removed outlier: 5.808A pdb=" N TYR D 175 " --> pdb=" O GLY D 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 151 through 154 Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 13 removed outlier: 5.873A pdb=" N LEU E 11 " --> pdb=" O GLU E 109 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP E 39 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 118 through 122 removed outlier: 5.706A pdb=" N TYR E 177 " --> pdb=" O ASN E 142 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 157 through 158 Processing sheet with id=AB8, first strand: chain 'F' and resid 3 through 5 Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.007A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU F 50 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N THR F 58 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 120 through 124 removed outlier: 3.562A pdb=" N SER F 179 " --> pdb=" O CYS F 140 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N TYR F 175 " --> pdb=" O GLY F 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 120 through 124 removed outlier: 3.562A pdb=" N SER F 179 " --> pdb=" O CYS F 140 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N TYR F 175 " --> pdb=" O GLY F 144 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 151 through 154 486 hydrogen bonds defined for protein. 1224 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: 1.64 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2086 1.33 - 1.45: 2503 1.45 - 1.58: 5259 1.58 - 1.71: 2 1.71 - 1.83: 76 Bond restraints: 9926 Sorted by residual: bond pdb=" NE ARG D 213 " pdb=" CZ ARG D 213 " ideal model delta sigma weight residual 1.326 1.375 -0.049 1.10e-02 8.26e+03 1.96e+01 bond pdb=" NE ARG F 213 " pdb=" CZ ARG F 213 " ideal model delta sigma weight residual 1.326 1.372 -0.046 1.10e-02 8.26e+03 1.71e+01 bond pdb=" CA SER A 92 " pdb=" CB SER A 92 " ideal model delta sigma weight residual 1.529 1.476 0.053 1.58e-02 4.01e+03 1.11e+01 bond pdb=" CB LEU B 11 " pdb=" CG LEU B 11 " ideal model delta sigma weight residual 1.530 1.597 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" CB LEU A 11 " pdb=" CG LEU A 11 " ideal model delta sigma weight residual 1.530 1.595 -0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 9921 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 11772 1.69 - 3.38: 1387 3.38 - 5.07: 248 5.07 - 6.76: 93 6.76 - 8.46: 20 Bond angle restraints: 13520 Sorted by residual: angle pdb=" C THR D 117 " pdb=" N PRO D 118 " pdb=" CA PRO D 118 " ideal model delta sigma weight residual 119.66 126.02 -6.36 7.20e-01 1.93e+00 7.81e+01 angle pdb=" C GLY F 8 " pdb=" N PRO F 9 " pdb=" CA PRO F 9 " ideal model delta sigma weight residual 119.85 127.88 -8.03 1.01e+00 9.80e-01 6.32e+01 angle pdb=" C LEU B 162 " pdb=" N PRO B 163 " pdb=" CA PRO B 163 " ideal model delta sigma weight residual 119.90 127.53 -7.63 1.02e+00 9.61e-01 5.60e+01 angle pdb=" C PRO D 118 " pdb=" N PRO D 119 " pdb=" CA PRO D 119 " ideal model delta sigma weight residual 119.85 127.12 -7.27 1.01e+00 9.80e-01 5.18e+01 angle pdb=" C ASN B 111 " pdb=" N PRO B 112 " pdb=" CA PRO B 112 " ideal model delta sigma weight residual 119.87 127.33 -7.46 1.04e+00 9.25e-01 5.14e+01 ... (remaining 13515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5655 17.91 - 35.81: 156 35.81 - 53.72: 33 53.72 - 71.63: 10 71.63 - 89.53: 12 Dihedral angle restraints: 5866 sinusoidal: 2244 harmonic: 3622 Sorted by residual: dihedral pdb=" CA GLU D 148 " pdb=" C GLU D 148 " pdb=" N PRO D 149 " pdb=" CA PRO D 149 " ideal model delta harmonic sigma weight residual -180.00 -147.91 -32.09 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" CA TYR D 80 " pdb=" C TYR D 80 " pdb=" N MET D 81 " pdb=" CA MET D 81 " ideal model delta harmonic sigma weight residual 180.00 162.93 17.07 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA PRO F 149 " pdb=" C PRO F 149 " pdb=" N VAL F 150 " pdb=" CA VAL F 150 " ideal model delta harmonic sigma weight residual 180.00 163.23 16.77 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 5863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1120 0.065 - 0.130: 336 0.130 - 0.195: 65 0.195 - 0.260: 8 0.260 - 0.325: 3 Chirality restraints: 1532 Sorted by residual: chirality pdb=" CG LEU A 11 " pdb=" CB LEU A 11 " pdb=" CD1 LEU A 11 " pdb=" CD2 LEU A 11 " both_signs ideal model delta sigma weight residual False -2.59 -2.91 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CG LEU B 11 " pdb=" CB LEU B 11 " pdb=" CD1 LEU B 11 " pdb=" CD2 LEU B 11 " both_signs ideal model delta sigma weight residual False -2.59 -2.91 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA TYR C 144 " pdb=" N TYR C 144 " pdb=" C TYR C 144 " pdb=" CB TYR C 144 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1529 not shown) Planarity restraints: 1702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 218 " 0.024 2.00e-02 2.50e+03 4.83e-02 2.34e+01 pdb=" C CYS C 218 " -0.084 2.00e-02 2.50e+03 pdb=" O CYS C 218 " 0.030 2.00e-02 2.50e+03 pdb=" OXT CYS C 218 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS E 218 " 0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C CYS E 218 " -0.057 2.00e-02 2.50e+03 pdb=" O CYS E 218 " 0.020 2.00e-02 2.50e+03 pdb=" OXT CYS E 218 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 144 " -0.032 2.00e-02 2.50e+03 1.64e-02 5.38e+00 pdb=" CG TYR C 144 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR C 144 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR C 144 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR C 144 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR C 144 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 144 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 144 " -0.022 2.00e-02 2.50e+03 ... (remaining 1699 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 3519 2.88 - 3.39: 8211 3.39 - 3.89: 15524 3.89 - 4.40: 16998 4.40 - 4.90: 29982 Nonbonded interactions: 74234 Sorted by model distance: nonbonded pdb=" O TYR C 190 " pdb=" OH TYR C 196 " model vdw 2.377 3.040 nonbonded pdb=" O TYR B 197 " pdb=" ND2 ASN E 95 " model vdw 2.414 3.120 nonbonded pdb=" NZ LYS E 24 " pdb=" OD1 ASP E 74 " model vdw 2.422 3.120 nonbonded pdb=" O PHE B 101 " pdb=" O THR B 104 " model vdw 2.449 3.040 nonbonded pdb=" O THR B 170 " pdb=" OG SER B 171 " model vdw 2.468 3.040 ... (remaining 74229 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' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.490 Find NCS groups from input model: 0.280 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 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 : 0.011 0.074 9926 Z= 0.624 Angle : 1.267 8.456 13520 Z= 0.861 Chirality : 0.064 0.325 1532 Planarity : 0.005 0.048 1702 Dihedral : 10.429 89.533 3546 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.21 % Favored : 95.30 % Rotamer: Outliers : 0.46 % Allowed : 0.74 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.24), residues: 1234 helix: -1.22 (0.33), residues: 204 sheet: 0.92 (0.22), residues: 504 loop : -0.34 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 40 TYR 0.032 0.004 TYR C 144 PHE 0.017 0.003 PHE A 51 TRP 0.015 0.003 TRP F 188 HIS 0.003 0.001 HIS E 193 Details of bonding type rmsd covalent geometry : bond 0.01134 ( 9926) covalent geometry : angle 1.26656 (13520) hydrogen bonds : bond 0.19665 ( 457) hydrogen bonds : angle 8.33765 ( 1224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 239 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: B 197 TYR cc_start: 0.7152 (p90) cc_final: 0.6813 (p90) REVERT: C 38 ASN cc_start: 0.7347 (m-40) cc_final: 0.7143 (m-40) REVERT: C 193 HIS cc_start: 0.4860 (m-70) cc_final: 0.4646 (m-70) REVERT: E 179 MET cc_start: 0.6414 (ttt) cc_final: 0.6070 (ttm) REVERT: E 180 SER cc_start: 0.7492 (t) cc_final: 0.7014 (m) REVERT: F 67 LYS cc_start: 0.6074 (mttp) cc_final: 0.5363 (tmtt) REVERT: F 143 LYS cc_start: 0.6918 (tttt) cc_final: 0.6494 (tptt) REVERT: F 152 VAL cc_start: 0.8055 (t) cc_final: 0.7755 (t) REVERT: F 208 LYS cc_start: 0.6954 (mmtt) cc_final: 0.6401 (tptt) outliers start: 5 outliers final: 2 residues processed: 241 average time/residue: 0.1452 time to fit residues: 44.9553 Evaluate side-chains 148 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 91 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 ASN B 119 ASN C 42 GLN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN E 142 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.226473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.186771 restraints weight = 11745.076| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 2.96 r_work: 0.3897 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9926 Z= 0.172 Angle : 0.662 7.871 13520 Z= 0.353 Chirality : 0.046 0.161 1532 Planarity : 0.005 0.064 1702 Dihedral : 5.183 55.617 1353 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.49 % Allowed : 2.84 % Favored : 96.68 % Rotamer: Outliers : 1.94 % Allowed : 6.94 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.24), residues: 1234 helix: 0.44 (0.37), residues: 204 sheet: 1.13 (0.23), residues: 498 loop : -0.59 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 215 TYR 0.019 0.002 TYR E 53 PHE 0.014 0.002 PHE D 146 TRP 0.013 0.001 TRP A 29 HIS 0.005 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 9926) covalent geometry : angle 0.66230 (13520) hydrogen bonds : bond 0.06019 ( 457) hydrogen bonds : angle 5.98051 ( 1224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.6557 (OUTLIER) cc_final: 0.5870 (mtt) REVERT: B 105 ARG cc_start: 0.7489 (mmt180) cc_final: 0.7076 (mpt180) REVERT: B 184 ARG cc_start: 0.8330 (mtp85) cc_final: 0.8090 (ttm-80) REVERT: B 197 TYR cc_start: 0.7350 (p90) cc_final: 0.7118 (p90) REVERT: D 18 MET cc_start: 0.7580 (ptm) cc_final: 0.7290 (ptm) REVERT: D 80 TYR cc_start: 0.6483 (m-80) cc_final: 0.6215 (m-80) REVERT: D 196 ASN cc_start: 0.7425 (OUTLIER) cc_final: 0.6453 (p0) REVERT: E 171 ASP cc_start: 0.7130 (t70) cc_final: 0.6857 (t70) REVERT: E 180 SER cc_start: 0.7568 (t) cc_final: 0.7362 (m) REVERT: F 18 MET cc_start: 0.6750 (mtm) cc_final: 0.5705 (ptp) REVERT: F 67 LYS cc_start: 0.6495 (mttp) cc_final: 0.5105 (tptp) REVERT: F 87 THR cc_start: 0.5852 (t) cc_final: 0.5408 (m) REVERT: F 143 LYS cc_start: 0.6909 (tttt) cc_final: 0.6620 (tptp) outliers start: 21 outliers final: 10 residues processed: 185 average time/residue: 0.1118 time to fit residues: 28.1259 Evaluate side-chains 149 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain F residue 46 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 73 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 58 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN E 57 ASN E 142 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.223329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.182046 restraints weight = 11774.363| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 3.39 r_work: 0.3841 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9926 Z= 0.168 Angle : 0.650 8.359 13520 Z= 0.339 Chirality : 0.045 0.151 1532 Planarity : 0.005 0.054 1702 Dihedral : 5.059 51.542 1353 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.05 % Favored : 95.46 % Rotamer: Outliers : 2.78 % Allowed : 8.89 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.24), residues: 1234 helix: 1.03 (0.38), residues: 204 sheet: 0.94 (0.23), residues: 516 loop : -0.80 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 99 TYR 0.019 0.002 TYR E 53 PHE 0.012 0.002 PHE E 143 TRP 0.017 0.001 TRP E 167 HIS 0.003 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9926) covalent geometry : angle 0.64958 (13520) hydrogen bonds : bond 0.05303 ( 457) hydrogen bonds : angle 5.56441 ( 1224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.367 Fit side-chains REVERT: A 89 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6044 (mtt) REVERT: A 107 MET cc_start: 0.7466 (mmt) cc_final: 0.7090 (mmt) REVERT: B 90 TRP cc_start: 0.7032 (OUTLIER) cc_final: 0.6780 (t60) REVERT: B 105 ARG cc_start: 0.7301 (mmt180) cc_final: 0.6944 (mpt180) REVERT: B 132 MET cc_start: 0.7165 (mtt) cc_final: 0.6957 (mtp) REVERT: B 183 GLN cc_start: 0.8086 (tp40) cc_final: 0.7604 (pt0) REVERT: B 198 ARG cc_start: 0.7170 (ttp-170) cc_final: 0.6939 (ttp-170) REVERT: C 193 HIS cc_start: 0.5063 (m-70) cc_final: 0.4631 (m-70) REVERT: D 19 LYS cc_start: 0.7029 (mmtt) cc_final: 0.6587 (mttm) REVERT: D 35 ASN cc_start: 0.7214 (m-40) cc_final: 0.6632 (m-40) REVERT: D 43 LYS cc_start: 0.6450 (tttm) cc_final: 0.6038 (tptt) REVERT: D 196 ASN cc_start: 0.7411 (OUTLIER) cc_final: 0.6361 (p0) REVERT: E 112 ARG cc_start: 0.4452 (OUTLIER) cc_final: 0.3995 (ppp-140) REVERT: E 171 ASP cc_start: 0.7130 (t70) cc_final: 0.6602 (t0) REVERT: E 180 SER cc_start: 0.7627 (t) cc_final: 0.7420 (m) REVERT: F 18 MET cc_start: 0.6633 (mtm) cc_final: 0.5515 (ptp) REVERT: F 19 LYS cc_start: 0.7491 (mmtt) cc_final: 0.7054 (mtmt) REVERT: F 143 LYS cc_start: 0.6873 (tttt) cc_final: 0.6587 (tptp) outliers start: 30 outliers final: 19 residues processed: 161 average time/residue: 0.1039 time to fit residues: 23.3357 Evaluate side-chains 156 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 90 TRP Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain F residue 46 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 5 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 32 optimal weight: 0.1980 chunk 95 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 57 ASN C 94 GLN ** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.222466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.181520 restraints weight = 11807.488| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 3.45 r_work: 0.3828 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9926 Z= 0.169 Angle : 0.634 7.468 13520 Z= 0.329 Chirality : 0.045 0.147 1532 Planarity : 0.005 0.052 1702 Dihedral : 4.957 45.979 1353 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.49 % Allowed : 3.57 % Favored : 95.95 % Rotamer: Outliers : 2.50 % Allowed : 10.09 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.24), residues: 1234 helix: 1.17 (0.38), residues: 204 sheet: 1.01 (0.23), residues: 506 loop : -1.02 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 99 TYR 0.021 0.002 TYR F 32 PHE 0.010 0.001 PHE E 143 TRP 0.020 0.001 TRP E 167 HIS 0.003 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 9926) covalent geometry : angle 0.63439 (13520) hydrogen bonds : bond 0.04988 ( 457) hydrogen bonds : angle 5.42776 ( 1224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6201 (mtt) REVERT: A 107 MET cc_start: 0.7522 (mmt) cc_final: 0.7148 (mmt) REVERT: B 132 MET cc_start: 0.7280 (mtt) cc_final: 0.6947 (mtp) REVERT: B 164 LYS cc_start: 0.8641 (mttt) cc_final: 0.8432 (mttp) REVERT: B 183 GLN cc_start: 0.8067 (tp40) cc_final: 0.7683 (pt0) REVERT: B 198 ARG cc_start: 0.7153 (ttp-170) cc_final: 0.6919 (ttp-110) REVERT: C 84 GLU cc_start: 0.7424 (tt0) cc_final: 0.7204 (tt0) REVERT: C 193 HIS cc_start: 0.5259 (m-70) cc_final: 0.4830 (m-70) REVERT: D 35 ASN cc_start: 0.7142 (m-40) cc_final: 0.6641 (m-40) REVERT: D 196 ASN cc_start: 0.7390 (OUTLIER) cc_final: 0.6370 (p0) REVERT: E 112 ARG cc_start: 0.4374 (OUTLIER) cc_final: 0.3826 (ppp-140) REVERT: E 171 ASP cc_start: 0.7207 (t70) cc_final: 0.6698 (t0) REVERT: E 180 SER cc_start: 0.7661 (t) cc_final: 0.7391 (t) REVERT: F 18 MET cc_start: 0.6626 (mtm) cc_final: 0.5182 (ptm) REVERT: F 19 LYS cc_start: 0.7449 (mmtt) cc_final: 0.7033 (mtmt) REVERT: F 143 LYS cc_start: 0.6846 (tttt) cc_final: 0.6545 (tptp) REVERT: F 166 PHE cc_start: 0.7148 (m-80) cc_final: 0.6160 (m-10) outliers start: 27 outliers final: 20 residues processed: 159 average time/residue: 0.1063 time to fit residues: 23.4436 Evaluate side-chains 152 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain F residue 46 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 96 ASN D 35 ASN E 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.219129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.179522 restraints weight = 11587.793| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.96 r_work: 0.3827 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9926 Z= 0.176 Angle : 0.645 8.236 13520 Z= 0.334 Chirality : 0.045 0.185 1532 Planarity : 0.005 0.050 1702 Dihedral : 4.884 35.349 1353 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.29 % Favored : 95.22 % Rotamer: Outliers : 3.06 % Allowed : 11.57 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.25), residues: 1234 helix: 1.20 (0.38), residues: 204 sheet: 0.96 (0.24), residues: 502 loop : -1.11 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 148 TYR 0.026 0.002 TYR F 32 PHE 0.012 0.002 PHE C 143 TRP 0.023 0.001 TRP E 167 HIS 0.003 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 9926) covalent geometry : angle 0.64503 (13520) hydrogen bonds : bond 0.04946 ( 457) hydrogen bonds : angle 5.36107 ( 1224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.6334 (mtt) REVERT: B 164 LYS cc_start: 0.8664 (mttt) cc_final: 0.8450 (mttp) REVERT: B 183 GLN cc_start: 0.8041 (tp40) cc_final: 0.7705 (pt0) REVERT: C 18 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7705 (ttm170) REVERT: D 19 LYS cc_start: 0.7109 (mmtt) cc_final: 0.6668 (mttm) REVERT: D 196 ASN cc_start: 0.7384 (OUTLIER) cc_final: 0.6335 (p0) REVERT: E 112 ARG cc_start: 0.4407 (OUTLIER) cc_final: 0.3765 (ppp-140) REVERT: E 142 ASN cc_start: 0.5861 (m110) cc_final: 0.5646 (m110) REVERT: E 171 ASP cc_start: 0.7296 (t70) cc_final: 0.6836 (t0) REVERT: F 143 LYS cc_start: 0.6730 (tttt) cc_final: 0.6493 (tptp) outliers start: 33 outliers final: 22 residues processed: 157 average time/residue: 0.1036 time to fit residues: 22.7733 Evaluate side-chains 154 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 163 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 39 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 80 optimal weight: 0.0060 chunk 116 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN D 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.224408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.184520 restraints weight = 11895.979| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 3.00 r_work: 0.3864 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9926 Z= 0.115 Angle : 0.569 7.293 13520 Z= 0.292 Chirality : 0.043 0.140 1532 Planarity : 0.004 0.047 1702 Dihedral : 4.452 36.131 1351 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.24 % Favored : 96.35 % Rotamer: Outliers : 1.94 % Allowed : 12.78 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.25), residues: 1234 helix: 1.48 (0.38), residues: 204 sheet: 0.82 (0.24), residues: 512 loop : -0.92 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 198 TYR 0.014 0.001 TYR F 95 PHE 0.007 0.001 PHE C 139 TRP 0.016 0.001 TRP E 167 HIS 0.002 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9926) covalent geometry : angle 0.56921 (13520) hydrogen bonds : bond 0.04016 ( 457) hydrogen bonds : angle 5.05386 ( 1224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.6662 (mpt) cc_final: 0.6309 (mtm) REVERT: B 132 MET cc_start: 0.7434 (mtt) cc_final: 0.7057 (mtp) REVERT: B 164 LYS cc_start: 0.8593 (mttt) cc_final: 0.8392 (mttp) REVERT: B 183 GLN cc_start: 0.8021 (tp40) cc_final: 0.7746 (pt0) REVERT: C 18 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8218 (ttm110) REVERT: C 193 HIS cc_start: 0.5444 (m-70) cc_final: 0.5052 (m-70) REVERT: D 19 LYS cc_start: 0.7130 (mmtt) cc_final: 0.6789 (mttm) REVERT: D 35 ASN cc_start: 0.7141 (m-40) cc_final: 0.6808 (m-40) REVERT: D 196 ASN cc_start: 0.7238 (OUTLIER) cc_final: 0.6991 (p0) REVERT: E 112 ARG cc_start: 0.4440 (OUTLIER) cc_final: 0.3838 (ppp-140) REVERT: E 171 ASP cc_start: 0.7252 (t70) cc_final: 0.6798 (t0) REVERT: F 19 LYS cc_start: 0.7537 (mmtt) cc_final: 0.7114 (mtmt) REVERT: F 143 LYS cc_start: 0.6688 (tttt) cc_final: 0.6453 (tptp) REVERT: F 166 PHE cc_start: 0.7147 (m-80) cc_final: 0.6155 (m-10) outliers start: 21 outliers final: 17 residues processed: 155 average time/residue: 0.1037 time to fit residues: 22.4291 Evaluate side-chains 149 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 46 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 6 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 ASN C 96 ASN D 6 GLN D 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.221176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.179068 restraints weight = 11905.953| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 3.02 r_work: 0.3835 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9926 Z= 0.160 Angle : 0.622 8.577 13520 Z= 0.322 Chirality : 0.044 0.146 1532 Planarity : 0.004 0.047 1702 Dihedral : 4.455 18.202 1348 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.38 % Favored : 95.14 % Rotamer: Outliers : 3.15 % Allowed : 11.94 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.25), residues: 1234 helix: 1.37 (0.38), residues: 204 sheet: 0.97 (0.24), residues: 498 loop : -1.10 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 172 TYR 0.025 0.002 TYR F 32 PHE 0.012 0.001 PHE D 146 TRP 0.016 0.001 TRP E 167 HIS 0.003 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9926) covalent geometry : angle 0.62244 (13520) hydrogen bonds : bond 0.04572 ( 457) hydrogen bonds : angle 5.14236 ( 1224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.6710 (mpt) cc_final: 0.6342 (mtm) REVERT: B 164 LYS cc_start: 0.8667 (mttt) cc_final: 0.8435 (mttm) REVERT: B 183 GLN cc_start: 0.8020 (tp40) cc_final: 0.7727 (pt0) REVERT: C 18 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8234 (ttm110) REVERT: C 193 HIS cc_start: 0.5679 (m-70) cc_final: 0.5265 (m-70) REVERT: D 19 LYS cc_start: 0.6998 (mmtt) cc_final: 0.6691 (mttm) REVERT: D 196 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.7043 (p0) REVERT: E 4 MET cc_start: 0.6715 (mtp) cc_final: 0.6499 (ttm) REVERT: E 112 ARG cc_start: 0.4545 (OUTLIER) cc_final: 0.4006 (ppp-140) REVERT: E 171 ASP cc_start: 0.7272 (t70) cc_final: 0.6827 (t0) REVERT: F 19 LYS cc_start: 0.7580 (mmtt) cc_final: 0.7226 (mtmt) REVERT: F 143 LYS cc_start: 0.6766 (tttt) cc_final: 0.6494 (tptp) REVERT: F 166 PHE cc_start: 0.7075 (m-80) cc_final: 0.5884 (m-10) outliers start: 34 outliers final: 27 residues processed: 150 average time/residue: 0.1054 time to fit residues: 22.1902 Evaluate side-chains 147 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 90 TRP Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 176 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN C 96 ASN D 35 ASN F 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.222772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.182555 restraints weight = 11777.950| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 2.96 r_work: 0.3869 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9926 Z= 0.119 Angle : 0.566 7.129 13520 Z= 0.294 Chirality : 0.043 0.139 1532 Planarity : 0.004 0.045 1702 Dihedral : 4.242 17.750 1348 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.48 % Favored : 96.19 % Rotamer: Outliers : 2.69 % Allowed : 12.59 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.25), residues: 1234 helix: 1.57 (0.38), residues: 204 sheet: 0.75 (0.24), residues: 508 loop : -0.91 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 172 TYR 0.014 0.001 TYR E 177 PHE 0.011 0.001 PHE B 110 TRP 0.013 0.001 TRP B 56 HIS 0.003 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9926) covalent geometry : angle 0.56607 (13520) hydrogen bonds : bond 0.03916 ( 457) hydrogen bonds : angle 4.92437 ( 1224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.7185 (mmm) cc_final: 0.6970 (mtm) REVERT: A 89 MET cc_start: 0.6663 (mpt) cc_final: 0.6232 (mtm) REVERT: A 107 MET cc_start: 0.7602 (mmt) cc_final: 0.7207 (mmt) REVERT: B 107 MET cc_start: 0.6038 (ptm) cc_final: 0.5199 (ptt) REVERT: B 132 MET cc_start: 0.7586 (mtt) cc_final: 0.7153 (mtp) REVERT: B 164 LYS cc_start: 0.8567 (mttt) cc_final: 0.8353 (mttm) REVERT: B 183 GLN cc_start: 0.8026 (tp40) cc_final: 0.7800 (pt0) REVERT: C 18 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8085 (ttm110) REVERT: C 193 HIS cc_start: 0.5700 (m-70) cc_final: 0.5282 (m-70) REVERT: D 19 LYS cc_start: 0.6970 (mmtt) cc_final: 0.6734 (mttm) REVERT: D 35 ASN cc_start: 0.7048 (m-40) cc_final: 0.6770 (m-40) REVERT: D 146 PHE cc_start: 0.7335 (t80) cc_final: 0.6317 (m-80) REVERT: E 112 ARG cc_start: 0.4499 (OUTLIER) cc_final: 0.4004 (ppp-140) REVERT: E 171 ASP cc_start: 0.7253 (t70) cc_final: 0.6802 (t0) REVERT: F 19 LYS cc_start: 0.7662 (mmtt) cc_final: 0.7266 (mtmt) REVERT: F 143 LYS cc_start: 0.6711 (tttt) cc_final: 0.6453 (tptp) REVERT: F 166 PHE cc_start: 0.7012 (m-80) cc_final: 0.5873 (m-10) outliers start: 29 outliers final: 25 residues processed: 144 average time/residue: 0.1115 time to fit residues: 21.9204 Evaluate side-chains 149 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 90 TRP Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 176 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 73 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 102 optimal weight: 0.0000 chunk 61 optimal weight: 3.9990 chunk 70 optimal weight: 0.0030 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.225125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.185260 restraints weight = 11738.956| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 2.98 r_work: 0.3883 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9926 Z= 0.108 Angle : 0.542 6.735 13520 Z= 0.282 Chirality : 0.043 0.136 1532 Planarity : 0.004 0.047 1702 Dihedral : 4.056 17.508 1348 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.38 % Favored : 95.30 % Rotamer: Outliers : 2.59 % Allowed : 12.59 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.25), residues: 1234 helix: 1.75 (0.39), residues: 204 sheet: 0.83 (0.24), residues: 518 loop : -0.83 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 184 TYR 0.012 0.001 TYR F 95 PHE 0.007 0.001 PHE E 213 TRP 0.012 0.001 TRP B 56 HIS 0.003 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9926) covalent geometry : angle 0.54204 (13520) hydrogen bonds : bond 0.03594 ( 457) hydrogen bonds : angle 4.75413 ( 1224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.7200 (mmm) cc_final: 0.6982 (mtm) REVERT: A 89 MET cc_start: 0.6552 (mpt) cc_final: 0.6202 (mtm) REVERT: A 107 MET cc_start: 0.7613 (mmt) cc_final: 0.7224 (mmt) REVERT: B 105 ARG cc_start: 0.6947 (mmt180) cc_final: 0.6733 (mpt180) REVERT: B 107 MET cc_start: 0.5814 (ptm) cc_final: 0.4994 (ptt) REVERT: B 132 MET cc_start: 0.7632 (mtt) cc_final: 0.7197 (mtp) REVERT: B 183 GLN cc_start: 0.8042 (tp40) cc_final: 0.7809 (pt0) REVERT: C 18 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7756 (ttm110) REVERT: C 193 HIS cc_start: 0.5745 (m-70) cc_final: 0.5313 (m-70) REVERT: E 112 ARG cc_start: 0.4358 (OUTLIER) cc_final: 0.3916 (ppp-140) REVERT: E 171 ASP cc_start: 0.7293 (t70) cc_final: 0.6882 (t0) REVERT: F 17 SER cc_start: 0.7478 (m) cc_final: 0.7024 (t) REVERT: F 19 LYS cc_start: 0.7687 (mmtt) cc_final: 0.7289 (mtmt) REVERT: F 143 LYS cc_start: 0.6551 (tttt) cc_final: 0.6327 (tptp) REVERT: F 166 PHE cc_start: 0.6966 (m-80) cc_final: 0.5808 (m-10) outliers start: 28 outliers final: 22 residues processed: 153 average time/residue: 0.0993 time to fit residues: 21.2639 Evaluate side-chains 152 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 SER Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 90 TRP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 176 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 43 optimal weight: 0.0370 chunk 94 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 85 optimal weight: 0.1980 chunk 119 optimal weight: 0.0050 chunk 13 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 106 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 overall best weight: 0.3272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 96 ASN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.226030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.188433 restraints weight = 11746.463| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 2.67 r_work: 0.3925 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9926 Z= 0.099 Angle : 0.533 8.120 13520 Z= 0.274 Chirality : 0.042 0.137 1532 Planarity : 0.004 0.047 1702 Dihedral : 3.924 17.068 1348 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.32 % Favored : 96.35 % Rotamer: Outliers : 1.85 % Allowed : 13.89 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.25), residues: 1234 helix: 1.85 (0.39), residues: 204 sheet: 0.89 (0.23), residues: 522 loop : -0.75 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 184 TYR 0.014 0.001 TYR F 95 PHE 0.007 0.001 PHE C 213 TRP 0.012 0.001 TRP B 56 HIS 0.003 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 9926) covalent geometry : angle 0.53336 (13520) hydrogen bonds : bond 0.03276 ( 457) hydrogen bonds : angle 4.58113 ( 1224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.369 Fit side-chains REVERT: A 60 LEU cc_start: 0.8294 (tt) cc_final: 0.8093 (tp) REVERT: A 107 MET cc_start: 0.7562 (mmt) cc_final: 0.7149 (mmt) REVERT: B 107 MET cc_start: 0.5663 (ptm) cc_final: 0.4854 (ptt) REVERT: B 132 MET cc_start: 0.7562 (mtt) cc_final: 0.7166 (mtp) REVERT: C 18 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7645 (ttm170) REVERT: C 193 HIS cc_start: 0.5693 (m-70) cc_final: 0.5270 (m-70) REVERT: D 19 LYS cc_start: 0.7381 (mttm) cc_final: 0.6990 (mmtt) REVERT: E 112 ARG cc_start: 0.4453 (OUTLIER) cc_final: 0.3984 (ppp-140) REVERT: E 171 ASP cc_start: 0.7337 (t70) cc_final: 0.7010 (t0) REVERT: E 180 SER cc_start: 0.7549 (t) cc_final: 0.7337 (t) REVERT: F 19 LYS cc_start: 0.7643 (mmtt) cc_final: 0.7325 (mtmt) REVERT: F 166 PHE cc_start: 0.7016 (m-80) cc_final: 0.5784 (m-10) outliers start: 20 outliers final: 17 residues processed: 150 average time/residue: 0.0912 time to fit residues: 19.8768 Evaluate side-chains 148 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain B residue 39 ASN Chi-restraints excluded: chain B residue 90 TRP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 195 ASN Chi-restraints excluded: chain B residue 197 TYR Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain D residue 195 CYS Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 112 ARG Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 163 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 44 optimal weight: 0.0970 chunk 97 optimal weight: 0.0070 chunk 2 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.227097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.186851 restraints weight = 11767.180| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 2.69 r_work: 0.3939 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9926 Z= 0.105 Angle : 0.548 7.349 13520 Z= 0.280 Chirality : 0.043 0.140 1532 Planarity : 0.004 0.047 1702 Dihedral : 3.914 17.310 1348 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.97 % Favored : 95.71 % Rotamer: Outliers : 2.22 % Allowed : 14.54 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.25), residues: 1234 helix: 1.85 (0.39), residues: 204 sheet: 0.92 (0.24), residues: 522 loop : -0.75 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 184 TYR 0.014 0.001 TYR F 95 PHE 0.007 0.001 PHE E 213 TRP 0.011 0.001 TRP B 56 HIS 0.003 0.001 HIS D 199 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9926) covalent geometry : angle 0.54798 (13520) hydrogen bonds : bond 0.03410 ( 457) hydrogen bonds : angle 4.58308 ( 1224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2643.94 seconds wall clock time: 46 minutes 10.13 seconds (2770.13 seconds total)