Starting phenix.real_space_refine on Tue Feb 11 15:54:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7czb_30508/02_2025/7czb_30508.cif Found real_map, /net/cci-nas-00/data/ceres_data/7czb_30508/02_2025/7czb_30508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7czb_30508/02_2025/7czb_30508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7czb_30508/02_2025/7czb_30508.map" model { file = "/net/cci-nas-00/data/ceres_data/7czb_30508/02_2025/7czb_30508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7czb_30508/02_2025/7czb_30508.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.055 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 40 5.16 5 C 4308 2.51 5 N 968 2.21 5 O 988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6304 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1576 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1576 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1576 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1576 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 4.45, per 1000 atoms: 0.71 Number of scatterers: 6304 At special positions: 0 Unit cell: (116.1, 124.7, 70.52, 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 40 16.00 O 988 8.00 N 968 7.00 C 4308 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 910.3 milliseconds 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1424 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 64.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 16 through 32 Proline residue: A 26 - end of helix removed outlier: 3.569A pdb=" N GLY A 32 " --> pdb=" O VAL A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 39 Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.924A pdb=" N TYR A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 89 removed outlier: 3.556A pdb=" N LEU A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.611A pdb=" N ASN A 105 " --> pdb=" O MET A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 removed outlier: 4.485A pdb=" N ILE A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 136 removed outlier: 3.549A pdb=" N ILE A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 166 Processing helix chain 'A' and resid 170 through 188 removed outlier: 3.683A pdb=" N ILE A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 176 " --> pdb=" O ASN A 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 31 Proline residue: B 26 - end of helix removed outlier: 3.512A pdb=" N LEU B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 39 Processing helix chain 'B' and resid 43 through 48 removed outlier: 4.452A pdb=" N TYR B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 70 through 90 removed outlier: 3.833A pdb=" N THR B 84 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG B 85 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU B 86 " --> pdb=" O TYR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 116 removed outlier: 4.277A pdb=" N TYR B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN B 105 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 137 removed outlier: 3.779A pdb=" N ILE B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 167 Processing helix chain 'B' and resid 173 through 189 removed outlier: 3.895A pdb=" N HIS B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 32 Proline residue: C 26 - end of helix removed outlier: 3.578A pdb=" N GLY C 32 " --> pdb=" O VAL C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 57 through 61 removed outlier: 3.948A pdb=" N TYR C 61 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 89 removed outlier: 3.550A pdb=" N LEU C 73 " --> pdb=" O GLY C 69 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR C 84 " --> pdb=" O TYR C 80 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG C 85 " --> pdb=" O GLN C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 removed outlier: 3.561A pdb=" N TYR C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN C 105 " --> pdb=" O MET C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 116 removed outlier: 4.540A pdb=" N ILE C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 136 removed outlier: 3.548A pdb=" N ILE C 126 " --> pdb=" O MET C 122 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 166 Processing helix chain 'C' and resid 170 through 188 removed outlier: 3.663A pdb=" N LEU C 174 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE C 175 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY C 176 " --> pdb=" O ASN C 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 31 Proline residue: D 26 - end of helix removed outlier: 3.555A pdb=" N LEU D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 43 through 48 removed outlier: 4.442A pdb=" N TYR D 48 " --> pdb=" O GLU D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 58 Processing helix chain 'D' and resid 70 through 90 removed outlier: 3.890A pdb=" N THR D 84 " --> pdb=" O TYR D 80 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG D 85 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU D 86 " --> pdb=" O TYR D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 116 removed outlier: 4.255A pdb=" N TYR D 98 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN D 105 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 137 removed outlier: 3.772A pdb=" N ILE D 126 " --> pdb=" O MET D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 167 Processing helix chain 'D' and resid 173 through 189 removed outlier: 3.880A pdb=" N HIS D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 870 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: 1.35 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1692 1.34 - 1.46: 1757 1.46 - 1.58: 3013 1.58 - 1.70: 2 1.70 - 1.82: 72 Bond restraints: 6536 Sorted by residual: bond pdb=" CA THR C 68 " pdb=" CB THR C 68 " ideal model delta sigma weight residual 1.526 1.566 -0.040 1.51e-02 4.39e+03 6.88e+00 bond pdb=" C ILE B 123 " pdb=" N PRO B 124 " ideal model delta sigma weight residual 1.336 1.363 -0.027 1.25e-02 6.40e+03 4.80e+00 bond pdb=" C ILE D 123 " pdb=" N PRO D 124 " ideal model delta sigma weight residual 1.336 1.363 -0.027 1.25e-02 6.40e+03 4.69e+00 bond pdb=" CB ASP C 139 " pdb=" CG ASP C 139 " ideal model delta sigma weight residual 1.516 1.567 -0.051 2.50e-02 1.60e+03 4.22e+00 bond pdb=" CB ASP A 139 " pdb=" CG ASP A 139 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.50e-02 1.60e+03 4.05e+00 ... (remaining 6531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 8550 2.41 - 4.83: 301 4.83 - 7.24: 47 7.24 - 9.66: 29 9.66 - 12.07: 1 Bond angle restraints: 8928 Sorted by residual: angle pdb=" C ARG C 138 " pdb=" N ASP C 139 " pdb=" CA ASP C 139 " ideal model delta sigma weight residual 121.54 133.61 -12.07 1.91e+00 2.74e-01 4.00e+01 angle pdb=" C ALA C 24 " pdb=" N VAL C 25 " pdb=" CA VAL C 25 " ideal model delta sigma weight residual 120.24 123.63 -3.39 6.30e-01 2.52e+00 2.89e+01 angle pdb=" C ALA A 24 " pdb=" N VAL A 25 " pdb=" CA VAL A 25 " ideal model delta sigma weight residual 120.24 123.49 -3.25 6.30e-01 2.52e+00 2.66e+01 angle pdb=" C ARG A 138 " pdb=" N ASP A 139 " pdb=" CA ASP A 139 " ideal model delta sigma weight residual 125.02 134.02 -9.00 1.76e+00 3.23e-01 2.61e+01 angle pdb=" C ALA D 152 " pdb=" N CYS D 153 " pdb=" CA CYS D 153 " ideal model delta sigma weight residual 121.54 129.78 -8.24 1.91e+00 2.74e-01 1.86e+01 ... (remaining 8923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 3073 15.62 - 31.23: 422 31.23 - 46.85: 115 46.85 - 62.46: 15 62.46 - 78.08: 11 Dihedral angle restraints: 3636 sinusoidal: 1384 harmonic: 2252 Sorted by residual: dihedral pdb=" CA ARG A 54 " pdb=" C ARG A 54 " pdb=" N PRO A 55 " pdb=" CA PRO A 55 " ideal model delta harmonic sigma weight residual 180.00 153.48 26.52 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA ARG C 54 " pdb=" C ARG C 54 " pdb=" N PRO C 55 " pdb=" CA PRO C 55 " ideal model delta harmonic sigma weight residual 180.00 154.78 25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA MET D 118 " pdb=" C MET D 118 " pdb=" N GLN D 119 " pdb=" CA GLN D 119 " ideal model delta harmonic sigma weight residual -180.00 -160.07 -19.93 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 3633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 837 0.091 - 0.183: 116 0.183 - 0.274: 9 0.274 - 0.365: 0 0.365 - 0.456: 2 Chirality restraints: 964 Sorted by residual: chirality pdb=" CB ILE C 11 " pdb=" CA ILE C 11 " pdb=" CG1 ILE C 11 " pdb=" CG2 ILE C 11 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.21e+00 chirality pdb=" CB ILE A 11 " pdb=" CA ILE A 11 " pdb=" CG1 ILE A 11 " pdb=" CG2 ILE A 11 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CA ARG C 94 " pdb=" N ARG C 94 " pdb=" C ARG C 94 " pdb=" CB ARG C 94 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 961 not shown) Planarity restraints: 1084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 54 " 0.054 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO C 55 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 54 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO A 55 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 55 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 55 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 25 " 0.036 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A 26 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " 0.030 5.00e-02 4.00e+02 ... (remaining 1081 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2187 2.87 - 3.38: 5885 3.38 - 3.88: 9807 3.88 - 4.39: 9919 4.39 - 4.90: 17266 Nonbonded interactions: 45064 Sorted by model distance: nonbonded pdb=" O ILE C 159 " pdb=" ND2 ASN C 163 " model vdw 2.360 3.120 nonbonded pdb=" O ILE A 159 " pdb=" ND2 ASN A 163 " model vdw 2.362 3.120 nonbonded pdb=" O TRP A 133 " pdb=" ND2 ASN A 137 " model vdw 2.375 3.120 nonbonded pdb=" O TRP C 133 " pdb=" ND2 ASN C 137 " model vdw 2.376 3.120 nonbonded pdb=" O TYR A 131 " pdb=" NE2 GLN A 135 " model vdw 2.383 3.120 ... (remaining 45059 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 17.410 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.005 0.058 6536 Z= 0.314 Angle : 1.117 12.073 8928 Z= 0.601 Chirality : 0.063 0.456 964 Planarity : 0.007 0.082 1084 Dihedral : 15.722 78.075 2212 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 0.47 % Allowed : 11.01 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.95 (0.24), residues: 768 helix: -2.64 (0.18), residues: 430 sheet: None (None), residues: 0 loop : -4.19 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 145 HIS 0.001 0.000 HIS A 181 PHE 0.030 0.002 PHE B 188 TYR 0.016 0.002 TYR A 183 ARG 0.005 0.001 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 233 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8599 (ttp) cc_final: 0.8369 (tmm) REVERT: A 183 TYR cc_start: 0.8821 (t80) cc_final: 0.8586 (t80) REVERT: B 59 THR cc_start: 0.9027 (p) cc_final: 0.8815 (m) REVERT: B 104 PHE cc_start: 0.8742 (t80) cc_final: 0.8368 (t80) REVERT: B 123 ILE cc_start: 0.8975 (mp) cc_final: 0.8457 (mm) REVERT: B 162 PHE cc_start: 0.7562 (m-10) cc_final: 0.7297 (m-80) REVERT: B 185 PHE cc_start: 0.8702 (t80) cc_final: 0.8494 (t80) REVERT: C 187 MET cc_start: 0.7799 (tmm) cc_final: 0.7245 (tmm) REVERT: D 85 ARG cc_start: 0.8550 (mmt90) cc_final: 0.8145 (mmm-85) REVERT: D 104 PHE cc_start: 0.8810 (t80) cc_final: 0.8351 (t80) REVERT: D 106 TRP cc_start: 0.8995 (t60) cc_final: 0.8347 (t60) REVERT: D 121 LEU cc_start: 0.9090 (tp) cc_final: 0.8878 (tp) REVERT: D 123 ILE cc_start: 0.9042 (mp) cc_final: 0.8460 (mm) outliers start: 3 outliers final: 0 residues processed: 234 average time/residue: 0.1907 time to fit residues: 57.1028 Evaluate side-chains 173 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 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 81 GLN B 172 ASN B 177 ASN D 137 ASN D 172 ASN D 177 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.142638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.116191 restraints weight = 14227.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.119195 restraints weight = 8501.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.121207 restraints weight = 6234.653| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6536 Z= 0.211 Angle : 0.776 8.970 8928 Z= 0.384 Chirality : 0.045 0.224 964 Planarity : 0.006 0.065 1084 Dihedral : 5.305 20.773 864 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 4.09 % Allowed : 20.60 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.29), residues: 768 helix: -1.05 (0.23), residues: 454 sheet: None (None), residues: 0 loop : -4.01 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 53 HIS 0.000 0.000 HIS D 181 PHE 0.013 0.001 PHE B 91 TYR 0.014 0.002 TYR B 77 ARG 0.006 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7435 (tmm) cc_final: 0.7023 (tmm) REVERT: B 104 PHE cc_start: 0.8739 (t80) cc_final: 0.8305 (t80) REVERT: B 106 TRP cc_start: 0.9031 (t60) cc_final: 0.8437 (t60) REVERT: B 136 LEU cc_start: 0.8721 (mm) cc_final: 0.8322 (mm) REVERT: C 187 MET cc_start: 0.7794 (tmm) cc_final: 0.7127 (tmm) REVERT: D 16 ARG cc_start: 0.7258 (ptt180) cc_final: 0.6984 (ptp-170) REVERT: D 85 ARG cc_start: 0.8606 (mmt90) cc_final: 0.8082 (mmm-85) REVERT: D 104 PHE cc_start: 0.8782 (t80) cc_final: 0.8399 (t80) outliers start: 26 outliers final: 16 residues processed: 203 average time/residue: 0.1711 time to fit residues: 45.7548 Evaluate side-chains 192 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TRP Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain C residue 42 TRP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 139 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 53 TRP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 188 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 17 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.137100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.110300 restraints weight = 14569.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113203 restraints weight = 8721.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.115115 restraints weight = 6384.786| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6536 Z= 0.298 Angle : 0.791 7.489 8928 Z= 0.390 Chirality : 0.047 0.212 964 Planarity : 0.005 0.065 1084 Dihedral : 5.128 20.591 864 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.89 % Favored : 87.11 % Rotamer: Outliers : 6.60 % Allowed : 21.54 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.30), residues: 768 helix: -0.48 (0.24), residues: 456 sheet: None (None), residues: 0 loop : -3.82 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 53 HIS 0.001 0.000 HIS D 181 PHE 0.020 0.001 PHE B 91 TYR 0.019 0.002 TYR B 98 ARG 0.005 0.001 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.6231 (OUTLIER) cc_final: 0.5901 (m-10) REVERT: A 183 TYR cc_start: 0.8842 (t80) cc_final: 0.8621 (t80) REVERT: A 187 MET cc_start: 0.7596 (tmm) cc_final: 0.6951 (tmm) REVERT: A 188 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7455 (m-10) REVERT: B 104 PHE cc_start: 0.8766 (t80) cc_final: 0.8318 (t80) REVERT: B 106 TRP cc_start: 0.9090 (t60) cc_final: 0.8510 (t60) REVERT: C 48 TYR cc_start: 0.6222 (OUTLIER) cc_final: 0.5951 (m-10) REVERT: C 178 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8384 (pp) REVERT: C 187 MET cc_start: 0.7888 (tmm) cc_final: 0.7122 (tmm) REVERT: D 85 ARG cc_start: 0.8692 (mmt90) cc_final: 0.8007 (tpp80) REVERT: D 104 PHE cc_start: 0.8811 (t80) cc_final: 0.8442 (t80) REVERT: D 118 MET cc_start: 0.6882 (tpp) cc_final: 0.6667 (tpt) outliers start: 42 outliers final: 25 residues processed: 199 average time/residue: 0.1692 time to fit residues: 44.4184 Evaluate side-chains 203 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TRP Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain C residue 42 TRP Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 188 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.0270 chunk 74 optimal weight: 0.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 181 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.141166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.114262 restraints weight = 14622.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.117294 restraints weight = 8781.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.119280 restraints weight = 6383.712| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6536 Z= 0.174 Angle : 0.727 8.854 8928 Z= 0.352 Chirality : 0.044 0.207 964 Planarity : 0.005 0.067 1084 Dihedral : 4.854 19.510 864 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 5.19 % Allowed : 25.63 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.31), residues: 768 helix: 0.04 (0.25), residues: 450 sheet: None (None), residues: 0 loop : -3.69 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 133 HIS 0.002 0.000 HIS D 181 PHE 0.019 0.001 PHE B 91 TYR 0.017 0.001 TYR C 98 ARG 0.005 0.001 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 TYR cc_start: 0.6260 (OUTLIER) cc_final: 0.6029 (m-10) REVERT: A 183 TYR cc_start: 0.8801 (t80) cc_final: 0.8586 (t80) REVERT: A 187 MET cc_start: 0.7629 (tmm) cc_final: 0.6953 (tmm) REVERT: B 103 LEU cc_start: 0.9390 (mm) cc_final: 0.9123 (mm) REVERT: B 104 PHE cc_start: 0.8777 (t80) cc_final: 0.8353 (t80) REVERT: B 106 TRP cc_start: 0.9038 (t60) cc_final: 0.8437 (t60) REVERT: C 48 TYR cc_start: 0.6312 (OUTLIER) cc_final: 0.6102 (m-10) REVERT: C 81 GLN cc_start: 0.9194 (tp40) cc_final: 0.8621 (tp40) REVERT: C 140 MET cc_start: 0.7999 (mpp) cc_final: 0.7675 (mpp) REVERT: C 178 LEU cc_start: 0.8614 (tt) cc_final: 0.8341 (pp) REVERT: C 187 MET cc_start: 0.7900 (tmm) cc_final: 0.7143 (tmm) REVERT: D 9 ARG cc_start: 0.6392 (mtt180) cc_final: 0.5697 (mtm180) REVERT: D 51 GLN cc_start: 0.7213 (tp-100) cc_final: 0.6969 (tp-100) REVERT: D 85 ARG cc_start: 0.8594 (mmt90) cc_final: 0.8046 (tpp80) REVERT: D 104 PHE cc_start: 0.8807 (t80) cc_final: 0.8459 (t80) outliers start: 33 outliers final: 18 residues processed: 217 average time/residue: 0.1666 time to fit residues: 47.9274 Evaluate side-chains 208 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 TRP Chi-restraints excluded: chain A residue 48 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain C residue 42 TRP Chi-restraints excluded: chain C residue 48 TYR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 188 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 0.0370 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 11 optimal weight: 0.0370 chunk 55 optimal weight: 1.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 135 GLN D 181 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.139830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113669 restraints weight = 14468.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.116638 restraints weight = 8516.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.118575 restraints weight = 6158.067| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6536 Z= 0.189 Angle : 0.723 7.705 8928 Z= 0.349 Chirality : 0.044 0.205 964 Planarity : 0.004 0.060 1084 Dihedral : 4.690 19.513 864 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 5.82 % Allowed : 27.67 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.32), residues: 768 helix: 0.24 (0.25), residues: 456 sheet: None (None), residues: 0 loop : -3.55 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 133 HIS 0.001 0.000 HIS D 181 PHE 0.017 0.001 PHE B 91 TYR 0.014 0.001 TYR A 82 ARG 0.006 0.001 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.9173 (tp40) cc_final: 0.8577 (tp40) REVERT: A 178 LEU cc_start: 0.8627 (tt) cc_final: 0.8284 (pp) REVERT: A 187 MET cc_start: 0.7622 (tmm) cc_final: 0.6885 (tmm) REVERT: B 71 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7725 (tt) REVERT: B 103 LEU cc_start: 0.9404 (mm) cc_final: 0.9139 (mm) REVERT: B 104 PHE cc_start: 0.8779 (t80) cc_final: 0.8355 (t80) REVERT: B 106 TRP cc_start: 0.9035 (t60) cc_final: 0.8467 (t60) REVERT: C 81 GLN cc_start: 0.9177 (tp40) cc_final: 0.8943 (tp40) REVERT: C 178 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8333 (pp) REVERT: C 183 TYR cc_start: 0.8849 (t80) cc_final: 0.8608 (t80) REVERT: C 187 MET cc_start: 0.7868 (tmm) cc_final: 0.7150 (tmm) REVERT: D 85 ARG cc_start: 0.8628 (mmt90) cc_final: 0.8145 (tpp80) REVERT: D 104 PHE cc_start: 0.8822 (t80) cc_final: 0.8472 (t80) outliers start: 37 outliers final: 25 residues processed: 209 average time/residue: 0.1720 time to fit residues: 46.8307 Evaluate side-chains 203 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 42 TRP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain C residue 42 TRP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 164 TYR Chi-restraints excluded: chain D residue 188 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 40 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 68 optimal weight: 0.0070 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 0.0270 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.141642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.115157 restraints weight = 14393.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.118148 restraints weight = 8594.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.120118 restraints weight = 6242.408| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6536 Z= 0.184 Angle : 0.743 10.003 8928 Z= 0.351 Chirality : 0.045 0.206 964 Planarity : 0.005 0.068 1084 Dihedral : 4.569 18.822 864 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 4.72 % Allowed : 29.25 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.32), residues: 768 helix: 0.44 (0.26), residues: 452 sheet: None (None), residues: 0 loop : -3.51 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 133 HIS 0.001 0.000 HIS A 181 PHE 0.016 0.001 PHE D 91 TYR 0.014 0.001 TYR C 82 ARG 0.007 0.001 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.9148 (tp40) cc_final: 0.8945 (tp40) REVERT: A 178 LEU cc_start: 0.8581 (tt) cc_final: 0.8248 (pp) REVERT: A 187 MET cc_start: 0.7784 (tmm) cc_final: 0.6974 (tmm) REVERT: B 71 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7693 (tt) REVERT: B 103 LEU cc_start: 0.9420 (mm) cc_final: 0.9148 (mm) REVERT: B 104 PHE cc_start: 0.8794 (t80) cc_final: 0.8383 (t80) REVERT: B 106 TRP cc_start: 0.9011 (t60) cc_final: 0.8466 (t60) REVERT: B 187 MET cc_start: 0.7415 (tmm) cc_final: 0.6719 (tmm) REVERT: C 81 GLN cc_start: 0.9156 (tp40) cc_final: 0.8927 (tp40) REVERT: C 178 LEU cc_start: 0.8612 (tt) cc_final: 0.8328 (pp) REVERT: C 187 MET cc_start: 0.7884 (tmm) cc_final: 0.7164 (tmm) REVERT: D 9 ARG cc_start: 0.6593 (mtt180) cc_final: 0.6260 (mtm180) REVERT: D 85 ARG cc_start: 0.8564 (mmt90) cc_final: 0.8115 (tpp80) REVERT: D 104 PHE cc_start: 0.8826 (t80) cc_final: 0.8481 (t80) outliers start: 30 outliers final: 21 residues processed: 207 average time/residue: 0.1608 time to fit residues: 44.6169 Evaluate side-chains 209 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 164 TYR Chi-restraints excluded: chain D residue 188 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 10 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 137 ASN D 181 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.138376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.110985 restraints weight = 14589.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113856 restraints weight = 8956.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115628 restraints weight = 6639.816| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6536 Z= 0.293 Angle : 0.794 8.632 8928 Z= 0.384 Chirality : 0.047 0.209 964 Planarity : 0.005 0.067 1084 Dihedral : 4.744 19.137 864 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.54 % Favored : 86.46 % Rotamer: Outliers : 6.29 % Allowed : 28.46 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.32), residues: 768 helix: 0.30 (0.25), residues: 456 sheet: None (None), residues: 0 loop : -3.56 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 133 HIS 0.002 0.001 HIS D 181 PHE 0.016 0.001 PHE B 91 TYR 0.013 0.002 TYR C 82 ARG 0.008 0.001 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.7893 (tmm) cc_final: 0.6994 (tmm) REVERT: B 103 LEU cc_start: 0.9451 (mm) cc_final: 0.9167 (mm) REVERT: B 104 PHE cc_start: 0.8854 (t80) cc_final: 0.8461 (t80) REVERT: B 106 TRP cc_start: 0.9076 (t60) cc_final: 0.8517 (t60) REVERT: B 123 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8847 (mp) REVERT: C 178 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8382 (pp) REVERT: C 187 MET cc_start: 0.7926 (tmm) cc_final: 0.7103 (tmm) REVERT: D 104 PHE cc_start: 0.8853 (t80) cc_final: 0.8542 (t80) REVERT: D 187 MET cc_start: 0.7550 (tmm) cc_final: 0.7011 (tmm) outliers start: 40 outliers final: 32 residues processed: 199 average time/residue: 0.1696 time to fit residues: 44.8211 Evaluate side-chains 213 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 42 TRP Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 42 TRP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 164 TYR Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 188 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 52 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 40 optimal weight: 0.0370 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.0770 chunk 73 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.141862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115678 restraints weight = 14310.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118583 restraints weight = 8577.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.120509 restraints weight = 6233.940| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6536 Z= 0.186 Angle : 0.775 10.719 8928 Z= 0.362 Chirality : 0.044 0.204 964 Planarity : 0.005 0.076 1084 Dihedral : 4.572 18.697 864 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 4.56 % Allowed : 31.45 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.32), residues: 768 helix: 0.48 (0.25), residues: 456 sheet: None (None), residues: 0 loop : -3.42 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 133 HIS 0.001 0.001 HIS A 181 PHE 0.015 0.001 PHE B 91 TYR 0.016 0.001 TYR A 183 ARG 0.008 0.001 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.9101 (tp40) cc_final: 0.8622 (tp40) REVERT: A 178 LEU cc_start: 0.8572 (tt) cc_final: 0.8265 (pp) REVERT: A 187 MET cc_start: 0.7826 (tmm) cc_final: 0.6916 (tmm) REVERT: A 188 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.7031 (m-80) REVERT: B 9 ARG cc_start: 0.6625 (mtt180) cc_final: 0.6277 (mtm180) REVERT: B 71 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7717 (tt) REVERT: B 103 LEU cc_start: 0.9435 (mm) cc_final: 0.9159 (mm) REVERT: B 104 PHE cc_start: 0.8876 (t80) cc_final: 0.8494 (t80) REVERT: B 106 TRP cc_start: 0.9019 (t60) cc_final: 0.8436 (t60) REVERT: B 187 MET cc_start: 0.7436 (tmm) cc_final: 0.6781 (tmm) REVERT: C 81 GLN cc_start: 0.9090 (tp40) cc_final: 0.8640 (tp40) REVERT: C 178 LEU cc_start: 0.8608 (tt) cc_final: 0.8318 (pp) REVERT: C 187 MET cc_start: 0.7924 (tmm) cc_final: 0.7041 (tmm) REVERT: D 51 GLN cc_start: 0.7104 (tp-100) cc_final: 0.6786 (tp-100) REVERT: D 104 PHE cc_start: 0.8873 (t80) cc_final: 0.8520 (t80) REVERT: D 187 MET cc_start: 0.7549 (tmm) cc_final: 0.7046 (tmm) outliers start: 29 outliers final: 22 residues processed: 216 average time/residue: 0.1701 time to fit residues: 49.3671 Evaluate side-chains 216 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 188 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 188 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 0.0670 chunk 50 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.0060 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 overall best weight: 0.4334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 181 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.142875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.116576 restraints weight = 14676.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.119562 restraints weight = 8632.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.121494 restraints weight = 6249.523| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6536 Z= 0.186 Angle : 0.780 10.361 8928 Z= 0.366 Chirality : 0.044 0.201 964 Planarity : 0.005 0.076 1084 Dihedral : 4.479 19.234 864 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 4.09 % Allowed : 32.23 % Favored : 63.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.33), residues: 768 helix: 0.51 (0.26), residues: 456 sheet: None (None), residues: 0 loop : -3.34 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 133 HIS 0.001 0.000 HIS C 181 PHE 0.014 0.001 PHE B 91 TYR 0.017 0.001 TYR A 183 ARG 0.007 0.001 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.9062 (tp40) cc_final: 0.8553 (tp40) REVERT: A 140 MET cc_start: 0.7527 (mpp) cc_final: 0.7293 (mpp) REVERT: A 178 LEU cc_start: 0.8586 (tt) cc_final: 0.8270 (pp) REVERT: A 187 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.6972 (tmm) REVERT: B 9 ARG cc_start: 0.6617 (mtt180) cc_final: 0.6273 (mtm180) REVERT: B 71 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7787 (tt) REVERT: B 103 LEU cc_start: 0.9454 (mm) cc_final: 0.9182 (mm) REVERT: B 104 PHE cc_start: 0.8871 (t80) cc_final: 0.8503 (t80) REVERT: B 106 TRP cc_start: 0.9027 (t60) cc_final: 0.8470 (t60) REVERT: B 187 MET cc_start: 0.7422 (tmm) cc_final: 0.6785 (tmm) REVERT: C 81 GLN cc_start: 0.9053 (tp40) cc_final: 0.8604 (tp40) REVERT: C 118 MET cc_start: 0.7625 (tpp) cc_final: 0.7340 (tpp) REVERT: C 178 LEU cc_start: 0.8585 (tt) cc_final: 0.8289 (pp) REVERT: C 187 MET cc_start: 0.7967 (tmm) cc_final: 0.7135 (tmm) REVERT: D 51 GLN cc_start: 0.7093 (tp-100) cc_final: 0.6744 (tp-100) REVERT: D 85 ARG cc_start: 0.8465 (mmm-85) cc_final: 0.8145 (mmm-85) REVERT: D 104 PHE cc_start: 0.8867 (t80) cc_final: 0.8540 (t80) REVERT: D 187 MET cc_start: 0.7515 (tmm) cc_final: 0.7011 (tmm) outliers start: 26 outliers final: 21 residues processed: 213 average time/residue: 0.1566 time to fit residues: 44.9496 Evaluate side-chains 209 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 188 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 23 optimal weight: 0.4980 chunk 30 optimal weight: 0.0050 chunk 64 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 ASN D 181 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.145441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.119224 restraints weight = 14433.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.122222 restraints weight = 8705.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.123980 restraints weight = 6346.271| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6536 Z= 0.191 Angle : 0.798 9.523 8928 Z= 0.375 Chirality : 0.045 0.205 964 Planarity : 0.005 0.070 1084 Dihedral : 4.533 18.124 864 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 3.62 % Allowed : 33.02 % Favored : 63.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.33), residues: 768 helix: 0.56 (0.26), residues: 456 sheet: None (None), residues: 0 loop : -3.29 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 133 HIS 0.002 0.001 HIS D 181 PHE 0.016 0.001 PHE D 144 TYR 0.018 0.001 TYR A 183 ARG 0.009 0.001 ARG B 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1536 Ramachandran restraints generated. 768 Oldfield, 0 Emsley, 768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.9057 (tp40) cc_final: 0.8557 (tp40) REVERT: A 178 LEU cc_start: 0.8587 (tt) cc_final: 0.8273 (pp) REVERT: A 187 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.6934 (tmm) REVERT: B 9 ARG cc_start: 0.6578 (mtt180) cc_final: 0.6250 (mtm180) REVERT: B 71 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7784 (tt) REVERT: B 103 LEU cc_start: 0.9440 (mm) cc_final: 0.9171 (mm) REVERT: B 104 PHE cc_start: 0.8881 (t80) cc_final: 0.8510 (t80) REVERT: B 106 TRP cc_start: 0.9039 (t60) cc_final: 0.8493 (t60) REVERT: B 187 MET cc_start: 0.7497 (tmm) cc_final: 0.6851 (tmm) REVERT: C 81 GLN cc_start: 0.9030 (tp40) cc_final: 0.8578 (tp40) REVERT: C 118 MET cc_start: 0.7585 (tpp) cc_final: 0.7368 (tpp) REVERT: C 178 LEU cc_start: 0.8583 (tt) cc_final: 0.8298 (pp) REVERT: C 187 MET cc_start: 0.7934 (tmm) cc_final: 0.7096 (tmm) REVERT: D 51 GLN cc_start: 0.7048 (tp-100) cc_final: 0.6723 (tp-100) REVERT: D 104 PHE cc_start: 0.8883 (t80) cc_final: 0.8534 (t80) REVERT: D 187 MET cc_start: 0.7543 (tmm) cc_final: 0.7038 (tmm) outliers start: 23 outliers final: 21 residues processed: 201 average time/residue: 0.1547 time to fit residues: 41.8769 Evaluate side-chains 207 residues out of total 664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 188 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 54 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 181 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.145499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.119333 restraints weight = 14724.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.122361 restraints weight = 8835.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.123773 restraints weight = 6439.676| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6536 Z= 0.192 Angle : 0.801 9.458 8928 Z= 0.379 Chirality : 0.045 0.205 964 Planarity : 0.005 0.071 1084 Dihedral : 4.597 20.587 864 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 4.40 % Allowed : 32.55 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.33), residues: 768 helix: 0.56 (0.26), residues: 456 sheet: None (None), residues: 0 loop : -3.21 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 133 HIS 0.002 0.000 HIS D 181 PHE 0.031 0.001 PHE B 162 TYR 0.015 0.001 TYR A 183 ARG 0.011 0.001 ARG D 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2115.44 seconds wall clock time: 38 minutes 33.10 seconds (2313.10 seconds total)