Starting phenix.real_space_refine on Fri Feb 14 10:53:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uba_42080/02_2025/8uba_42080.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uba_42080/02_2025/8uba_42080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uba_42080/02_2025/8uba_42080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uba_42080/02_2025/8uba_42080.map" model { file = "/net/cci-nas-00/data/ceres_data/8uba_42080/02_2025/8uba_42080.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uba_42080/02_2025/8uba_42080.cif" } resolution = 3.2 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 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.67, per 1000 atoms: 0.65 Number of scatterers: 10299 At special positions: 0 Unit cell: (84, 100, 147, 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: 2.76 Conformation dependent library (CDL) restraints added in 913.6 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: 43 helices and 3 sheets defined 75.0% alpha, 2.9% beta 46 base pairs and 90 stacking pairs defined. Time for finding SS restraints: 4.67 Creating SS restraints... Processing helix chain 'A' and resid 7 through 13 removed outlier: 4.259A pdb=" N GLN A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 27 removed outlier: 3.522A pdb=" N ASP A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 40 removed outlier: 3.773A pdb=" N GLU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 54 Processing helix chain 'A' and resid 80 through 94 removed outlier: 3.911A 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 150 through 154 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 183 through 203 removed outlier: 3.558A pdb=" N ALA A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.264A 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: 3.857A 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 33 removed outlier: 3.634A pdb=" N ARG B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.579A 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 50 through 61 removed outlier: 4.404A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) 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: 3.653A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.784A 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 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 50 through 62 removed outlier: 4.389A pdb=" N GLU C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 88 removed outlier: 3.591A 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: 3.713A pdb=" N ARG D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.543A 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: 3.568A pdb=" N LEU D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 removed outlier: 3.934A pdb=" N LEU D 68 " --> pdb=" O GLN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 123 removed outlier: 4.030A pdb=" N GLN D 103 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 34 removed outlier: 3.639A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.629A 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 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: 3.788A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.618A 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 63 Processing helix chain 'F' and resid 64 through 87 removed outlier: 3.867A pdb=" N GLY F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.304A 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 65 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 213 removed outlier: 3.839A 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 260 487 hydrogen bonds defined for protein. 1440 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 120 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 90 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1948 1.33 - 1.46: 4266 1.46 - 1.59: 4279 1.59 - 1.72: 265 1.72 - 1.85: 62 Bond restraints: 10820 Sorted by residual: bond pdb=" CG HIS E 38 " pdb=" CD2 HIS E 38 " ideal model delta sigma weight residual 1.354 1.276 0.078 1.10e-02 8.26e+03 4.99e+01 bond pdb=" CE1 HIS E 38 " pdb=" NE2 HIS E 38 " ideal model delta sigma weight residual 1.321 1.257 0.064 1.00e-02 1.00e+04 4.15e+01 bond pdb=" CA ARG B 36 " pdb=" CB ARG B 36 " ideal model delta sigma weight residual 1.530 1.630 -0.099 1.69e-02 3.50e+03 3.45e+01 bond pdb=" CA GLU F 100 " pdb=" CB GLU F 100 " ideal model delta sigma weight residual 1.529 1.608 -0.079 1.58e-02 4.01e+03 2.52e+01 bond pdb=" CA ASN C 63 " pdb=" CB ASN C 63 " ideal model delta sigma weight residual 1.535 1.609 -0.074 1.51e-02 4.39e+03 2.39e+01 ... (remaining 10815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 14019 2.11 - 4.21: 1135 4.21 - 6.32: 130 6.32 - 8.42: 25 8.42 - 10.53: 7 Bond angle restraints: 15316 Sorted by residual: angle pdb=" N PRO C 91 " pdb=" CA PRO C 91 " pdb=" CB PRO C 91 " ideal model delta sigma weight residual 103.25 96.08 7.17 1.05e+00 9.07e-01 4.66e+01 angle pdb=" C3' U I 67 " pdb=" O3' U I 67 " pdb=" P C I 68 " ideal model delta sigma weight residual 120.20 110.57 9.63 1.50e+00 4.44e-01 4.12e+01 angle pdb=" C3' A I 119 " pdb=" O3' A I 119 " pdb=" P U I 120 " ideal model delta sigma weight residual 120.20 111.20 9.00 1.50e+00 4.44e-01 3.60e+01 angle pdb=" C3' U I 120 " pdb=" O3' U I 120 " pdb=" P G I 121 " ideal model delta sigma weight residual 120.20 111.70 8.50 1.50e+00 4.44e-01 3.21e+01 angle pdb=" C3' U I 7 " pdb=" O3' U I 7 " pdb=" P C I 8 " ideal model delta sigma weight residual 120.20 112.11 8.09 1.50e+00 4.44e-01 2.91e+01 ... (remaining 15311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 6009 35.39 - 70.77: 637 70.77 - 106.16: 62 106.16 - 141.55: 1 141.55 - 176.93: 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 55.07 176.93 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 -91.97 -68.03 1 1.50e+01 4.44e-03 2.67e+01 dihedral pdb=" CA LYS D 90 " pdb=" C LYS D 90 " pdb=" N PRO D 91 " pdb=" CA PRO D 91 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 6709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 1589 0.137 - 0.273: 208 0.273 - 0.410: 5 0.410 - 0.547: 9 0.547 - 0.683: 2 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 3.09 -0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" P U I 47 " pdb=" OP1 U I 47 " pdb=" OP2 U I 47 " pdb=" O5' U I 47 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.65e+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 -2.95 -0.54 2.00e-01 2.50e+01 7.39e+00 ... (remaining 1810 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " 0.063 2.00e-02 2.50e+03 3.34e-02 2.23e+01 pdb=" CG TYR C 28 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U I 7 " 0.063 2.00e-02 2.50e+03 3.12e-02 2.20e+01 pdb=" N1 U I 7 " -0.034 2.00e-02 2.50e+03 pdb=" C2 U I 7 " -0.031 2.00e-02 2.50e+03 pdb=" O2 U I 7 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U I 7 " -0.018 2.00e-02 2.50e+03 pdb=" C4 U I 7 " 0.012 2.00e-02 2.50e+03 pdb=" O4 U I 7 " 0.035 2.00e-02 2.50e+03 pdb=" C5 U I 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 U I 7 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 28 " -0.041 2.00e-02 2.50e+03 3.02e-02 1.83e+01 pdb=" CG TYR E 28 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR E 28 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR E 28 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR E 28 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR E 28 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR E 28 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 28 " -0.049 2.00e-02 2.50e+03 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1317 2.74 - 3.28: 10909 3.28 - 3.82: 21452 3.82 - 4.36: 26920 4.36 - 4.90: 38269 Nonbonded interactions: 98867 Sorted by model distance: nonbonded pdb=" NZ LYS A 3 " pdb=" N7 G I 108 " model vdw 2.202 3.200 nonbonded pdb=" OH TYR A 152 " pdb=" O LEU A 168 " model vdw 2.230 3.040 nonbonded pdb=" O LYS A 113 " pdb=" O2' C H 120 " model vdw 2.250 3.040 nonbonded pdb=" NH1 ARG A 264 " pdb=" O LEU A 272 " model vdw 2.260 3.120 nonbonded pdb=" OH TYR A 152 " pdb=" O LEU A 172 " model vdw 2.261 3.040 ... (remaining 98862 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: 2.620 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: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.970 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 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 0.129 10820 Z= 0.692 Angle : 1.251 10.528 15316 Z= 0.755 Chirality : 0.095 0.683 1813 Planarity : 0.010 0.087 1402 Dihedral : 23.380 176.931 5028 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 28.19 Ramachandran Plot: Outliers : 2.03 % Allowed : 8.25 % Favored : 89.72 % Rotamer: Outliers : 7.20 % Allowed : 14.67 % Favored : 78.13 % 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: -3.80 (0.23), residues: 885 helix: -1.84 (0.16), residues: 648 sheet: -4.28 (0.74), residues: 24 loop : -3.93 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.009 TRP A 15 HIS 0.016 0.003 HIS F 97 PHE 0.035 0.008 PHE A 98 TYR 0.063 0.009 TYR C 28 ARG 0.034 0.003 ARG A 208 *********************** 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 301 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 247 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7260 (ptp-170) REVERT: A 16 GLU cc_start: 0.8875 (mp0) cc_final: 0.8265 (tm-30) REVERT: A 24 LYS cc_start: 0.8314 (mttp) cc_final: 0.7958 (mtmt) REVERT: A 31 ARG cc_start: 0.8553 (mtp85) cc_final: 0.8025 (mtm110) REVERT: A 68 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.7815 (p) REVERT: A 70 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7670 (tp30) REVERT: A 116 HIS cc_start: 0.7549 (t70) cc_final: 0.7193 (m90) REVERT: A 141 LYS cc_start: 0.8008 (mmtp) cc_final: 0.7792 (mtmm) REVERT: A 161 CYS cc_start: 0.8944 (t) cc_final: 0.8547 (t) REVERT: B 25 SER cc_start: 0.9399 (t) cc_final: 0.9144 (p) REVERT: B 90 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7475 (mttt) REVERT: C 14 MET cc_start: 0.7722 (tpt) cc_final: 0.7259 (mtt) REVERT: C 40 VAL cc_start: 0.9047 (t) cc_final: 0.8807 (t) REVERT: C 67 LYS cc_start: 0.8549 (mmtp) cc_final: 0.8335 (mmtm) REVERT: C 117 ILE cc_start: 0.8584 (mt) cc_final: 0.8347 (mt) REVERT: C 121 ASN cc_start: 0.8277 (m-40) cc_final: 0.8051 (m-40) REVERT: D 26 TYR cc_start: 0.8455 (t80) cc_final: 0.7419 (t80) REVERT: D 37 LYS cc_start: 0.7956 (mmtm) cc_final: 0.7466 (ttmm) REVERT: D 44 MET cc_start: 0.8500 (mtp) cc_final: 0.8287 (mtt) REVERT: D 69 TYR cc_start: 0.8095 (m-80) cc_final: 0.7879 (m-80) REVERT: D 98 GLN cc_start: 0.8439 (mt0) cc_final: 0.8098 (mt0) REVERT: E 14 MET cc_start: 0.6281 (tpp) cc_final: 0.5837 (tpp) REVERT: E 64 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7716 (mt0) REVERT: E 79 ARG cc_start: 0.8287 (mtt90) cc_final: 0.7870 (mtt-85) REVERT: E 98 GLN cc_start: 0.8233 (mt0) cc_final: 0.7905 (mt0) REVERT: E 111 ARG cc_start: 0.8778 (mtm180) cc_final: 0.8283 (ptt90) REVERT: F 14 MET cc_start: 0.6758 (mmt) cc_final: 0.5789 (tmm) REVERT: F 19 ARG cc_start: 0.8107 (mmm160) cc_final: 0.7901 (mmm160) REVERT: F 26 TYR cc_start: 0.8473 (t80) cc_final: 0.8179 (t80) REVERT: F 43 GLU cc_start: 0.8488 (tt0) cc_final: 0.7889 (mt-10) REVERT: F 89 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7993 (mp10) outliers start: 54 outliers final: 14 residues processed: 278 average time/residue: 0.3231 time to fit residues: 113.9957 Evaluate side-chains 210 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 6 ARG 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 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 101 THR 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: 0.5980 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN B 32 GLN B 92 HIS C 89 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 121 ASN F 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.152637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.119191 restraints weight = 15675.864| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.65 r_work: 0.3426 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10820 Z= 0.268 Angle : 0.699 11.795 15316 Z= 0.358 Chirality : 0.041 0.241 1813 Planarity : 0.007 0.153 1402 Dihedral : 23.542 175.359 3315 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.44 % Favored : 92.99 % Rotamer: Outliers : 5.47 % Allowed : 16.40 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -1.72 (0.26), residues: 885 helix: -0.32 (0.18), residues: 667 sheet: -4.19 (0.70), residues: 28 loop : -3.27 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 81 HIS 0.006 0.001 HIS A 88 PHE 0.024 0.002 PHE A 231 TYR 0.019 0.002 TYR D 26 ARG 0.007 0.001 ARG D 111 *********************** 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 255 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8238 (p) REVERT: A 69 TYR cc_start: 0.5537 (OUTLIER) cc_final: 0.4944 (p90) REVERT: A 113 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6868 (mttm) REVERT: A 184 LEU cc_start: 0.8798 (tp) cc_final: 0.8592 (tp) REVERT: B 90 LYS cc_start: 0.7539 (ttpp) cc_final: 0.7111 (mttp) REVERT: B 108 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: C 67 LYS cc_start: 0.8806 (mmtp) cc_final: 0.8504 (mmtm) REVERT: C 89 GLN cc_start: 0.7116 (tt0) cc_final: 0.6846 (tm-30) REVERT: D 21 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7729 (mm-30) REVERT: D 37 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7840 (ttmm) REVERT: D 63 ASN cc_start: 0.7014 (m-40) cc_final: 0.6779 (t0) REVERT: D 108 GLU cc_start: 0.7751 (tp30) cc_final: 0.7132 (tp30) REVERT: E 14 MET cc_start: 0.6783 (tpp) cc_final: 0.6339 (tpp) REVERT: E 54 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7738 (tp30) REVERT: E 72 ASP cc_start: 0.8481 (t70) cc_final: 0.7895 (t70) REVERT: F 14 MET cc_start: 0.6493 (mmt) cc_final: 0.6074 (tmm) REVERT: F 19 ARG cc_start: 0.7334 (mmm160) cc_final: 0.6497 (mmm160) outliers start: 41 outliers final: 15 residues processed: 242 average time/residue: 0.3025 time to fit residues: 95.4432 Evaluate side-chains 199 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 115 SER 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: 0.6980 chunk 81 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.154184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.121634 restraints weight = 16133.267| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.60 r_work: 0.3451 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10820 Z= 0.252 Angle : 0.647 8.711 15316 Z= 0.330 Chirality : 0.038 0.202 1813 Planarity : 0.006 0.131 1402 Dihedral : 23.011 178.583 3289 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.55 % Favored : 92.88 % Rotamer: Outliers : 5.20 % Allowed : 18.27 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.94 (0.27), residues: 885 helix: 0.25 (0.19), residues: 666 sheet: -3.60 (0.83), residues: 28 loop : -3.08 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 116 HIS 0.007 0.001 HIS B 38 PHE 0.027 0.002 PHE B 80 TYR 0.021 0.002 TYR D 26 ARG 0.004 0.000 ARG B 36 *********************** 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 234 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.6118 (mpt-90) REVERT: A 31 ARG cc_start: 0.8270 (mtm110) cc_final: 0.8031 (ttm110) REVERT: A 109 CYS cc_start: 0.8352 (m) cc_final: 0.8089 (p) REVERT: A 113 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.7025 (mttm) REVERT: B 1 MET cc_start: 0.8475 (ppp) cc_final: 0.8245 (ppp) REVERT: D 22 ARG cc_start: 0.8548 (mtm-85) cc_final: 0.8310 (mtt-85) REVERT: D 52 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: D 63 ASN cc_start: 0.7008 (m-40) cc_final: 0.6776 (t0) REVERT: D 108 GLU cc_start: 0.7883 (tp30) cc_final: 0.7295 (tp30) REVERT: F 14 MET cc_start: 0.6454 (mmt) cc_final: 0.6234 (tmm) REVERT: F 19 ARG cc_start: 0.6937 (mmm160) cc_final: 0.6362 (mmm160) REVERT: F 37 LYS cc_start: 0.8525 (tttm) cc_final: 0.8287 (tttm) REVERT: F 94 MET cc_start: 0.6567 (ttp) cc_final: 0.6309 (ttm) outliers start: 39 outliers final: 18 residues processed: 220 average time/residue: 0.2988 time to fit residues: 85.7385 Evaluate side-chains 200 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 78 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 E residue 16 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 95 THR 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: 0.7980 chunk 3 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 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 87 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.154253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.122069 restraints weight = 15985.103| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.57 r_work: 0.3458 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10820 Z= 0.257 Angle : 0.634 8.759 15316 Z= 0.322 Chirality : 0.038 0.205 1813 Planarity : 0.006 0.126 1402 Dihedral : 22.686 176.661 3281 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.21 % Favored : 93.33 % Rotamer: Outliers : 5.20 % Allowed : 19.87 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.54 (0.28), residues: 885 helix: 0.46 (0.19), residues: 664 sheet: -2.99 (0.86), residues: 28 loop : -2.63 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 309 HIS 0.007 0.001 HIS A 88 PHE 0.032 0.002 PHE B 80 TYR 0.018 0.002 TYR F 20 ARG 0.010 0.001 ARG F 36 *********************** 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 226 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 187 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.9011 (tp) cc_final: 0.8592 (tp) REVERT: A 227 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7816 (mp) REVERT: D 14 MET cc_start: 0.7595 (tpt) cc_final: 0.7113 (tpt) REVERT: D 22 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8342 (mtt-85) REVERT: D 52 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8225 (tm-30) REVERT: D 108 GLU cc_start: 0.7860 (tp30) cc_final: 0.7417 (tp30) REVERT: E 42 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8546 (ptm160) REVERT: E 54 GLU cc_start: 0.7781 (tp30) cc_final: 0.7479 (tp30) REVERT: F 37 LYS cc_start: 0.8539 (tttm) cc_final: 0.8324 (tttm) outliers start: 39 outliers final: 25 residues processed: 207 average time/residue: 0.2873 time to fit residues: 79.4994 Evaluate side-chains 207 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 78 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 E residue 16 ILE Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 103 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 0.0470 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN C 13 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.155222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.121507 restraints weight = 16037.377| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.73 r_work: 0.3454 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10820 Z= 0.216 Angle : 0.619 9.113 15316 Z= 0.316 Chirality : 0.037 0.208 1813 Planarity : 0.006 0.122 1402 Dihedral : 22.390 176.516 3277 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.65 % Favored : 93.79 % Rotamer: Outliers : 4.27 % Allowed : 20.67 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.34 (0.28), residues: 885 helix: 0.59 (0.19), residues: 668 sheet: -2.49 (0.92), residues: 28 loop : -2.68 (0.45), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 266 HIS 0.006 0.001 HIS D 38 PHE 0.026 0.002 PHE B 80 TYR 0.030 0.002 TYR F 20 ARG 0.006 0.001 ARG F 36 *********************** 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 231 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8547 (mttp) cc_final: 0.8158 (mtmt) REVERT: A 92 ASN cc_start: 0.8749 (m-40) cc_final: 0.8209 (m-40) REVERT: A 184 LEU cc_start: 0.8926 (tp) cc_final: 0.8578 (tp) REVERT: A 227 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7746 (mp) REVERT: B 1 MET cc_start: 0.8441 (ppp) cc_final: 0.8226 (ppp) REVERT: B 22 ARG cc_start: 0.8673 (mtm110) cc_final: 0.8401 (mtm-85) REVERT: C 64 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: C 67 LYS cc_start: 0.8757 (mmtm) cc_final: 0.8414 (mmtp) REVERT: D 18 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6964 (mm-30) REVERT: D 19 ARG cc_start: 0.7919 (mmt-90) cc_final: 0.7661 (mmt-90) REVERT: D 37 LYS cc_start: 0.8434 (ttmm) cc_final: 0.8231 (ttmm) REVERT: D 103 GLN cc_start: 0.8642 (mt0) cc_final: 0.8433 (mt0) REVERT: D 108 GLU cc_start: 0.7859 (tp30) cc_final: 0.7221 (tp30) REVERT: E 26 TYR cc_start: 0.7971 (t80) cc_final: 0.7218 (t80) REVERT: E 54 GLU cc_start: 0.7835 (tp30) cc_final: 0.7469 (tp30) REVERT: F 14 MET cc_start: 0.6588 (tmm) cc_final: 0.6264 (tpp) outliers start: 32 outliers final: 19 residues processed: 223 average time/residue: 0.3065 time to fit residues: 90.0196 Evaluate side-chains 205 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 78 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 E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 103 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN C 13 GLN ** D 32 GLN ** 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 = 0.4064 r_free = 0.4064 target = 0.154499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.121339 restraints weight = 16325.737| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.73 r_work: 0.3440 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10820 Z= 0.229 Angle : 0.643 17.706 15316 Z= 0.321 Chirality : 0.038 0.208 1813 Planarity : 0.007 0.171 1402 Dihedral : 22.316 176.360 3274 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.65 % Favored : 93.79 % Rotamer: Outliers : 4.27 % Allowed : 22.13 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.27 (0.28), residues: 885 helix: 0.64 (0.19), residues: 668 sheet: -2.06 (0.98), residues: 28 loop : -2.70 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 266 HIS 0.005 0.001 HIS B 92 PHE 0.030 0.002 PHE B 80 TYR 0.026 0.002 TYR C 28 ARG 0.006 0.001 ARG F 22 *********************** 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 222 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8593 (mttp) cc_final: 0.8202 (mtmt) REVERT: A 92 ASN cc_start: 0.8730 (m-40) cc_final: 0.8117 (m-40) REVERT: A 184 LEU cc_start: 0.8910 (tp) cc_final: 0.8573 (tp) REVERT: A 227 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7720 (mp) REVERT: B 1 MET cc_start: 0.8488 (ppp) cc_final: 0.8130 (ppp) REVERT: C 64 GLN cc_start: 0.7973 (pm20) cc_final: 0.7704 (pm20) REVERT: C 67 LYS cc_start: 0.8760 (mmtm) cc_final: 0.8409 (mmtp) REVERT: D 52 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8399 (tm-30) REVERT: D 108 GLU cc_start: 0.8044 (tp30) cc_final: 0.7715 (tp30) REVERT: E 54 GLU cc_start: 0.7885 (tp30) cc_final: 0.7508 (tp30) REVERT: F 14 MET cc_start: 0.6891 (tmm) cc_final: 0.6503 (tpp) REVERT: F 22 ARG cc_start: 0.7118 (mtt90) cc_final: 0.6909 (mtt90) REVERT: F 37 LYS cc_start: 0.8477 (tttm) cc_final: 0.8265 (tttm) outliers start: 32 outliers final: 25 residues processed: 213 average time/residue: 0.2925 time to fit residues: 81.6230 Evaluate side-chains 209 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 78 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 E residue 16 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 103 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 64 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 7 optimal weight: 0.0040 chunk 36 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 92 HIS C 13 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.154517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.121199 restraints weight = 16433.122| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.66 r_work: 0.3447 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10820 Z= 0.232 Angle : 0.634 11.867 15316 Z= 0.322 Chirality : 0.038 0.209 1813 Planarity : 0.006 0.149 1402 Dihedral : 22.273 176.610 3274 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.10 % Favored : 93.33 % Rotamer: Outliers : 5.07 % Allowed : 21.20 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.12 (0.28), residues: 885 helix: 0.71 (0.19), residues: 666 sheet: -1.86 (1.07), residues: 28 loop : -2.47 (0.46), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 309 HIS 0.009 0.001 HIS B 97 PHE 0.027 0.002 PHE B 80 TYR 0.025 0.002 TYR F 20 ARG 0.009 0.001 ARG F 36 *********************** 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 225 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8579 (mttp) cc_final: 0.8175 (mtmt) REVERT: A 92 ASN cc_start: 0.8777 (m-40) cc_final: 0.8201 (m-40) REVERT: A 184 LEU cc_start: 0.8919 (tp) cc_final: 0.8564 (tp) REVERT: A 227 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7641 (mp) REVERT: A 273 ARG cc_start: 0.7576 (mtm110) cc_final: 0.7313 (mtm110) REVERT: B 1 MET cc_start: 0.8460 (ppp) cc_final: 0.8244 (ppp) REVERT: C 67 LYS cc_start: 0.8776 (mmtm) cc_final: 0.8535 (mmtp) REVERT: D 108 GLU cc_start: 0.8095 (tp30) cc_final: 0.7730 (tp30) REVERT: E 54 GLU cc_start: 0.7943 (tp30) cc_final: 0.7711 (tp30) REVERT: E 96 PRO cc_start: 0.8212 (Cg_exo) cc_final: 0.8009 (Cg_endo) REVERT: F 14 MET cc_start: 0.6805 (tmm) cc_final: 0.6504 (tpp) REVERT: F 113 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7991 (tt) outliers start: 38 outliers final: 28 residues processed: 209 average time/residue: 0.3084 time to fit residues: 83.9210 Evaluate side-chains 208 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 78 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 E residue 16 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN C 13 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.153410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.119500 restraints weight = 16277.064| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.74 r_work: 0.3420 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10820 Z= 0.264 Angle : 0.654 9.425 15316 Z= 0.330 Chirality : 0.038 0.205 1813 Planarity : 0.007 0.139 1402 Dihedral : 22.204 177.241 3274 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.99 % Favored : 93.45 % Rotamer: Outliers : 4.40 % Allowed : 22.67 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: -0.09 (0.28), residues: 885 helix: 0.71 (0.19), residues: 666 sheet: -1.88 (1.07), residues: 28 loop : -2.34 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 309 HIS 0.012 0.001 HIS B 92 PHE 0.027 0.002 PHE B 80 TYR 0.022 0.002 TYR C 28 ARG 0.014 0.001 ARG F 22 *********************** 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 220 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8683 (mttp) cc_final: 0.8276 (mtmt) REVERT: A 92 ASN cc_start: 0.8810 (m-40) cc_final: 0.8367 (m-40) REVERT: A 184 LEU cc_start: 0.8962 (tp) cc_final: 0.8538 (tp) REVERT: A 227 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7691 (mp) REVERT: B 1 MET cc_start: 0.8537 (ppp) cc_final: 0.8264 (ppp) REVERT: C 64 GLN cc_start: 0.7937 (pm20) cc_final: 0.7599 (pm20) REVERT: C 67 LYS cc_start: 0.8772 (mmtm) cc_final: 0.8377 (mmtp) REVERT: D 18 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7001 (mm-30) REVERT: D 52 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8393 (tm-30) REVERT: D 108 GLU cc_start: 0.8058 (tp30) cc_final: 0.7486 (tp30) REVERT: F 19 ARG cc_start: 0.7429 (mmm160) cc_final: 0.7217 (mmm-85) REVERT: F 113 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8045 (tt) outliers start: 33 outliers final: 26 residues processed: 209 average time/residue: 0.2961 time to fit residues: 80.5504 Evaluate side-chains 209 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 78 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 E residue 16 ILE Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 113 LEU 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: 0.7980 chunk 81 optimal weight: 0.0970 chunk 40 optimal weight: 0.7980 chunk 67 optimal weight: 0.0980 chunk 59 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 46 optimal weight: 0.0370 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 92 HIS C 13 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN E 103 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.157507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.123278 restraints weight = 16599.650| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.95 r_work: 0.3479 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10820 Z= 0.181 Angle : 0.624 9.406 15316 Z= 0.317 Chirality : 0.037 0.201 1813 Planarity : 0.006 0.134 1402 Dihedral : 22.033 175.557 3274 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.76 % Favored : 93.67 % Rotamer: Outliers : 4.13 % Allowed : 22.67 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: 0.12 (0.29), residues: 885 helix: 0.89 (0.19), residues: 666 sheet: -1.63 (1.11), residues: 28 loop : -2.42 (0.48), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 266 HIS 0.012 0.001 HIS B 92 PHE 0.021 0.002 PHE B 80 TYR 0.023 0.002 TYR C 69 ARG 0.007 0.001 ARG A 31 *********************** 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 229 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8412 (mttp) cc_final: 0.7997 (mtmt) REVERT: A 31 ARG cc_start: 0.8110 (ttm110) cc_final: 0.7895 (mtp-110) REVERT: A 92 ASN cc_start: 0.8830 (m-40) cc_final: 0.8151 (m-40) REVERT: A 184 LEU cc_start: 0.8836 (tp) cc_final: 0.8452 (tp) REVERT: B 1 MET cc_start: 0.8424 (ppp) cc_final: 0.8064 (ppp) REVERT: B 90 LYS cc_start: 0.7554 (tptp) cc_final: 0.7028 (mttp) REVERT: C 64 GLN cc_start: 0.7903 (pm20) cc_final: 0.7648 (pm20) REVERT: C 67 LYS cc_start: 0.8794 (mmtm) cc_final: 0.8430 (mmtp) REVERT: C 69 TYR cc_start: 0.8553 (m-80) cc_final: 0.8176 (m-80) REVERT: D 18 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6936 (mm-30) REVERT: D 52 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8425 (tm-30) REVERT: D 108 GLU cc_start: 0.8127 (tp30) cc_final: 0.7555 (tp30) REVERT: E 54 GLU cc_start: 0.7595 (tp30) cc_final: 0.7310 (tp30) REVERT: F 113 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7988 (tt) outliers start: 31 outliers final: 23 residues processed: 219 average time/residue: 0.3214 time to fit residues: 90.1194 Evaluate side-chains 206 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 78 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 E residue 62 SER Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 60 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 94 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.155241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.120615 restraints weight = 16420.688| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.93 r_work: 0.3438 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10820 Z= 0.255 Angle : 0.663 10.483 15316 Z= 0.335 Chirality : 0.038 0.197 1813 Planarity : 0.006 0.133 1402 Dihedral : 22.051 176.670 3274 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.88 % Favored : 93.67 % Rotamer: Outliers : 3.47 % Allowed : 24.00 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: 0.09 (0.29), residues: 885 helix: 0.82 (0.20), residues: 663 sheet: -1.72 (1.09), residues: 28 loop : -2.18 (0.49), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 81 HIS 0.009 0.001 HIS B 38 PHE 0.027 0.002 PHE B 80 TYR 0.035 0.002 TYR C 28 ARG 0.012 0.001 ARG F 36 ********************** 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 205 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7933 (mtp-110) REVERT: A 184 LEU cc_start: 0.8907 (tp) cc_final: 0.8543 (tp) REVERT: B 1 MET cc_start: 0.8528 (ppp) cc_final: 0.8111 (ppp) REVERT: B 90 LYS cc_start: 0.7577 (tptp) cc_final: 0.7080 (mttp) REVERT: C 64 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7648 (pm20) REVERT: C 67 LYS cc_start: 0.8785 (mmtm) cc_final: 0.8393 (mmtp) REVERT: C 69 TYR cc_start: 0.8562 (m-80) cc_final: 0.8227 (m-80) REVERT: D 18 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6874 (mm-30) REVERT: D 52 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8304 (tm-30) REVERT: E 54 GLU cc_start: 0.7795 (tp30) cc_final: 0.7568 (tp30) REVERT: F 113 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7977 (tt) outliers start: 26 outliers final: 21 residues processed: 194 average time/residue: 0.3021 time to fit residues: 76.5166 Evaluate side-chains 202 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ARG Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 306 HIS Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 78 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 E residue 62 SER Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 99 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.156868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.122316 restraints weight = 16365.812| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.94 r_work: 0.3462 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.6003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10820 Z= 0.212 Angle : 0.647 9.729 15316 Z= 0.328 Chirality : 0.037 0.193 1813 Planarity : 0.006 0.132 1402 Dihedral : 22.038 175.966 3274 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.99 % Favored : 93.56 % Rotamer: Outliers : 3.60 % Allowed : 24.53 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: 0.13 (0.29), residues: 885 helix: 0.86 (0.20), residues: 663 sheet: -1.64 (1.10), residues: 28 loop : -2.21 (0.49), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 266 HIS 0.008 0.001 HIS B 97 PHE 0.023 0.002 PHE B 80 TYR 0.033 0.002 TYR C 28 ARG 0.013 0.001 ARG F 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4723.47 seconds wall clock time: 84 minutes 56.98 seconds (5096.98 seconds total)