Starting phenix.real_space_refine on Thu May 1 02:05:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ub8_42078/05_2025/8ub8_42078.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ub8_42078/05_2025/8ub8_42078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ub8_42078/05_2025/8ub8_42078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ub8_42078/05_2025/8ub8_42078.map" model { file = "/net/cci-nas-00/data/ceres_data/8ub8_42078/05_2025/8ub8_42078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ub8_42078/05_2025/8ub8_42078.cif" } resolution = 3.28 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= -0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 143 5.49 5 S 37 5.16 5 C 6036 2.51 5 N 1861 2.21 5 O 2222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10299 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2690 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain: "B" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "C" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 914 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "D" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 893 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 876 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "F" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "G" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 311 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 3} Link IDs: {'rna3p': 13} Chain: "H" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 270 Classifications: {'RNA': 13} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 8} Link IDs: {'rna3p': 12} Chain: "I" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2481 Classifications: {'RNA': 116} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 51, 'rna3p_pyr': 48} Link IDs: {'rna2p': 17, 'rna3p': 98} Chain breaks: 2 Time building chain proxies: 7.10, per 1000 atoms: 0.69 Number of scatterers: 10299 At special positions: 0 Unit cell: (86, 98, 149, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 P 143 15.00 O 2222 8.00 N 1861 7.00 C 6036 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: 2.83 Conformation dependent library (CDL) restraints added in 965.1 milliseconds 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 3 sheets defined 75.0% alpha, 3.6% beta 43 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 4.74 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 14 through 27 removed outlier: 3.560A pdb=" N ASP A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 40 removed outlier: 3.857A pdb=" N GLU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.532A pdb=" N LEU A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 94 removed outlier: 3.957A pdb=" N ILE A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 98 Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.574A pdb=" N ILE A 146 " --> pdb=" O PHE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 183 through 203 removed outlier: 3.588A pdb=" N ALA A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 241 Processing helix chain 'A' and resid 273 through 289 Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.842A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 324 Processing helix chain 'B' and resid 10 through 32 removed outlier: 3.682A pdb=" N ARG B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 38 through 50 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 65 through 88 Processing helix chain 'B' and resid 95 through 122 Processing helix chain 'C' and resid 11 through 34 removed outlier: 3.657A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 51 through 62 removed outlier: 3.514A pdb=" N LEU C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 88 removed outlier: 3.592A pdb=" N LEU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 122 Processing helix chain 'D' and resid 14 through 34 removed outlier: 3.720A pdb=" N ARG D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 51 through 62 removed outlier: 3.590A pdb=" N LEU D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 removed outlier: 3.874A pdb=" N LEU D 68 " --> pdb=" O GLN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 121 removed outlier: 3.810A pdb=" N GLN D 103 " --> pdb=" O VAL D 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 34 removed outlier: 3.697A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Proline residue: E 29 - end of helix Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 51 through 62 removed outlier: 3.519A pdb=" N LEU E 55 " --> pdb=" O GLY E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 86 Processing helix chain 'E' and resid 95 through 121 Processing helix chain 'F' and resid 14 through 28 removed outlier: 3.605A pdb=" N GLU F 18 " --> pdb=" O MET F 14 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 64 through 87 removed outlier: 3.631A pdb=" N GLY F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 93 Proline residue: F 91 - end of helix No H-bonds generated for 'chain 'F' and resid 88 through 93' Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.118A pdb=" N LEU F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 213 removed outlier: 3.929A pdb=" N HIS A 248 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 260 484 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 109 hydrogen bonds 174 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 3.50 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 1743 1.33 - 1.46: 4503 1.46 - 1.60: 4271 1.60 - 1.74: 241 1.74 - 1.87: 62 Bond restraints: 10820 Sorted by residual: bond pdb=" CA GLN F 64 " pdb=" CB GLN F 64 " ideal model delta sigma weight residual 1.529 1.641 -0.112 1.64e-02 3.72e+03 4.66e+01 bond pdb=" O5' U I 24 " pdb=" C5' U I 24 " ideal model delta sigma weight residual 1.420 1.505 -0.085 1.50e-02 4.44e+03 3.23e+01 bond pdb=" CA ARG E 36 " pdb=" CB ARG E 36 " ideal model delta sigma weight residual 1.529 1.442 0.086 1.64e-02 3.72e+03 2.77e+01 bond pdb=" C PRO F 29 " pdb=" O PRO F 29 " ideal model delta sigma weight residual 1.237 1.190 0.048 1.32e-02 5.74e+03 1.31e+01 bond pdb=" CA ASN C 63 " pdb=" CB ASN C 63 " ideal model delta sigma weight residual 1.536 1.479 0.057 1.58e-02 4.01e+03 1.30e+01 ... (remaining 10815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 13778 2.26 - 4.51: 1349 4.51 - 6.76: 158 6.76 - 9.02: 26 9.02 - 11.27: 5 Bond angle restraints: 15316 Sorted by residual: angle pdb=" N VAL A 170 " pdb=" CA VAL A 170 " pdb=" C VAL A 170 " ideal model delta sigma weight residual 112.96 104.20 8.76 1.00e+00 1.00e+00 7.67e+01 angle pdb=" N ILE F 88 " pdb=" CA ILE F 88 " pdb=" C ILE F 88 " ideal model delta sigma weight residual 113.47 105.05 8.42 1.01e+00 9.80e-01 6.96e+01 angle pdb=" C3' G G 370 " pdb=" O3' G G 370 " pdb=" P G G 371 " ideal model delta sigma weight residual 120.20 108.93 11.27 1.50e+00 4.44e-01 5.65e+01 angle pdb=" C3' G G 372 " pdb=" O3' G G 372 " pdb=" P C G 373 " ideal model delta sigma weight residual 120.20 108.93 11.27 1.50e+00 4.44e-01 5.64e+01 angle pdb=" C3' G G 371 " pdb=" O3' G G 371 " pdb=" P G G 372 " ideal model delta sigma weight residual 120.20 109.25 10.95 1.50e+00 4.44e-01 5.33e+01 ... (remaining 15311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 6022 35.75 - 71.49: 622 71.49 - 107.24: 63 107.24 - 142.98: 2 142.98 - 178.73: 3 Dihedral angle restraints: 6712 sinusoidal: 4101 harmonic: 2611 Sorted by residual: dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual 232.00 53.27 178.73 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U I 3 " pdb=" C1' U I 3 " pdb=" N1 U I 3 " pdb=" C2 U I 3 " ideal model delta sinusoidal sigma weight residual -160.00 -83.65 -76.35 1 1.50e+01 4.44e-03 3.26e+01 dihedral pdb=" CA HIS A 5 " pdb=" C HIS A 5 " pdb=" N ARG A 6 " pdb=" CA ARG A 6 " ideal model delta harmonic sigma weight residual -180.00 -152.74 -27.26 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 6709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1479 0.133 - 0.266: 292 0.266 - 0.399: 30 0.399 - 0.532: 8 0.532 - 0.665: 4 Chirality restraints: 1813 Sorted by residual: chirality pdb=" P G H 117 " pdb=" OP1 G H 117 " pdb=" OP2 G H 117 " pdb=" O5' G H 117 " both_signs ideal model delta sigma weight residual True 2.41 3.08 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" P G G 369 " pdb=" OP1 G G 369 " pdb=" OP2 G G 369 " pdb=" O5' G G 369 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.06e+00 chirality pdb=" P U I 3 " pdb=" OP1 U I 3 " pdb=" OP2 U I 3 " pdb=" O5' U I 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.98e+00 ... (remaining 1810 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 28 " 0.091 2.00e-02 2.50e+03 4.79e-02 4.59e+01 pdb=" CG TYR F 28 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR F 28 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR F 28 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR F 28 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR F 28 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR F 28 " 0.034 2.00e-02 2.50e+03 pdb=" OH TYR F 28 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " 0.080 2.00e-02 2.50e+03 4.06e-02 3.30e+01 pdb=" CG TYR C 28 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 81 " 0.005 2.00e-02 2.50e+03 3.57e-02 3.18e+01 pdb=" CG TRP E 81 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP E 81 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP E 81 " 0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP E 81 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TRP E 81 " 0.038 2.00e-02 2.50e+03 pdb=" CE3 TRP E 81 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 81 " 0.033 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 81 " -0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP E 81 " -0.027 2.00e-02 2.50e+03 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 47 2.49 - 3.09: 7487 3.09 - 3.69: 19014 3.69 - 4.30: 28523 4.30 - 4.90: 41089 Nonbonded interactions: 96160 Sorted by model distance: nonbonded pdb=" O ARG A 6 " pdb=" OD1 ASN A 7 " model vdw 1.887 3.040 nonbonded pdb=" O ASN F 121 " pdb=" NH1 ARG F 122 " model vdw 2.083 3.120 nonbonded pdb=" OE1 GLN D 52 " pdb=" CE2 PHE D 56 " model vdw 2.198 3.340 nonbonded pdb=" OE1 GLU F 108 " pdb=" NH2 ARG F 111 " model vdw 2.285 3.120 nonbonded pdb=" O GLU D 21 " pdb=" OG SER D 25 " model vdw 2.289 3.040 ... (remaining 96155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = (chain 'D' and resid 13 through 121) selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } 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=0.00 max=1.00 mean=0.99 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: 2.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 31.270 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.112 10820 Z= 0.656 Angle : 1.426 11.275 15316 Z= 0.910 Chirality : 0.109 0.665 1813 Planarity : 0.013 0.124 1402 Dihedral : 23.559 178.728 5028 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 27.19 Ramachandran Plot: Outliers : 2.26 % Allowed : 8.70 % Favored : 89.04 % Rotamer: Outliers : 6.27 % Allowed : 16.53 % Favored : 77.20 % 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: -4.02 (0.22), residues: 885 helix: -2.01 (0.16), residues: 656 sheet: -4.26 (0.80), residues: 26 loop : -4.02 (0.35), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.013 TRP E 81 HIS 0.026 0.005 HIS A 88 PHE 0.062 0.012 PHE E 84 TYR 0.091 0.014 TYR F 28 ARG 0.036 0.004 ARG A 127 Details of bonding type rmsd hydrogen bonds : bond 0.19784 ( 593) hydrogen bonds : angle 9.02641 ( 1599) covalent geometry : bond 0.01074 (10820) covalent geometry : angle 1.42638 (15316) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.5413 (OUTLIER) cc_final: 0.5071 (p90) REVERT: A 111 PRO cc_start: 0.7939 (Cg_exo) cc_final: 0.7738 (Cg_endo) REVERT: A 112 ASP cc_start: 0.8570 (m-30) cc_final: 0.8269 (t0) REVERT: A 309 TRP cc_start: 0.6882 (m100) cc_final: 0.6657 (m100) REVERT: B 77 MET cc_start: 0.8180 (tpt) cc_final: 0.7837 (tpt) REVERT: C 91 PRO cc_start: 0.8287 (OUTLIER) cc_final: 0.7904 (Cg_endo) REVERT: D 18 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7220 (tp30) REVERT: D 26 TYR cc_start: 0.8019 (t80) cc_final: 0.7809 (t80) REVERT: D 95 THR cc_start: 0.7279 (p) cc_final: 0.7070 (p) REVERT: E 63 ASN cc_start: 0.7839 (t0) cc_final: 0.6734 (p0) outliers start: 47 outliers final: 16 residues processed: 195 average time/residue: 0.3114 time to fit residues: 78.1908 Evaluate side-chains 164 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 180 PRO Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 91 PRO Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 103 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 306 HIS B 92 HIS D 32 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 92 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.168154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128673 restraints weight = 13158.765| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.47 r_work: 0.3347 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10820 Z= 0.186 Angle : 0.703 8.659 15316 Z= 0.362 Chirality : 0.041 0.233 1813 Planarity : 0.006 0.043 1402 Dihedral : 23.588 177.237 3313 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.33 % Favored : 93.11 % Rotamer: Outliers : 4.93 % Allowed : 17.07 % Favored : 78.00 % 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: -1.80 (0.26), residues: 885 helix: -0.38 (0.18), residues: 670 sheet: -3.85 (0.72), residues: 26 loop : -3.42 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 81 HIS 0.012 0.001 HIS C 38 PHE 0.019 0.002 PHE D 56 TYR 0.016 0.002 TYR A 152 ARG 0.005 0.001 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.04953 ( 593) hydrogen bonds : angle 4.66096 ( 1599) covalent geometry : bond 0.00407 (10820) covalent geometry : angle 0.70344 (15316) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8439 (m-40) REVERT: A 69 TYR cc_start: 0.5802 (OUTLIER) cc_final: 0.5378 (p90) REVERT: A 72 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7516 (ttpp) REVERT: A 278 LYS cc_start: 0.7368 (mtpt) cc_final: 0.6645 (mmtt) REVERT: B 44 MET cc_start: 0.8989 (mtp) cc_final: 0.8587 (mtp) REVERT: B 108 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7509 (mm-30) REVERT: C 111 ARG cc_start: 0.8521 (ttm-80) cc_final: 0.8137 (ttp80) REVERT: D 62 SER cc_start: 0.8204 (OUTLIER) cc_final: 0.7714 (p) REVERT: D 95 THR cc_start: 0.7612 (p) cc_final: 0.7259 (p) outliers start: 37 outliers final: 14 residues processed: 188 average time/residue: 0.4119 time to fit residues: 99.3972 Evaluate side-chains 167 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 14 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.167525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.128891 restraints weight = 13354.708| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.43 r_work: 0.3345 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10820 Z= 0.185 Angle : 0.649 10.647 15316 Z= 0.331 Chirality : 0.038 0.189 1813 Planarity : 0.005 0.047 1402 Dihedral : 23.123 179.863 3292 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.44 % Favored : 92.99 % Rotamer: Outliers : 4.93 % Allowed : 18.27 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.28), residues: 885 helix: 0.35 (0.19), residues: 667 sheet: -3.08 (0.86), residues: 26 loop : -3.14 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 116 HIS 0.006 0.001 HIS A 27 PHE 0.017 0.002 PHE D 80 TYR 0.018 0.002 TYR D 26 ARG 0.010 0.001 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.04788 ( 593) hydrogen bonds : angle 4.37639 ( 1599) covalent geometry : bond 0.00415 (10820) covalent geometry : angle 0.64918 (15316) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8768 (m-40) cc_final: 0.8465 (m-40) REVERT: A 72 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7327 (ttpp) REVERT: A 278 LYS cc_start: 0.7365 (mtpt) cc_final: 0.6606 (mmtt) REVERT: B 44 MET cc_start: 0.8996 (mtp) cc_final: 0.8742 (mtp) REVERT: B 108 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7383 (mm-30) REVERT: C 111 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.8161 (ttp80) REVERT: D 67 LYS cc_start: 0.7757 (mtmt) cc_final: 0.7503 (mtmt) REVERT: D 95 THR cc_start: 0.7753 (p) cc_final: 0.7400 (p) outliers start: 37 outliers final: 17 residues processed: 172 average time/residue: 0.3281 time to fit residues: 72.0444 Evaluate side-chains 158 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS A 306 HIS A 313 HIS ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.162949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.123712 restraints weight = 13185.374| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.42 r_work: 0.3264 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10820 Z= 0.275 Angle : 0.702 8.504 15316 Z= 0.355 Chirality : 0.040 0.179 1813 Planarity : 0.005 0.044 1402 Dihedral : 23.014 179.691 3282 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.01 % Favored : 92.43 % Rotamer: Outliers : 4.80 % Allowed : 20.27 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.28), residues: 885 helix: 0.43 (0.19), residues: 666 sheet: -2.45 (0.90), residues: 26 loop : -3.09 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 318 HIS 0.011 0.002 HIS A 313 PHE 0.022 0.003 PHE D 80 TYR 0.019 0.002 TYR D 26 ARG 0.009 0.001 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.05012 ( 593) hydrogen bonds : angle 4.45386 ( 1599) covalent geometry : bond 0.00627 (10820) covalent geometry : angle 0.70203 (15316) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 2.879 Fit side-chains revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8881 (m-40) cc_final: 0.8510 (m-40) REVERT: A 67 LEU cc_start: 0.6426 (pp) cc_final: 0.6052 (mp) REVERT: A 110 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8290 (mtp180) REVERT: A 215 ASP cc_start: 0.8496 (p0) cc_final: 0.8258 (p0) REVERT: A 256 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7943 (mmt90) REVERT: A 278 LYS cc_start: 0.7375 (mtpt) cc_final: 0.6602 (mmtt) REVERT: B 44 MET cc_start: 0.9037 (mtp) cc_final: 0.8757 (mtp) REVERT: B 108 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7420 (mm-30) REVERT: C 111 ARG cc_start: 0.8603 (ttm-80) cc_final: 0.8123 (ttp80) REVERT: D 13 GLN cc_start: 0.4727 (pm20) cc_final: 0.4474 (pm20) REVERT: D 21 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7459 (mt-10) REVERT: D 95 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7644 (p) outliers start: 36 outliers final: 23 residues processed: 175 average time/residue: 0.3466 time to fit residues: 80.2567 Evaluate side-chains 171 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 70 optimal weight: 0.0370 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.168600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.128480 restraints weight = 13043.232| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.50 r_work: 0.3328 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10820 Z= 0.142 Angle : 0.598 7.085 15316 Z= 0.307 Chirality : 0.036 0.200 1813 Planarity : 0.005 0.053 1402 Dihedral : 22.819 179.963 3282 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.21 % Favored : 93.33 % Rotamer: Outliers : 4.80 % Allowed : 20.53 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.29), residues: 885 helix: 0.77 (0.20), residues: 667 sheet: -1.76 (0.96), residues: 26 loop : -3.14 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 116 HIS 0.010 0.001 HIS D 38 PHE 0.016 0.002 PHE A 231 TYR 0.017 0.001 TYR D 26 ARG 0.009 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.04416 ( 593) hydrogen bonds : angle 4.14007 ( 1599) covalent geometry : bond 0.00310 (10820) covalent geometry : angle 0.59840 (15316) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8899 (m-40) cc_final: 0.8573 (m-40) REVERT: A 67 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.6073 (mp) REVERT: A 275 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8267 (t) REVERT: A 278 LYS cc_start: 0.7233 (mtpt) cc_final: 0.6528 (mmtt) REVERT: B 44 MET cc_start: 0.8972 (mtp) cc_final: 0.8669 (mtp) REVERT: B 108 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7343 (mm-30) REVERT: C 64 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8154 (tp-100) REVERT: C 111 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.7963 (ttp80) REVERT: D 17 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8143 (p) REVERT: D 21 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7397 (mt-10) REVERT: D 95 THR cc_start: 0.7872 (p) cc_final: 0.7555 (p) outliers start: 36 outliers final: 19 residues processed: 169 average time/residue: 0.3195 time to fit residues: 69.8401 Evaluate side-chains 163 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 36 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.167457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.126743 restraints weight = 13198.543| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.52 r_work: 0.3316 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10820 Z= 0.172 Angle : 0.620 8.119 15316 Z= 0.317 Chirality : 0.036 0.218 1813 Planarity : 0.005 0.056 1402 Dihedral : 22.638 179.794 3278 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.89 % Favored : 92.66 % Rotamer: Outliers : 5.07 % Allowed : 21.07 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.28), residues: 885 helix: 0.91 (0.20), residues: 658 sheet: -1.01 (1.01), residues: 26 loop : -2.89 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 116 HIS 0.005 0.001 HIS A 313 PHE 0.018 0.002 PHE D 80 TYR 0.016 0.002 TYR D 26 ARG 0.012 0.001 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 593) hydrogen bonds : angle 4.16513 ( 1599) covalent geometry : bond 0.00388 (10820) covalent geometry : angle 0.61971 (15316) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8921 (m-40) cc_final: 0.8553 (m-40) REVERT: A 67 LEU cc_start: 0.6375 (OUTLIER) cc_final: 0.6161 (mp) REVERT: A 278 LYS cc_start: 0.7226 (mtpt) cc_final: 0.6533 (mmtt) REVERT: B 44 MET cc_start: 0.8991 (mtp) cc_final: 0.8729 (mtp) REVERT: B 108 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7390 (mm-30) REVERT: C 64 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8169 (tp-100) REVERT: C 111 ARG cc_start: 0.8457 (ttm-80) cc_final: 0.8074 (ttp80) REVERT: D 14 MET cc_start: 0.6607 (tpt) cc_final: 0.6345 (tpt) REVERT: D 21 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7382 (mt-10) REVERT: D 62 SER cc_start: 0.8026 (OUTLIER) cc_final: 0.7392 (p) REVERT: D 67 LYS cc_start: 0.7825 (mtmt) cc_final: 0.7451 (mtmt) REVERT: D 68 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8287 (mp) REVERT: D 95 THR cc_start: 0.7925 (OUTLIER) cc_final: 0.7607 (p) REVERT: F 89 GLN cc_start: 0.8014 (pt0) cc_final: 0.7758 (pm20) outliers start: 38 outliers final: 25 residues processed: 166 average time/residue: 0.3209 time to fit residues: 68.3783 Evaluate side-chains 169 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 64 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 313 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.169803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.129874 restraints weight = 13275.255| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.45 r_work: 0.3368 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10820 Z= 0.139 Angle : 0.586 6.944 15316 Z= 0.302 Chirality : 0.035 0.223 1813 Planarity : 0.005 0.057 1402 Dihedral : 22.474 179.335 3278 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.10 % Favored : 93.45 % Rotamer: Outliers : 4.53 % Allowed : 21.87 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.29), residues: 885 helix: 1.06 (0.20), residues: 661 sheet: -0.46 (1.06), residues: 26 loop : -2.93 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 116 HIS 0.007 0.001 HIS A 313 PHE 0.016 0.002 PHE A 231 TYR 0.017 0.001 TYR D 26 ARG 0.011 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.04322 ( 593) hydrogen bonds : angle 4.07420 ( 1599) covalent geometry : bond 0.00307 (10820) covalent geometry : angle 0.58638 (15316) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8826 (m-40) cc_final: 0.8472 (m-40) REVERT: A 67 LEU cc_start: 0.6220 (OUTLIER) cc_final: 0.5944 (mp) REVERT: A 116 HIS cc_start: 0.8471 (t-90) cc_final: 0.8200 (t70) REVERT: A 275 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8283 (t) REVERT: A 278 LYS cc_start: 0.7201 (mtpt) cc_final: 0.6505 (mmtt) REVERT: B 42 ARG cc_start: 0.8612 (ttp-170) cc_final: 0.8405 (ttp-170) REVERT: B 44 MET cc_start: 0.8935 (mtp) cc_final: 0.8639 (mtp) REVERT: B 108 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7285 (mm-30) REVERT: C 64 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8209 (tp-100) REVERT: C 111 ARG cc_start: 0.8327 (ttm-80) cc_final: 0.7992 (ttp80) REVERT: D 21 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7327 (mt-10) REVERT: D 62 SER cc_start: 0.7831 (OUTLIER) cc_final: 0.7162 (p) REVERT: D 67 LYS cc_start: 0.7709 (mtmt) cc_final: 0.7249 (mtmt) REVERT: D 68 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8180 (mp) REVERT: D 95 THR cc_start: 0.7835 (OUTLIER) cc_final: 0.7517 (p) REVERT: F 89 GLN cc_start: 0.7983 (pt0) cc_final: 0.7730 (pm20) outliers start: 34 outliers final: 20 residues processed: 161 average time/residue: 0.3275 time to fit residues: 68.4605 Evaluate side-chains 164 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.168434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.128838 restraints weight = 13078.191| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.43 r_work: 0.3348 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10820 Z= 0.155 Angle : 0.597 6.986 15316 Z= 0.306 Chirality : 0.035 0.229 1813 Planarity : 0.005 0.057 1402 Dihedral : 22.398 179.620 3278 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.10 % Favored : 93.45 % Rotamer: Outliers : 4.13 % Allowed : 22.27 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.29), residues: 885 helix: 1.08 (0.20), residues: 662 sheet: -0.12 (1.09), residues: 26 loop : -2.91 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 116 HIS 0.004 0.001 HIS A 27 PHE 0.016 0.002 PHE D 80 TYR 0.019 0.002 TYR D 26 ARG 0.014 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 593) hydrogen bonds : angle 4.09187 ( 1599) covalent geometry : bond 0.00348 (10820) covalent geometry : angle 0.59724 (15316) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8822 (m-40) cc_final: 0.8466 (m-40) REVERT: A 67 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.6031 (mp) REVERT: A 116 HIS cc_start: 0.8397 (t-90) cc_final: 0.8102 (t70) REVERT: B 42 ARG cc_start: 0.8624 (ttp-170) cc_final: 0.8399 (ttp-170) REVERT: B 44 MET cc_start: 0.8964 (mtp) cc_final: 0.8700 (mtp) REVERT: B 77 MET cc_start: 0.8983 (tpt) cc_final: 0.8337 (tpt) REVERT: B 108 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7177 (mm-30) REVERT: C 64 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8212 (tp-100) REVERT: C 111 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.7999 (ttp80) REVERT: D 21 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7325 (mt-10) REVERT: D 62 SER cc_start: 0.7837 (OUTLIER) cc_final: 0.7186 (p) REVERT: D 67 LYS cc_start: 0.7701 (mtmt) cc_final: 0.7261 (mtmt) REVERT: D 68 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8176 (mp) REVERT: D 95 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7509 (p) REVERT: D 98 GLN cc_start: 0.8201 (mt0) cc_final: 0.7777 (mt0) outliers start: 31 outliers final: 22 residues processed: 158 average time/residue: 0.3641 time to fit residues: 74.3175 Evaluate side-chains 164 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 59 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 97 optimal weight: 8.9990 chunk 56 optimal weight: 0.4980 chunk 88 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.169274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129278 restraints weight = 13112.588| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.48 r_work: 0.3343 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10820 Z= 0.153 Angle : 0.598 7.335 15316 Z= 0.307 Chirality : 0.035 0.232 1813 Planarity : 0.005 0.057 1402 Dihedral : 22.346 179.569 3277 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.88 % Favored : 93.56 % Rotamer: Outliers : 3.73 % Allowed : 22.67 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.29), residues: 885 helix: 1.10 (0.20), residues: 661 sheet: 0.09 (1.10), residues: 26 loop : -2.85 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 116 HIS 0.004 0.001 HIS A 27 PHE 0.016 0.002 PHE D 80 TYR 0.021 0.002 TYR D 26 ARG 0.014 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 593) hydrogen bonds : angle 4.09404 ( 1599) covalent geometry : bond 0.00343 (10820) covalent geometry : angle 0.59819 (15316) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8897 (m-40) cc_final: 0.8516 (m-40) REVERT: A 116 HIS cc_start: 0.8369 (t-90) cc_final: 0.8080 (t70) REVERT: A 275 SER cc_start: 0.8796 (OUTLIER) cc_final: 0.8307 (t) REVERT: B 44 MET cc_start: 0.8971 (mtp) cc_final: 0.8691 (mtp) REVERT: B 77 MET cc_start: 0.8988 (tpt) cc_final: 0.8428 (tpt) REVERT: B 108 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7164 (mm-30) REVERT: C 64 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8189 (tp-100) REVERT: C 111 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.8000 (ttp80) REVERT: D 21 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7330 (mt-10) REVERT: D 68 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8193 (mp) REVERT: D 95 THR cc_start: 0.7969 (OUTLIER) cc_final: 0.7652 (p) outliers start: 28 outliers final: 22 residues processed: 155 average time/residue: 0.3525 time to fit residues: 70.7897 Evaluate side-chains 163 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 97 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 60 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.167517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.126859 restraints weight = 13095.720| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.48 r_work: 0.3311 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10820 Z= 0.193 Angle : 0.630 8.158 15316 Z= 0.323 Chirality : 0.037 0.240 1813 Planarity : 0.005 0.055 1402 Dihedral : 22.411 179.728 3277 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.10 % Favored : 93.33 % Rotamer: Outliers : 4.00 % Allowed : 21.87 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.29), residues: 885 helix: 1.00 (0.20), residues: 660 sheet: 0.26 (1.13), residues: 26 loop : -2.74 (0.46), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 309 HIS 0.004 0.001 HIS A 27 PHE 0.018 0.002 PHE D 80 TYR 0.024 0.002 TYR D 26 ARG 0.014 0.001 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 593) hydrogen bonds : angle 4.24401 ( 1599) covalent geometry : bond 0.00441 (10820) covalent geometry : angle 0.63020 (15316) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8858 (m-40) cc_final: 0.8496 (m-40) REVERT: A 116 HIS cc_start: 0.8331 (t-90) cc_final: 0.7993 (t70) REVERT: B 44 MET cc_start: 0.8983 (mtp) cc_final: 0.8742 (mtp) REVERT: B 77 MET cc_start: 0.9017 (tpt) cc_final: 0.8474 (tpt) REVERT: B 108 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7235 (mm-30) REVERT: C 111 ARG cc_start: 0.8489 (ttm-80) cc_final: 0.8113 (ttp80) REVERT: D 21 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7394 (mt-10) REVERT: D 62 SER cc_start: 0.7967 (OUTLIER) cc_final: 0.7694 (p) REVERT: D 95 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7542 (p) REVERT: F 90 LYS cc_start: 0.7370 (mptt) cc_final: 0.7061 (tptt) outliers start: 30 outliers final: 22 residues processed: 163 average time/residue: 0.3100 time to fit residues: 65.3350 Evaluate side-chains 162 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 97 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.0980 chunk 87 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.167802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.126935 restraints weight = 13006.076| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.51 r_work: 0.3317 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10820 Z= 0.183 Angle : 0.628 9.512 15316 Z= 0.322 Chirality : 0.036 0.241 1813 Planarity : 0.005 0.055 1402 Dihedral : 22.386 179.949 3275 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.76 % Favored : 93.67 % Rotamer: Outliers : 3.33 % Allowed : 22.27 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.29), residues: 885 helix: 1.02 (0.20), residues: 659 sheet: 0.38 (1.13), residues: 26 loop : -2.68 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 309 HIS 0.004 0.001 HIS A 27 PHE 0.022 0.002 PHE F 80 TYR 0.020 0.002 TYR D 26 ARG 0.014 0.000 ARG F 111 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 593) hydrogen bonds : angle 4.23019 ( 1599) covalent geometry : bond 0.00417 (10820) covalent geometry : angle 0.62769 (15316) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5943.38 seconds wall clock time: 106 minutes 0.99 seconds (6360.99 seconds total)