Starting phenix.real_space_refine on Tue Jan 13 14:09:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fvi_29488/01_2026/8fvi_29488.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fvi_29488/01_2026/8fvi_29488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fvi_29488/01_2026/8fvi_29488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fvi_29488/01_2026/8fvi_29488.map" model { file = "/net/cci-nas-00/data/ceres_data/8fvi_29488/01_2026/8fvi_29488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fvi_29488/01_2026/8fvi_29488.cif" } resolution = 3.24 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= 0.005 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 18 5.49 5 S 38 5.16 5 C 4256 2.51 5 N 1180 2.21 5 O 1280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6774 Number of models: 1 Model: "" Number of chains: 10 Chain: "0" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1139 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "1" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1332 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 8, 'TRANS': 151} Chain breaks: 3 Chain: "A" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1500 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 169} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 9} Link IDs: {'rna3p': 9} Chain: "C" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 177 Classifications: {'DNA': 1, 'RNA': 8} Modifications used: {'5*END': 1, 'rna3p_pur': 8} Link IDs: {'rna3p': 8} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "x" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1054 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "y" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 676 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain breaks: 1 Chain: "z" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 691 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain breaks: 1 Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2047 SG CYS 1 114 51.214 46.880 68.310 1.00 47.00 S ATOM 2194 SG CYS 1 133 52.611 50.239 66.801 1.00 51.18 S ATOM 3159 SG CYS A 85 33.533 42.839 33.330 1.00 41.86 S ATOM 3177 SG CYS A 88 30.209 41.819 34.540 1.00 32.60 S Time building chain proxies: 1.65, per 1000 atoms: 0.24 Number of scatterers: 6774 At special positions: 0 Unit cell: (75.48, 92.82, 120.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 38 16.00 P 18 15.00 O 1280 8.00 N 1180 7.00 C 4256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 58 " distance=2.03 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: 0.66 Conformation dependent library (CDL) restraints added in 267.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 1 201 " pdb="ZN ZN 1 201 " - pdb=" NE2 HIS 1 108 " pdb="ZN ZN 1 201 " - pdb=" NE2 HIS 1 139 " pdb="ZN ZN 1 201 " - pdb=" SG CYS 1 133 " pdb="ZN ZN 1 201 " - pdb=" SG CYS 1 114 " pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" ND1 HIS A 54 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 88 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 85 " Number of angles added : 2 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 49.5% alpha, 13.9% beta 8 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain '0' and resid 7 through 15 removed outlier: 3.894A pdb=" N PHE 0 12 " --> pdb=" O GLN 0 8 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU 0 13 " --> pdb=" O ARG 0 9 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN 0 14 " --> pdb=" O SER 0 10 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU 0 15 " --> pdb=" O LYS 0 11 " (cutoff:3.500A) Processing helix chain '0' and resid 15 through 22 Processing helix chain '0' and resid 36 through 50 removed outlier: 3.564A pdb=" N ASP 0 50 " --> pdb=" O ASN 0 46 " (cutoff:3.500A) Processing helix chain '0' and resid 72 through 74 No H-bonds generated for 'chain '0' and resid 72 through 74' Processing helix chain '0' and resid 128 through 135 Processing helix chain '0' and resid 137 through 149 Processing helix chain '1' and resid 14 through 30 removed outlier: 3.533A pdb=" N ILE 1 18 " --> pdb=" O ASP 1 14 " (cutoff:3.500A) Processing helix chain '1' and resid 99 through 109 Processing helix chain '1' and resid 116 through 118 No H-bonds generated for 'chain '1' and resid 116 through 118' Processing helix chain '1' and resid 119 through 126 Processing helix chain '1' and resid 135 through 139 Processing helix chain '1' and resid 145 through 155 Processing helix chain '1' and resid 166 through 171 removed outlier: 3.530A pdb=" N LEU 1 170 " --> pdb=" O SER 1 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 54 through 67 removed outlier: 3.742A pdb=" N GLY A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 99 Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 137 through 148 Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.635A pdb=" N LYS A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing helix chain 'x' and resid 18 through 30 Proline residue: x 24 - end of helix Processing helix chain 'x' and resid 31 through 33 No H-bonds generated for 'chain 'x' and resid 31 through 33' Processing helix chain 'x' and resid 36 through 54 removed outlier: 4.003A pdb=" N ASP x 54 " --> pdb=" O VAL x 50 " (cutoff:3.500A) Processing helix chain 'x' and resid 56 through 82 removed outlier: 3.518A pdb=" N LYS x 60 " --> pdb=" O LYS x 56 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N HIS x 62 " --> pdb=" O PRO x 58 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER x 82 " --> pdb=" O ALA x 78 " (cutoff:3.500A) Processing helix chain 'x' and resid 85 through 107 Processing helix chain 'x' and resid 111 through 118 removed outlier: 4.362A pdb=" N GLU x 115 " --> pdb=" O PHE x 111 " (cutoff:3.500A) Processing helix chain 'x' and resid 134 through 147 Processing helix chain 'y' and resid 23 through 28 Processing helix chain 'y' and resid 31 through 36 removed outlier: 3.523A pdb=" N ILE y 34 " --> pdb=" O VAL y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 56 through 61 removed outlier: 3.522A pdb=" N CYS y 60 " --> pdb=" O THR y 56 " (cutoff:3.500A) Processing helix chain 'y' and resid 63 through 67 Processing helix chain 'z' and resid 32 through 37 Processing helix chain 'z' and resid 39 through 47 removed outlier: 3.758A pdb=" N SER z 47 " --> pdb=" O LYS z 43 " (cutoff:3.500A) Processing helix chain 'z' and resid 66 through 84 removed outlier: 4.380A pdb=" N LYS z 72 " --> pdb=" O HIS z 68 " (cutoff:3.500A) Processing helix chain 'z' and resid 96 through 111 removed outlier: 4.012A pdb=" N LEU z 101 " --> pdb=" O PRO z 97 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLU z 102 " --> pdb=" O GLU z 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '0' and resid 99 through 103 removed outlier: 4.497A pdb=" N ALA 0 56 " --> pdb=" O THR 0 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 51 through 59 removed outlier: 6.469A pdb=" N THR 1 68 " --> pdb=" O SER 1 52 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU 1 54 " --> pdb=" O ILE 1 66 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE 1 66 " --> pdb=" O GLU 1 54 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N HIS 1 56 " --> pdb=" O LEU 1 64 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU 1 64 " --> pdb=" O HIS 1 56 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA 1 62 " --> pdb=" O PRO 1 58 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY 1 84 " --> pdb=" O TYR 1 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 48 removed outlier: 6.810A pdb=" N TYR A 74 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ARG A 105 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 76 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N PHE A 107 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N CYS A 78 " --> pdb=" O PHE A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'y' and resid 12 through 18 removed outlier: 4.263A pdb=" N ALA y 73 " --> pdb=" O PHE y 4 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET y 6 " --> pdb=" O ALA y 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'z' and resid 28 through 31 295 hydrogen bonds defined for protein. 837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1898 1.33 - 1.45: 1292 1.45 - 1.57: 3685 1.57 - 1.69: 35 1.69 - 1.81: 54 Bond restraints: 6964 Sorted by residual: bond pdb=" CA ASN A 49 " pdb=" C ASN A 49 " ideal model delta sigma weight residual 1.531 1.507 0.024 1.12e-02 7.97e+03 4.59e+00 bond pdb=" CA CYS A 58 " pdb=" C CYS A 58 " ideal model delta sigma weight residual 1.524 1.504 0.020 1.29e-02 6.01e+03 2.38e+00 bond pdb=" CA ARG y 29 " pdb=" C ARG y 29 " ideal model delta sigma weight residual 1.526 1.515 0.011 9.20e-03 1.18e+04 1.48e+00 bond pdb=" CA ALA A 55 " pdb=" CB ALA A 55 " ideal model delta sigma weight residual 1.529 1.512 0.018 1.58e-02 4.01e+03 1.27e+00 bond pdb=" C ASN A 158 " pdb=" N PRO A 159 " ideal model delta sigma weight residual 1.333 1.349 -0.016 1.44e-02 4.82e+03 1.23e+00 ... (remaining 6959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 9203 1.50 - 2.99: 227 2.99 - 4.49: 37 4.49 - 5.99: 10 5.99 - 7.48: 3 Bond angle restraints: 9480 Sorted by residual: angle pdb=" N ILE y 30 " pdb=" CA ILE y 30 " pdb=" C ILE y 30 " ideal model delta sigma weight residual 112.96 109.74 3.22 1.00e+00 1.00e+00 1.04e+01 angle pdb=" N GLY 0 75 " pdb=" CA GLY 0 75 " pdb=" C GLY 0 75 " ideal model delta sigma weight residual 112.65 108.47 4.18 1.30e+00 5.92e-01 1.04e+01 angle pdb=" N CYS A 58 " pdb=" CA CYS A 58 " pdb=" C CYS A 58 " ideal model delta sigma weight residual 111.36 108.12 3.24 1.09e+00 8.42e-01 8.81e+00 angle pdb=" N TYR A 160 " pdb=" CA TYR A 160 " pdb=" C TYR A 160 " ideal model delta sigma weight residual 111.11 107.66 3.45 1.20e+00 6.94e-01 8.28e+00 angle pdb=" C GLY y 54 " pdb=" N LYS y 55 " pdb=" CA LYS y 55 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 7.99e+00 ... (remaining 9475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.04: 3514 19.04 - 38.09: 491 38.09 - 57.13: 145 57.13 - 76.18: 30 76.18 - 95.22: 12 Dihedral angle restraints: 4192 sinusoidal: 1909 harmonic: 2283 Sorted by residual: dihedral pdb=" CB CYS A 53 " pdb=" SG CYS A 53 " pdb=" SG CYS A 58 " pdb=" CB CYS A 58 " ideal model delta sinusoidal sigma weight residual 93.00 179.82 -86.82 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CA TRP 1 70 " pdb=" C TRP 1 70 " pdb=" N GLY 1 71 " pdb=" CA GLY 1 71 " ideal model delta harmonic sigma weight residual 180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA HIS 1 110 " pdb=" C HIS 1 110 " pdb=" N TYR 1 111 " pdb=" CA TYR 1 111 " ideal model delta harmonic sigma weight residual -180.00 -161.05 -18.95 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 4189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 639 0.028 - 0.057: 243 0.057 - 0.085: 93 0.085 - 0.113: 45 0.113 - 0.142: 16 Chirality restraints: 1036 Sorted by residual: chirality pdb=" CG LEU A 125 " pdb=" CB LEU A 125 " pdb=" CD1 LEU A 125 " pdb=" CD2 LEU A 125 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CB THR y 56 " pdb=" CA THR y 56 " pdb=" OG1 THR y 56 " pdb=" CG2 THR y 56 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ARG 1 93 " pdb=" N ARG 1 93 " pdb=" C ARG 1 93 " pdb=" CB ARG 1 93 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 1033 not shown) Planarity restraints: 1146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE x 100 " -0.012 2.00e-02 2.50e+03 1.49e-02 3.87e+00 pdb=" CG PHE x 100 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE x 100 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE x 100 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE x 100 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE x 100 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE x 100 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG 0 35 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO 0 36 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO 0 36 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO 0 36 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY x 57 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO x 58 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO x 58 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO x 58 " -0.021 5.00e-02 4.00e+02 ... (remaining 1143 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 82 2.59 - 3.17: 5626 3.17 - 3.75: 11021 3.75 - 4.32: 14633 4.32 - 4.90: 24080 Nonbonded interactions: 55442 Sorted by model distance: nonbonded pdb=" O LEU A 11 " pdb=" OH TYR A 24 " model vdw 2.016 3.040 nonbonded pdb=" O PRO 1 58 " pdb=" OH TYR 1 111 " model vdw 2.191 3.040 nonbonded pdb=" O LYS z 80 " pdb=" OG1 THR z 84 " model vdw 2.197 3.040 nonbonded pdb=" NH2 ARG y 8 " pdb=" O GLU y 91 " model vdw 2.209 3.120 nonbonded pdb=" O SER A 129 " pdb=" OG SER A 129 " model vdw 2.221 3.040 ... (remaining 55437 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 30.090 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: 0.280 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.920 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 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 : 0.004 0.229 6972 Z= 0.180 Angle : 0.573 7.485 9484 Z= 0.310 Chirality : 0.040 0.142 1036 Planarity : 0.004 0.043 1146 Dihedral : 19.316 95.219 2695 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.15 % Allowed : 32.42 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.31), residues: 749 helix: 0.50 (0.30), residues: 326 sheet: -0.21 (0.53), residues: 101 loop : -1.29 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG y 68 TYR 0.014 0.002 TYR 1 148 PHE 0.034 0.002 PHE x 100 TRP 0.009 0.001 TRP 1 70 HIS 0.004 0.001 HIS 1 28 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6964) covalent geometry : angle 0.57228 ( 9480) SS BOND : bond 0.00052 ( 1) SS BOND : angle 1.69224 ( 2) hydrogen bonds : bond 0.13290 ( 311) hydrogen bonds : angle 5.70351 ( 869) metal coordination : bond 0.08675 ( 7) metal coordination : angle 1.54365 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7012 (mtp180) cc_final: 0.6741 (mtp180) REVERT: A 49 ASN cc_start: 0.6934 (m-40) cc_final: 0.6640 (t0) REVERT: A 148 PHE cc_start: 0.5291 (m-80) cc_final: 0.4800 (m-80) REVERT: x 101 PHE cc_start: 0.7247 (m-10) cc_final: 0.6967 (m-80) outliers start: 15 outliers final: 4 residues processed: 111 average time/residue: 0.1287 time to fit residues: 17.4597 Evaluate side-chains 86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 76 GLU Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 160 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 6 GLN 1 48 HIS ** 1 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 105 GLN 1 136 GLN x 62 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.185276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.149927 restraints weight = 9197.747| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.06 r_work: 0.3796 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6972 Z= 0.164 Angle : 0.585 6.758 9484 Z= 0.306 Chirality : 0.041 0.131 1036 Planarity : 0.005 0.058 1146 Dihedral : 10.044 94.774 1100 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.73 % Allowed : 30.13 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.31), residues: 749 helix: 0.46 (0.29), residues: 335 sheet: -0.57 (0.51), residues: 101 loop : -1.32 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG y 68 TYR 0.018 0.002 TYR 1 148 PHE 0.012 0.002 PHE 0 127 TRP 0.011 0.001 TRP x 19 HIS 0.004 0.001 HIS 1 43 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 6964) covalent geometry : angle 0.58325 ( 9480) SS BOND : bond 0.00135 ( 1) SS BOND : angle 1.94506 ( 2) hydrogen bonds : bond 0.04081 ( 311) hydrogen bonds : angle 4.75586 ( 869) metal coordination : bond 0.00678 ( 7) metal coordination : angle 2.97109 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 160 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6916 (mm) REVERT: x 96 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7050 (mm-30) REVERT: z 103 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7418 (tt) outliers start: 33 outliers final: 18 residues processed: 116 average time/residue: 0.1012 time to fit residues: 15.1197 Evaluate side-chains 103 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 55 ILE Chi-restraints excluded: chain 0 residue 97 LEU Chi-restraints excluded: chain 0 residue 106 VAL Chi-restraints excluded: chain 1 residue 6 GLN Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 32 SER Chi-restraints excluded: chain 1 residue 70 TRP Chi-restraints excluded: chain 1 residue 96 THR Chi-restraints excluded: chain 1 residue 160 ILE Chi-restraints excluded: chain 1 residue 170 LEU Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain x residue 61 ILE Chi-restraints excluded: chain x residue 134 ILE Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain z residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 0.0770 chunk 24 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 6 GLN ** 1 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 122 ASN x 62 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.185267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.149557 restraints weight = 9085.288| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.04 r_work: 0.3797 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6972 Z= 0.152 Angle : 0.560 6.388 9484 Z= 0.293 Chirality : 0.041 0.128 1036 Planarity : 0.005 0.048 1146 Dihedral : 9.655 96.234 1094 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.02 % Allowed : 30.56 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.31), residues: 749 helix: 0.43 (0.29), residues: 335 sheet: -0.88 (0.49), residues: 104 loop : -1.36 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG y 68 TYR 0.016 0.001 TYR 1 148 PHE 0.040 0.002 PHE x 101 TRP 0.019 0.001 TRP x 19 HIS 0.003 0.001 HIS 1 28 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 6964) covalent geometry : angle 0.55733 ( 9480) SS BOND : bond 0.00229 ( 1) SS BOND : angle 2.13380 ( 2) hydrogen bonds : bond 0.03771 ( 311) hydrogen bonds : angle 4.70897 ( 869) metal coordination : bond 0.00523 ( 7) metal coordination : angle 3.01189 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 70 TRP cc_start: 0.7186 (OUTLIER) cc_final: 0.6646 (m100) REVERT: 1 160 ILE cc_start: 0.7242 (OUTLIER) cc_final: 0.6900 (mm) REVERT: x 96 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7053 (mm-30) REVERT: z 103 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7450 (tt) outliers start: 35 outliers final: 19 residues processed: 118 average time/residue: 0.0979 time to fit residues: 14.9784 Evaluate side-chains 104 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 55 ILE Chi-restraints excluded: chain 0 residue 97 LEU Chi-restraints excluded: chain 0 residue 106 VAL Chi-restraints excluded: chain 1 residue 6 GLN Chi-restraints excluded: chain 1 residue 8 MET Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 32 SER Chi-restraints excluded: chain 1 residue 70 TRP Chi-restraints excluded: chain 1 residue 96 THR Chi-restraints excluded: chain 1 residue 145 SER Chi-restraints excluded: chain 1 residue 160 ILE Chi-restraints excluded: chain 1 residue 170 LEU Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain x residue 35 VAL Chi-restraints excluded: chain x residue 43 LEU Chi-restraints excluded: chain x residue 61 ILE Chi-restraints excluded: chain x residue 134 ILE Chi-restraints excluded: chain y residue 56 THR Chi-restraints excluded: chain z residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 46 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 49 optimal weight: 0.0870 chunk 29 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 6 GLN ** 1 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 140 ASN x 62 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.186473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.151190 restraints weight = 9201.679| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.08 r_work: 0.3813 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6972 Z= 0.127 Angle : 0.553 12.921 9484 Z= 0.283 Chirality : 0.040 0.128 1036 Planarity : 0.005 0.043 1146 Dihedral : 9.279 96.602 1091 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 5.60 % Allowed : 29.99 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.31), residues: 749 helix: 0.54 (0.29), residues: 335 sheet: -0.80 (0.49), residues: 104 loop : -1.34 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG y 68 TYR 0.014 0.001 TYR 1 148 PHE 0.045 0.002 PHE x 101 TRP 0.018 0.001 TRP x 19 HIS 0.003 0.001 HIS 1 28 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6964) covalent geometry : angle 0.55115 ( 9480) SS BOND : bond 0.00246 ( 1) SS BOND : angle 2.14428 ( 2) hydrogen bonds : bond 0.03501 ( 311) hydrogen bonds : angle 4.60614 ( 869) metal coordination : bond 0.00454 ( 7) metal coordination : angle 2.33217 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 88 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 149 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6882 (ptm-80) REVERT: 1 70 TRP cc_start: 0.7020 (OUTLIER) cc_final: 0.6607 (m100) REVERT: 1 160 ILE cc_start: 0.7222 (OUTLIER) cc_final: 0.6886 (mm) REVERT: x 77 GLN cc_start: 0.2808 (OUTLIER) cc_final: 0.1640 (mt0) REVERT: x 96 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7082 (mm-30) REVERT: z 103 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7457 (tt) outliers start: 39 outliers final: 18 residues processed: 119 average time/residue: 0.0884 time to fit residues: 14.0861 Evaluate side-chains 108 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 55 ILE Chi-restraints excluded: chain 0 residue 97 LEU Chi-restraints excluded: chain 0 residue 149 ARG Chi-restraints excluded: chain 1 residue 6 GLN Chi-restraints excluded: chain 1 residue 8 MET Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 32 SER Chi-restraints excluded: chain 1 residue 70 TRP Chi-restraints excluded: chain 1 residue 96 THR Chi-restraints excluded: chain 1 residue 160 ILE Chi-restraints excluded: chain 1 residue 170 LEU Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain x residue 35 VAL Chi-restraints excluded: chain x residue 61 ILE Chi-restraints excluded: chain x residue 77 GLN Chi-restraints excluded: chain x residue 134 ILE Chi-restraints excluded: chain y residue 56 THR Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain z residue 24 SER Chi-restraints excluded: chain z residue 103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 16 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 6 GLN ** 1 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 62 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.184781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.149221 restraints weight = 9247.497| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 1.95 r_work: 0.3795 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6972 Z= 0.162 Angle : 0.587 9.829 9484 Z= 0.299 Chirality : 0.041 0.132 1036 Planarity : 0.005 0.044 1146 Dihedral : 9.287 97.733 1091 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.16 % Allowed : 30.42 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.30), residues: 749 helix: 0.49 (0.29), residues: 334 sheet: -0.96 (0.49), residues: 104 loop : -1.43 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG y 68 TYR 0.020 0.002 TYR 1 148 PHE 0.038 0.002 PHE x 101 TRP 0.018 0.001 TRP x 19 HIS 0.004 0.001 HIS 1 28 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 6964) covalent geometry : angle 0.58433 ( 9480) SS BOND : bond 0.00243 ( 1) SS BOND : angle 2.14524 ( 2) hydrogen bonds : bond 0.03720 ( 311) hydrogen bonds : angle 4.69023 ( 869) metal coordination : bond 0.00554 ( 7) metal coordination : angle 3.60936 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 149 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.6354 (ptm-80) REVERT: 1 160 ILE cc_start: 0.7348 (OUTLIER) cc_final: 0.7038 (mm) REVERT: 1 168 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7540 (ptt180) REVERT: 1 169 LYS cc_start: 0.7372 (tmmt) cc_final: 0.7077 (tptm) REVERT: x 77 GLN cc_start: 0.2760 (OUTLIER) cc_final: 0.1517 (mt0) REVERT: x 96 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7144 (mm-30) REVERT: z 103 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7533 (tt) outliers start: 36 outliers final: 24 residues processed: 111 average time/residue: 0.0975 time to fit residues: 14.1520 Evaluate side-chains 110 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 55 ILE Chi-restraints excluded: chain 0 residue 88 LEU Chi-restraints excluded: chain 0 residue 97 LEU Chi-restraints excluded: chain 0 residue 149 ARG Chi-restraints excluded: chain 1 residue 6 GLN Chi-restraints excluded: chain 1 residue 8 MET Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 32 SER Chi-restraints excluded: chain 1 residue 70 TRP Chi-restraints excluded: chain 1 residue 96 THR Chi-restraints excluded: chain 1 residue 145 SER Chi-restraints excluded: chain 1 residue 160 ILE Chi-restraints excluded: chain 1 residue 168 ARG Chi-restraints excluded: chain 1 residue 170 LEU Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain x residue 35 VAL Chi-restraints excluded: chain x residue 43 LEU Chi-restraints excluded: chain x residue 61 ILE Chi-restraints excluded: chain x residue 77 GLN Chi-restraints excluded: chain x residue 98 ARG Chi-restraints excluded: chain x residue 134 ILE Chi-restraints excluded: chain y residue 56 THR Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain z residue 24 SER Chi-restraints excluded: chain z residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.0070 chunk 72 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 0.0970 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 6 GLN 1 83 GLN x 62 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.186300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.151115 restraints weight = 9252.651| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.08 r_work: 0.3819 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6972 Z= 0.129 Angle : 0.555 9.080 9484 Z= 0.284 Chirality : 0.040 0.127 1036 Planarity : 0.005 0.043 1146 Dihedral : 9.203 97.495 1091 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 5.60 % Allowed : 30.56 % Favored : 63.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.31), residues: 749 helix: 0.61 (0.29), residues: 334 sheet: -0.88 (0.49), residues: 104 loop : -1.40 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG y 68 TYR 0.017 0.001 TYR 1 148 PHE 0.034 0.002 PHE x 101 TRP 0.018 0.001 TRP x 19 HIS 0.003 0.001 HIS 1 28 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 6964) covalent geometry : angle 0.55353 ( 9480) SS BOND : bond 0.00242 ( 1) SS BOND : angle 2.09016 ( 2) hydrogen bonds : bond 0.03449 ( 311) hydrogen bonds : angle 4.58804 ( 869) metal coordination : bond 0.00501 ( 7) metal coordination : angle 2.49881 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 86 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 149 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6312 (ptm-80) REVERT: 1 70 TRP cc_start: 0.6947 (OUTLIER) cc_final: 0.6653 (m100) REVERT: 1 160 ILE cc_start: 0.7265 (OUTLIER) cc_final: 0.6932 (mm) REVERT: 1 169 LYS cc_start: 0.7292 (tmmt) cc_final: 0.6946 (tptm) REVERT: x 77 GLN cc_start: 0.2687 (OUTLIER) cc_final: 0.1474 (mt0) REVERT: z 103 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7486 (tt) outliers start: 39 outliers final: 25 residues processed: 116 average time/residue: 0.0894 time to fit residues: 13.7906 Evaluate side-chains 111 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 37 HIS Chi-restraints excluded: chain 0 residue 55 ILE Chi-restraints excluded: chain 0 residue 88 LEU Chi-restraints excluded: chain 0 residue 97 LEU Chi-restraints excluded: chain 0 residue 106 VAL Chi-restraints excluded: chain 0 residue 149 ARG Chi-restraints excluded: chain 1 residue 6 GLN Chi-restraints excluded: chain 1 residue 8 MET Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 32 SER Chi-restraints excluded: chain 1 residue 70 TRP Chi-restraints excluded: chain 1 residue 96 THR Chi-restraints excluded: chain 1 residue 145 SER Chi-restraints excluded: chain 1 residue 160 ILE Chi-restraints excluded: chain 1 residue 170 LEU Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain x residue 35 VAL Chi-restraints excluded: chain x residue 43 LEU Chi-restraints excluded: chain x residue 61 ILE Chi-restraints excluded: chain x residue 77 GLN Chi-restraints excluded: chain x residue 98 ARG Chi-restraints excluded: chain x residue 134 ILE Chi-restraints excluded: chain y residue 56 THR Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain z residue 24 SER Chi-restraints excluded: chain z residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 6 GLN ** x 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 62 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.185321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.149961 restraints weight = 9170.469| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.05 r_work: 0.3806 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6972 Z= 0.152 Angle : 0.584 8.382 9484 Z= 0.300 Chirality : 0.041 0.129 1036 Planarity : 0.005 0.043 1146 Dihedral : 9.204 96.990 1091 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 5.45 % Allowed : 31.28 % Favored : 63.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.30), residues: 749 helix: 0.52 (0.29), residues: 334 sheet: -0.93 (0.49), residues: 104 loop : -1.44 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG y 68 TYR 0.018 0.001 TYR 1 148 PHE 0.031 0.002 PHE x 101 TRP 0.021 0.001 TRP x 19 HIS 0.004 0.001 HIS 1 28 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6964) covalent geometry : angle 0.58093 ( 9480) SS BOND : bond 0.00233 ( 1) SS BOND : angle 2.09594 ( 2) hydrogen bonds : bond 0.03589 ( 311) hydrogen bonds : angle 4.63445 ( 869) metal coordination : bond 0.00509 ( 7) metal coordination : angle 3.30731 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 79 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 149 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6401 (ptm-80) REVERT: 1 70 TRP cc_start: 0.7076 (OUTLIER) cc_final: 0.6584 (m100) REVERT: 1 160 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.6992 (mm) REVERT: 1 169 LYS cc_start: 0.7309 (tmmt) cc_final: 0.6960 (tptm) REVERT: x 77 GLN cc_start: 0.2699 (OUTLIER) cc_final: 0.1425 (mt0) REVERT: z 103 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7506 (tt) outliers start: 38 outliers final: 25 residues processed: 109 average time/residue: 0.0821 time to fit residues: 11.8359 Evaluate side-chains 104 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 37 HIS Chi-restraints excluded: chain 0 residue 55 ILE Chi-restraints excluded: chain 0 residue 88 LEU Chi-restraints excluded: chain 0 residue 97 LEU Chi-restraints excluded: chain 0 residue 106 VAL Chi-restraints excluded: chain 0 residue 149 ARG Chi-restraints excluded: chain 1 residue 6 GLN Chi-restraints excluded: chain 1 residue 8 MET Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 32 SER Chi-restraints excluded: chain 1 residue 70 TRP Chi-restraints excluded: chain 1 residue 96 THR Chi-restraints excluded: chain 1 residue 145 SER Chi-restraints excluded: chain 1 residue 160 ILE Chi-restraints excluded: chain 1 residue 170 LEU Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain x residue 35 VAL Chi-restraints excluded: chain x residue 61 ILE Chi-restraints excluded: chain x residue 77 GLN Chi-restraints excluded: chain x residue 98 ARG Chi-restraints excluded: chain x residue 134 ILE Chi-restraints excluded: chain y residue 56 THR Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 75 VAL Chi-restraints excluded: chain z residue 24 SER Chi-restraints excluded: chain z residue 103 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 0.0050 chunk 67 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 6 GLN ** x 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 62 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.185741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.150609 restraints weight = 9244.908| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.07 r_work: 0.3815 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6972 Z= 0.137 Angle : 0.568 8.135 9484 Z= 0.292 Chirality : 0.040 0.129 1036 Planarity : 0.005 0.043 1146 Dihedral : 9.160 95.788 1091 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.88 % Allowed : 30.85 % Favored : 63.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.31), residues: 749 helix: 0.58 (0.29), residues: 334 sheet: -0.88 (0.50), residues: 104 loop : -1.41 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG y 68 TYR 0.017 0.001 TYR 1 148 PHE 0.029 0.002 PHE x 101 TRP 0.023 0.001 TRP x 19 HIS 0.003 0.001 HIS 1 28 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6964) covalent geometry : angle 0.56610 ( 9480) SS BOND : bond 0.00226 ( 1) SS BOND : angle 2.05589 ( 2) hydrogen bonds : bond 0.03457 ( 311) hydrogen bonds : angle 4.58966 ( 869) metal coordination : bond 0.00477 ( 7) metal coordination : angle 2.75980 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 83 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 96 TYR cc_start: 0.2815 (OUTLIER) cc_final: 0.2329 (m-80) REVERT: 0 149 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6400 (ptm-80) REVERT: 1 70 TRP cc_start: 0.6963 (OUTLIER) cc_final: 0.6687 (m100) REVERT: 1 160 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.6959 (mm) REVERT: 1 168 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7518 (ptt180) REVERT: 1 169 LYS cc_start: 0.7281 (tmmt) cc_final: 0.6933 (tptm) REVERT: x 77 GLN cc_start: 0.2665 (OUTLIER) cc_final: 0.1413 (mt0) REVERT: x 96 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6949 (mm-30) REVERT: z 103 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7510 (tt) outliers start: 41 outliers final: 27 residues processed: 115 average time/residue: 0.0988 time to fit residues: 14.8237 Evaluate side-chains 109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 37 HIS Chi-restraints excluded: chain 0 residue 55 ILE Chi-restraints excluded: chain 0 residue 62 THR Chi-restraints excluded: chain 0 residue 88 LEU Chi-restraints excluded: chain 0 residue 96 TYR Chi-restraints excluded: chain 0 residue 97 LEU Chi-restraints excluded: chain 0 residue 106 VAL Chi-restraints excluded: chain 0 residue 149 ARG Chi-restraints excluded: chain 1 residue 6 GLN Chi-restraints excluded: chain 1 residue 8 MET Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 32 SER Chi-restraints excluded: chain 1 residue 70 TRP Chi-restraints excluded: chain 1 residue 96 THR Chi-restraints excluded: chain 1 residue 145 SER Chi-restraints excluded: chain 1 residue 160 ILE Chi-restraints excluded: chain 1 residue 168 ARG Chi-restraints excluded: chain 1 residue 170 LEU Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain x residue 35 VAL Chi-restraints excluded: chain x residue 43 LEU Chi-restraints excluded: chain x residue 61 ILE Chi-restraints excluded: chain x residue 77 GLN Chi-restraints excluded: chain x residue 98 ARG Chi-restraints excluded: chain x residue 134 ILE Chi-restraints excluded: chain y residue 56 THR Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 75 VAL Chi-restraints excluded: chain z residue 24 SER Chi-restraints excluded: chain z residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 67 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 6 GLN x 32 GLN x 62 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.185458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.149785 restraints weight = 9211.674| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.15 r_work: 0.3798 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6972 Z= 0.148 Angle : 0.595 14.037 9484 Z= 0.301 Chirality : 0.041 0.127 1036 Planarity : 0.005 0.043 1146 Dihedral : 9.149 95.127 1091 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.74 % Allowed : 30.42 % Favored : 63.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.31), residues: 749 helix: 0.55 (0.29), residues: 334 sheet: -0.92 (0.49), residues: 104 loop : -1.43 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG y 68 TYR 0.022 0.001 TYR 1 148 PHE 0.026 0.002 PHE x 101 TRP 0.036 0.002 TRP x 19 HIS 0.004 0.001 HIS 1 28 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6964) covalent geometry : angle 0.59251 ( 9480) SS BOND : bond 0.00221 ( 1) SS BOND : angle 2.05337 ( 2) hydrogen bonds : bond 0.03544 ( 311) hydrogen bonds : angle 4.61170 ( 869) metal coordination : bond 0.00510 ( 7) metal coordination : angle 2.98259 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 79 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 96 TYR cc_start: 0.2843 (OUTLIER) cc_final: 0.2335 (m-80) REVERT: 0 149 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.6427 (ptm-80) REVERT: 1 70 TRP cc_start: 0.6999 (OUTLIER) cc_final: 0.6625 (m100) REVERT: 1 160 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.7021 (mm) REVERT: 1 168 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7531 (ptt180) REVERT: 1 169 LYS cc_start: 0.7306 (tmmt) cc_final: 0.6959 (tptm) REVERT: x 77 GLN cc_start: 0.2693 (OUTLIER) cc_final: 0.1786 (mt0) REVERT: x 96 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6975 (mm-30) REVERT: y 20 GLU cc_start: 0.5901 (mp0) cc_final: 0.5496 (mp0) REVERT: y 43 ARG cc_start: 0.4634 (OUTLIER) cc_final: 0.4323 (ptp90) REVERT: z 103 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7523 (tt) outliers start: 40 outliers final: 27 residues processed: 112 average time/residue: 0.1006 time to fit residues: 14.6080 Evaluate side-chains 111 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 37 HIS Chi-restraints excluded: chain 0 residue 55 ILE Chi-restraints excluded: chain 0 residue 62 THR Chi-restraints excluded: chain 0 residue 88 LEU Chi-restraints excluded: chain 0 residue 96 TYR Chi-restraints excluded: chain 0 residue 97 LEU Chi-restraints excluded: chain 0 residue 106 VAL Chi-restraints excluded: chain 0 residue 149 ARG Chi-restraints excluded: chain 1 residue 6 GLN Chi-restraints excluded: chain 1 residue 8 MET Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 32 SER Chi-restraints excluded: chain 1 residue 70 TRP Chi-restraints excluded: chain 1 residue 96 THR Chi-restraints excluded: chain 1 residue 145 SER Chi-restraints excluded: chain 1 residue 160 ILE Chi-restraints excluded: chain 1 residue 168 ARG Chi-restraints excluded: chain 1 residue 170 LEU Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain x residue 35 VAL Chi-restraints excluded: chain x residue 61 ILE Chi-restraints excluded: chain x residue 77 GLN Chi-restraints excluded: chain x residue 98 ARG Chi-restraints excluded: chain x residue 134 ILE Chi-restraints excluded: chain y residue 23 THR Chi-restraints excluded: chain y residue 43 ARG Chi-restraints excluded: chain y residue 56 THR Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 75 VAL Chi-restraints excluded: chain z residue 24 SER Chi-restraints excluded: chain z residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 18 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 0.0040 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 6 GLN ** x 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 62 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.186279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.152322 restraints weight = 9161.649| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.04 r_work: 0.3821 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6972 Z= 0.139 Angle : 0.604 12.351 9484 Z= 0.308 Chirality : 0.040 0.126 1036 Planarity : 0.005 0.043 1146 Dihedral : 9.118 94.139 1091 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.02 % Allowed : 31.56 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.31), residues: 749 helix: 0.56 (0.29), residues: 333 sheet: -0.87 (0.49), residues: 104 loop : -1.40 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG y 68 TYR 0.021 0.001 TYR 1 148 PHE 0.048 0.002 PHE x 101 TRP 0.034 0.001 TRP x 19 HIS 0.003 0.001 HIS 1 28 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 6964) covalent geometry : angle 0.60283 ( 9480) SS BOND : bond 0.00222 ( 1) SS BOND : angle 2.01843 ( 2) hydrogen bonds : bond 0.03524 ( 311) hydrogen bonds : angle 4.60692 ( 869) metal coordination : bond 0.00516 ( 7) metal coordination : angle 2.42672 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 96 TYR cc_start: 0.2818 (OUTLIER) cc_final: 0.2309 (m-80) REVERT: 0 149 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.6428 (ptm-80) REVERT: 1 160 ILE cc_start: 0.7287 (OUTLIER) cc_final: 0.6958 (mm) REVERT: 1 168 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7518 (ptt180) REVERT: 1 169 LYS cc_start: 0.7277 (tmmt) cc_final: 0.6932 (tptm) REVERT: x 77 GLN cc_start: 0.2686 (OUTLIER) cc_final: 0.1812 (mt0) REVERT: x 96 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7001 (mm-30) REVERT: y 20 GLU cc_start: 0.5926 (mp0) cc_final: 0.5526 (mp0) REVERT: y 43 ARG cc_start: 0.4604 (OUTLIER) cc_final: 0.4308 (ptp90) REVERT: z 103 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7491 (tt) outliers start: 35 outliers final: 24 residues processed: 111 average time/residue: 0.1024 time to fit residues: 14.7348 Evaluate side-chains 112 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 37 HIS Chi-restraints excluded: chain 0 residue 55 ILE Chi-restraints excluded: chain 0 residue 62 THR Chi-restraints excluded: chain 0 residue 96 TYR Chi-restraints excluded: chain 0 residue 97 LEU Chi-restraints excluded: chain 0 residue 106 VAL Chi-restraints excluded: chain 0 residue 149 ARG Chi-restraints excluded: chain 1 residue 6 GLN Chi-restraints excluded: chain 1 residue 8 MET Chi-restraints excluded: chain 1 residue 13 VAL Chi-restraints excluded: chain 1 residue 32 SER Chi-restraints excluded: chain 1 residue 96 THR Chi-restraints excluded: chain 1 residue 145 SER Chi-restraints excluded: chain 1 residue 160 ILE Chi-restraints excluded: chain 1 residue 168 ARG Chi-restraints excluded: chain 1 residue 170 LEU Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain x residue 35 VAL Chi-restraints excluded: chain x residue 61 ILE Chi-restraints excluded: chain x residue 77 GLN Chi-restraints excluded: chain x residue 134 ILE Chi-restraints excluded: chain y residue 43 ARG Chi-restraints excluded: chain y residue 56 THR Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 75 VAL Chi-restraints excluded: chain z residue 24 SER Chi-restraints excluded: chain z residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 16 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 7 optimal weight: 0.0770 chunk 29 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 0.0980 chunk 41 optimal weight: 0.5980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 6 GLN ** x 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 62 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.186872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.151964 restraints weight = 9187.229| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.05 r_work: 0.3828 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6972 Z= 0.128 Angle : 0.594 12.620 9484 Z= 0.303 Chirality : 0.040 0.126 1036 Planarity : 0.005 0.048 1146 Dihedral : 9.055 93.040 1091 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 5.16 % Allowed : 31.56 % Favored : 63.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.31), residues: 749 helix: 0.61 (0.29), residues: 333 sheet: -0.75 (0.51), residues: 99 loop : -1.39 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG y 68 TYR 0.019 0.001 TYR 1 148 PHE 0.024 0.002 PHE x 21 TRP 0.032 0.002 TRP x 19 HIS 0.003 0.001 HIS 1 28 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6964) covalent geometry : angle 0.59248 ( 9480) SS BOND : bond 0.00223 ( 1) SS BOND : angle 2.00003 ( 2) hydrogen bonds : bond 0.03382 ( 311) hydrogen bonds : angle 4.58052 ( 869) metal coordination : bond 0.00509 ( 7) metal coordination : angle 1.93585 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2547.52 seconds wall clock time: 44 minutes 27.03 seconds (2667.03 seconds total)