Starting phenix.real_space_refine on Sat Nov 16 01:56:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uba_42080/11_2024/8uba_42080.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uba_42080/11_2024/8uba_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uba_42080/11_2024/8uba_42080.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uba_42080/11_2024/8uba_42080.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uba_42080/11_2024/8uba_42080.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uba_42080/11_2024/8uba_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 6.73, 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: 2.58 Conformation dependent library (CDL) restraints added in 853.4 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: 4.28 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: 3.25 Time building geometry restraints manager: 2.96 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: 2.480 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 28.030 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: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.900 ------------------------------------------------------------------------------- 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 : 0.947 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: 0.3307 time to fit residues: 117.0674 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 : 0.951 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.8061 (ptm160) cc_final: 0.7795 (ptp-170) REVERT: A 16 GLU cc_start: 0.8824 (mp0) cc_final: 0.8367 (tm-30) REVERT: A 31 ARG cc_start: 0.8756 (mtp85) cc_final: 0.8066 (mtm110) REVERT: A 68 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7600 (p) REVERT: A 69 TYR cc_start: 0.4860 (OUTLIER) cc_final: 0.4585 (p90) REVERT: A 70 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7397 (tp30) REVERT: A 113 LYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6902 (mttm) REVERT: A 116 HIS cc_start: 0.7655 (t70) cc_final: 0.7277 (m90) REVERT: A 164 THR cc_start: 0.8724 (m) cc_final: 0.8494 (m) REVERT: A 241 ARG cc_start: 0.8883 (tpp80) cc_final: 0.8644 (mmm160) REVERT: B 90 LYS cc_start: 0.8031 (ttpp) cc_final: 0.7319 (mttp) REVERT: B 108 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8530 (tm-30) REVERT: C 14 MET cc_start: 0.7450 (tpt) cc_final: 0.7043 (mtt) REVERT: C 43 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: C 47 LYS cc_start: 0.8915 (ttpt) cc_final: 0.8607 (mtpp) REVERT: C 67 LYS cc_start: 0.8616 (mmtp) cc_final: 0.8240 (mmtm) REVERT: C 89 GLN cc_start: 0.8003 (tt0) cc_final: 0.7722 (tm-30) REVERT: D 21 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7986 (mm-30) REVERT: D 37 LYS cc_start: 0.7933 (mmtm) cc_final: 0.7486 (ttmm) REVERT: D 63 ASN cc_start: 0.7298 (m-40) cc_final: 0.6940 (t0) REVERT: D 89 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7668 (mm-40) REVERT: D 100 GLU cc_start: 0.8555 (tp30) cc_final: 0.8124 (tt0) REVERT: D 108 GLU cc_start: 0.7600 (tp30) cc_final: 0.7246 (tp30) REVERT: E 14 MET cc_start: 0.6047 (tpp) cc_final: 0.5745 (tpp) REVERT: E 72 ASP cc_start: 0.8183 (t70) cc_final: 0.7742 (t70) REVERT: E 79 ARG cc_start: 0.8117 (mtt90) cc_final: 0.7722 (mtt-85) REVERT: F 14 MET cc_start: 0.6038 (mmt) cc_final: 0.5413 (tmm) REVERT: F 19 ARG cc_start: 0.7576 (mmm160) cc_final: 0.7249 (mmm160) REVERT: F 20 TYR cc_start: 0.8827 (t80) cc_final: 0.8584 (t80) REVERT: F 22 ARG cc_start: 0.8356 (mmm-85) cc_final: 0.7975 (mpt180) REVERT: F 26 TYR cc_start: 0.8389 (t80) cc_final: 0.8064 (t80) REVERT: F 44 MET cc_start: 0.8567 (mtp) cc_final: 0.8314 (mtp) REVERT: F 95 THR cc_start: 0.7717 (p) cc_final: 0.7503 (t) REVERT: F 101 THR cc_start: 0.7986 (t) cc_final: 0.7758 (p) outliers start: 41 outliers final: 15 residues processed: 242 average time/residue: 0.3027 time to fit residues: 94.9358 Evaluate side-chains 209 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 70 GLU 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 43 GLU Chi-restraints excluded: chain C residue 66 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 89 GLN 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 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 50 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 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 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10820 Z= 0.252 Angle : 0.641 8.725 15316 Z= 0.328 Chirality : 0.038 0.204 1813 Planarity : 0.006 0.131 1402 Dihedral : 22.951 179.254 3292 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.12 % Favored : 92.43 % Rotamer: Outliers : 5.07 % Allowed : 18.27 % Favored : 76.67 % 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: -0.92 (0.27), residues: 885 helix: 0.25 (0.19), residues: 668 sheet: -3.64 (0.82), residues: 28 loop : -3.04 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 116 HIS 0.008 0.001 HIS B 38 PHE 0.028 0.002 PHE B 80 TYR 0.022 0.002 TYR D 26 ARG 0.005 0.001 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 238 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.5593 (mpt-90) REVERT: A 16 GLU cc_start: 0.8855 (mp0) cc_final: 0.8442 (tm-30) REVERT: A 70 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7402 (tp30) REVERT: A 109 CYS cc_start: 0.8428 (m) cc_final: 0.7948 (p) REVERT: A 116 HIS cc_start: 0.7403 (t70) cc_final: 0.7088 (m90) REVERT: A 164 THR cc_start: 0.8755 (m) cc_final: 0.8518 (m) REVERT: A 184 LEU cc_start: 0.8685 (tp) cc_final: 0.8404 (tp) REVERT: A 309 TRP cc_start: 0.5426 (m-90) cc_final: 0.4985 (m-10) REVERT: A 313 HIS cc_start: 0.4673 (OUTLIER) cc_final: 0.4425 (t-170) REVERT: B 1 MET cc_start: 0.8544 (ppp) cc_final: 0.8187 (ppp) REVERT: C 14 MET cc_start: 0.7446 (tpt) cc_final: 0.6991 (mtt) REVERT: C 43 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: C 47 LYS cc_start: 0.8919 (ttpt) cc_final: 0.8607 (mttm) REVERT: D 18 GLU cc_start: 0.8016 (tp30) cc_final: 0.7671 (mm-30) REVERT: D 22 ARG cc_start: 0.8155 (mtm-85) cc_final: 0.7730 (mtt-85) REVERT: D 52 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8432 (tm-30) REVERT: D 63 ASN cc_start: 0.7433 (m-40) cc_final: 0.7063 (t0) REVERT: D 108 GLU cc_start: 0.7714 (tp30) cc_final: 0.7341 (tp30) REVERT: E 79 ARG cc_start: 0.8047 (mtt90) cc_final: 0.7706 (mtt-85) REVERT: F 14 MET cc_start: 0.5880 (mmt) cc_final: 0.5361 (tmm) REVERT: F 19 ARG cc_start: 0.7563 (mmm160) cc_final: 0.7111 (mmm160) REVERT: F 20 TYR cc_start: 0.8917 (t80) cc_final: 0.8706 (t80) REVERT: F 22 ARG cc_start: 0.8350 (mmm-85) cc_final: 0.7962 (mpt180) REVERT: F 26 TYR cc_start: 0.8313 (t80) cc_final: 0.7950 (t80) REVERT: F 44 MET cc_start: 0.8571 (mtp) cc_final: 0.8307 (mtp) outliers start: 38 outliers final: 17 residues processed: 224 average time/residue: 0.2933 time to fit residues: 85.7637 Evaluate side-chains 209 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 70 GLU 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 A residue 313 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain C residue 43 GLU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 81 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS F 13 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10820 Z= 0.221 Angle : 0.611 8.334 15316 Z= 0.311 Chirality : 0.037 0.206 1813 Planarity : 0.006 0.125 1402 Dihedral : 22.482 175.762 3284 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.88 % Favored : 93.67 % Rotamer: Outliers : 4.40 % Allowed : 19.73 % Favored : 75.87 % 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: -0.56 (0.28), residues: 885 helix: 0.47 (0.19), residues: 669 sheet: -2.90 (0.86), residues: 28 loop : -2.85 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 309 HIS 0.006 0.001 HIS B 92 PHE 0.033 0.002 PHE B 80 TYR 0.017 0.002 TYR C 69 ARG 0.009 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 233 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8884 (mp0) cc_final: 0.8505 (tm-30) REVERT: A 24 LYS cc_start: 0.8166 (mttp) cc_final: 0.7736 (mtmt) REVERT: A 70 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7567 (tp30) REVERT: A 92 ASN cc_start: 0.8869 (m-40) cc_final: 0.8518 (m-40) REVERT: A 116 HIS cc_start: 0.7491 (t70) cc_final: 0.7229 (m90) REVERT: A 158 LYS cc_start: 0.8124 (mttp) cc_final: 0.7603 (mmtt) REVERT: A 164 THR cc_start: 0.8635 (m) cc_final: 0.8380 (m) REVERT: A 309 TRP cc_start: 0.5126 (m-90) cc_final: 0.4869 (m-10) REVERT: B 1 MET cc_start: 0.8475 (ppp) cc_final: 0.8255 (ppp) REVERT: B 108 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8448 (mt-10) REVERT: C 14 MET cc_start: 0.7438 (tpt) cc_final: 0.6961 (mtt) REVERT: C 47 LYS cc_start: 0.8918 (ttpt) cc_final: 0.8595 (mttm) REVERT: D 18 GLU cc_start: 0.8118 (tp30) cc_final: 0.7736 (mm-30) REVERT: D 19 ARG cc_start: 0.7897 (mpt180) cc_final: 0.7524 (mmt-90) REVERT: D 22 ARG cc_start: 0.8208 (mtm-85) cc_final: 0.7872 (mtt-85) REVERT: D 63 ASN cc_start: 0.7274 (m-40) cc_final: 0.6974 (t0) REVERT: D 108 GLU cc_start: 0.7784 (tp30) cc_final: 0.7480 (tp30) REVERT: E 42 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8138 (ptm160) REVERT: E 54 GLU cc_start: 0.8450 (tp30) cc_final: 0.8249 (tp30) REVERT: E 79 ARG cc_start: 0.8014 (mtt90) cc_final: 0.7715 (mtt-85) REVERT: F 14 MET cc_start: 0.5659 (mmt) cc_final: 0.5226 (tmm) REVERT: F 19 ARG cc_start: 0.7488 (mmm160) cc_final: 0.7067 (mmm160) REVERT: F 22 ARG cc_start: 0.8241 (mmm-85) cc_final: 0.7841 (mpt180) REVERT: F 26 TYR cc_start: 0.8442 (t80) cc_final: 0.8231 (t80) REVERT: F 44 MET cc_start: 0.8547 (mtp) cc_final: 0.8248 (mtp) REVERT: F 98 GLN cc_start: 0.7393 (mt0) cc_final: 0.7159 (mt0) outliers start: 33 outliers final: 20 residues processed: 223 average time/residue: 0.3173 time to fit residues: 93.4899 Evaluate side-chains 209 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 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 256 ARG Chi-restraints excluded: chain B residue 8 THR 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 92 HIS 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 42 ARG Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 95 THR 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 55 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 24 optimal weight: 0.0670 chunk 32 optimal weight: 0.3980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 38 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10820 Z= 0.206 Angle : 0.610 9.522 15316 Z= 0.312 Chirality : 0.037 0.209 1813 Planarity : 0.005 0.122 1402 Dihedral : 22.317 176.028 3278 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.76 % Favored : 93.67 % 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 : 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: -0.29 (0.28), residues: 885 helix: 0.65 (0.20), residues: 671 sheet: -2.25 (0.93), residues: 28 loop : -2.80 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 309 HIS 0.005 0.001 HIS A 88 PHE 0.027 0.002 PHE B 80 TYR 0.022 0.002 TYR F 20 ARG 0.007 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 235 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8812 (mp0) cc_final: 0.8128 (tm-30) REVERT: A 20 ASP cc_start: 0.8395 (t0) cc_final: 0.8117 (m-30) REVERT: A 24 LYS cc_start: 0.8111 (mttp) cc_final: 0.7684 (mtmt) REVERT: A 68 VAL cc_start: 0.7926 (OUTLIER) cc_final: 0.7627 (t) REVERT: A 70 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7600 (tp30) REVERT: A 92 ASN cc_start: 0.8882 (m-40) cc_final: 0.8560 (m-40) REVERT: A 116 HIS cc_start: 0.7472 (t70) cc_final: 0.7209 (m90) REVERT: A 158 LYS cc_start: 0.8163 (mttp) cc_final: 0.7654 (mmtt) REVERT: A 164 THR cc_start: 0.8629 (m) cc_final: 0.8361 (m) REVERT: A 241 ARG cc_start: 0.8791 (tpp80) cc_final: 0.8583 (mmm160) REVERT: B 1 MET cc_start: 0.8460 (ppp) cc_final: 0.7901 (ppp) REVERT: B 108 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8377 (mt-10) REVERT: C 14 MET cc_start: 0.7428 (tpt) cc_final: 0.6947 (mtt) REVERT: C 47 LYS cc_start: 0.8989 (ttpt) cc_final: 0.8646 (mttm) REVERT: C 67 LYS cc_start: 0.8386 (mmtm) cc_final: 0.8062 (mmtp) REVERT: D 18 GLU cc_start: 0.8055 (tp30) cc_final: 0.7710 (mm-30) REVERT: D 19 ARG cc_start: 0.7837 (mpt180) cc_final: 0.7581 (mmt-90) REVERT: D 22 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.7941 (mtt-85) REVERT: D 108 GLU cc_start: 0.7765 (tp30) cc_final: 0.7445 (tp30) REVERT: E 42 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8206 (ptm160) REVERT: E 79 ARG cc_start: 0.7988 (mtt90) cc_final: 0.7674 (mtt-85) REVERT: E 94 MET cc_start: 0.9215 (mtp) cc_final: 0.8922 (mtp) REVERT: F 14 MET cc_start: 0.5601 (mmt) cc_final: 0.5343 (tmm) REVERT: F 44 MET cc_start: 0.8426 (mtp) cc_final: 0.8108 (mtp) REVERT: F 113 LEU cc_start: 0.7804 (tp) cc_final: 0.7602 (tt) outliers start: 36 outliers final: 23 residues processed: 225 average time/residue: 0.2859 time to fit residues: 84.6890 Evaluate side-chains 208 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 GLU 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 184 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 4 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 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 42 ARG 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 95 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 chunk 97 optimal weight: 8.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 chunk 94 optimal weight: 7.9990 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 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** D 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10820 Z= 0.205 Angle : 0.630 17.906 15316 Z= 0.314 Chirality : 0.037 0.209 1813 Planarity : 0.006 0.171 1402 Dihedral : 22.220 175.948 3278 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.88 % Favored : 93.56 % Rotamer: Outliers : 4.40 % Allowed : 21.87 % 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: -0.13 (0.28), residues: 885 helix: 0.72 (0.20), residues: 670 sheet: -1.80 (0.99), residues: 28 loop : -2.64 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 309 HIS 0.005 0.001 HIS A 121 PHE 0.036 0.002 PHE B 80 TYR 0.011 0.002 TYR A 35 ARG 0.006 0.000 ARG C 19 *********************** 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 227 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8797 (mp0) cc_final: 0.8400 (tm-30) REVERT: A 24 LYS cc_start: 0.8125 (mttp) cc_final: 0.7711 (mtmt) REVERT: A 68 VAL cc_start: 0.7907 (OUTLIER) cc_final: 0.7623 (t) REVERT: A 70 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7595 (tp30) REVERT: A 116 HIS cc_start: 0.7638 (t70) cc_final: 0.7224 (m90) REVERT: A 158 LYS cc_start: 0.8155 (mttp) cc_final: 0.7619 (mmtt) REVERT: A 164 THR cc_start: 0.8648 (m) cc_final: 0.8395 (m) REVERT: A 184 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8519 (tp) REVERT: B 1 MET cc_start: 0.8474 (ppp) cc_final: 0.7877 (ppp) REVERT: B 108 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8377 (mt-10) REVERT: C 14 MET cc_start: 0.7375 (tpt) cc_final: 0.6922 (mtt) REVERT: C 47 LYS cc_start: 0.8980 (ttpt) cc_final: 0.8638 (mttm) REVERT: C 56 PHE cc_start: 0.9016 (m-80) cc_final: 0.8781 (m-80) REVERT: C 67 LYS cc_start: 0.8391 (mmtm) cc_final: 0.8064 (mmtp) REVERT: D 18 GLU cc_start: 0.8041 (tp30) cc_final: 0.7722 (mm-30) REVERT: D 19 ARG cc_start: 0.7872 (mpt180) cc_final: 0.7468 (mmt-90) REVERT: D 22 ARG cc_start: 0.8278 (mtm-85) cc_final: 0.7947 (mtt-85) REVERT: D 52 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8401 (tm-30) REVERT: D 108 GLU cc_start: 0.7881 (tp30) cc_final: 0.7607 (tp30) REVERT: E 79 ARG cc_start: 0.7874 (mtt90) cc_final: 0.7579 (mtt-85) outliers start: 33 outliers final: 21 residues processed: 218 average time/residue: 0.3033 time to fit residues: 86.6606 Evaluate side-chains 211 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 115 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 200 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 0.0010 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.0170 chunk 58 optimal weight: 0.5980 overall best weight: 0.3824 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10820 Z= 0.190 Angle : 0.626 11.271 15316 Z= 0.314 Chirality : 0.037 0.208 1813 Planarity : 0.006 0.146 1402 Dihedral : 22.121 175.586 3278 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.76 % Favored : 93.67 % Rotamer: Outliers : 4.27 % Allowed : 21.73 % Favored : 74.00 % 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: 0.05 (0.28), residues: 885 helix: 0.84 (0.20), residues: 671 sheet: -1.59 (1.02), residues: 28 loop : -2.56 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 309 HIS 0.010 0.001 HIS B 97 PHE 0.025 0.002 PHE B 80 TYR 0.025 0.002 TYR F 20 ARG 0.008 0.000 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 228 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8783 (mp0) cc_final: 0.8391 (tm-30) REVERT: A 24 LYS cc_start: 0.8111 (mttp) cc_final: 0.7786 (mtmt) REVERT: A 68 VAL cc_start: 0.7911 (t) cc_final: 0.7647 (t) REVERT: A 70 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7560 (tp30) REVERT: A 116 HIS cc_start: 0.7590 (t70) cc_final: 0.7282 (m90) REVERT: A 158 LYS cc_start: 0.8163 (mttp) cc_final: 0.7632 (mmtt) REVERT: A 164 THR cc_start: 0.8633 (m) cc_final: 0.8392 (m) REVERT: A 184 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8569 (tp) REVERT: A 309 TRP cc_start: 0.5556 (m-10) cc_final: 0.4900 (m-10) REVERT: B 1 MET cc_start: 0.8357 (ppp) cc_final: 0.7848 (ppp) REVERT: C 14 MET cc_start: 0.7317 (tpt) cc_final: 0.6913 (ptp) REVERT: C 47 LYS cc_start: 0.9027 (ttpt) cc_final: 0.8700 (mttm) REVERT: C 56 PHE cc_start: 0.9019 (m-80) cc_final: 0.8802 (m-80) REVERT: C 67 LYS cc_start: 0.8397 (mmtm) cc_final: 0.8078 (mmtp) REVERT: D 19 ARG cc_start: 0.7852 (mpt180) cc_final: 0.7441 (mmt-90) REVERT: D 22 ARG cc_start: 0.8262 (mtm-85) cc_final: 0.7967 (mtt-85) REVERT: D 108 GLU cc_start: 0.7815 (tp30) cc_final: 0.7511 (tp30) REVERT: E 79 ARG cc_start: 0.7856 (mtt90) cc_final: 0.7558 (mtt-85) REVERT: E 94 MET cc_start: 0.9021 (mtp) cc_final: 0.8778 (mtp) REVERT: E 96 PRO cc_start: 0.8516 (Cg_exo) cc_final: 0.8292 (Cg_endo) REVERT: F 14 MET cc_start: 0.6001 (tmm) cc_final: 0.5758 (tpp) outliers start: 32 outliers final: 26 residues processed: 215 average time/residue: 0.3011 time to fit residues: 84.8519 Evaluate side-chains 215 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 70 GLU 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 184 LEU Chi-restraints excluded: chain A residue 200 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 95 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 16 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 66 SER 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 95 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 chunk 76 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 85 optimal weight: 0.0570 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.5594 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= 0.202 Angle : 0.633 9.742 15316 Z= 0.318 Chirality : 0.037 0.205 1813 Planarity : 0.006 0.137 1402 Dihedral : 22.052 175.690 3277 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.99 % Favored : 93.45 % Rotamer: Outliers : 3.87 % Allowed : 22.53 % 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: 0.17 (0.29), residues: 885 helix: 0.88 (0.20), residues: 670 sheet: -1.42 (1.05), residues: 28 loop : -2.33 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 309 HIS 0.009 0.001 HIS B 97 PHE 0.026 0.002 PHE B 80 TYR 0.019 0.002 TYR C 28 ARG 0.007 0.001 ARG F 36 *********************** 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 215 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8774 (mp0) cc_final: 0.8394 (tm-30) REVERT: A 24 LYS cc_start: 0.8141 (mttp) cc_final: 0.7809 (mtmt) REVERT: A 68 VAL cc_start: 0.7876 (t) cc_final: 0.7614 (t) REVERT: A 70 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7554 (tp30) REVERT: A 92 ASN cc_start: 0.8872 (m-40) cc_final: 0.8613 (m-40) REVERT: A 116 HIS cc_start: 0.7556 (t70) cc_final: 0.7269 (m90) REVERT: A 158 LYS cc_start: 0.8174 (mttp) cc_final: 0.7641 (mmtt) REVERT: A 164 THR cc_start: 0.8638 (m) cc_final: 0.8402 (m) REVERT: A 184 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8591 (tp) REVERT: A 309 TRP cc_start: 0.5533 (m-10) cc_final: 0.5027 (m-10) REVERT: B 1 MET cc_start: 0.8356 (ppp) cc_final: 0.7823 (ppp) REVERT: C 14 MET cc_start: 0.7243 (tpt) cc_final: 0.6832 (ptp) REVERT: C 47 LYS cc_start: 0.9006 (ttpt) cc_final: 0.8665 (mttm) REVERT: C 56 PHE cc_start: 0.9001 (m-80) cc_final: 0.8780 (m-80) REVERT: C 67 LYS cc_start: 0.8405 (mmtm) cc_final: 0.8086 (mmtp) REVERT: D 19 ARG cc_start: 0.7948 (mpt180) cc_final: 0.7560 (mmt-90) REVERT: D 22 ARG cc_start: 0.8219 (mtm-85) cc_final: 0.7952 (mtt-85) REVERT: D 52 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8387 (tm-30) REVERT: D 108 GLU cc_start: 0.7973 (tp30) cc_final: 0.7707 (tp30) REVERT: E 79 ARG cc_start: 0.7879 (mtt90) cc_final: 0.7583 (mtt-85) outliers start: 29 outliers final: 23 residues processed: 205 average time/residue: 0.2856 time to fit residues: 77.6313 Evaluate side-chains 204 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 70 GLU 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 184 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 256 ARG 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 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 65 VAL Chi-restraints excluded: chain D residue 66 SER 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 F residue 16 ILE Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 0.0570 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 58 optimal weight: 0.5980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10820 Z= 0.225 Angle : 0.639 10.208 15316 Z= 0.323 Chirality : 0.037 0.201 1813 Planarity : 0.006 0.133 1402 Dihedral : 22.028 175.847 3277 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.88 % Favored : 93.56 % Rotamer: Outliers : 3.87 % Allowed : 23.20 % 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: 0.15 (0.29), residues: 885 helix: 0.86 (0.20), residues: 670 sheet: -1.21 (1.07), residues: 28 loop : -2.34 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 309 HIS 0.008 0.001 HIS B 97 PHE 0.028 0.002 PHE B 80 TYR 0.016 0.002 TYR F 20 ARG 0.007 0.001 ARG A 273 *********************** 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 207 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8766 (mp0) cc_final: 0.8400 (tm-30) REVERT: A 24 LYS cc_start: 0.8036 (mttp) cc_final: 0.7627 (mtmt) REVERT: A 68 VAL cc_start: 0.7920 (t) cc_final: 0.7660 (t) REVERT: A 70 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7589 (tp30) REVERT: A 92 ASN cc_start: 0.8886 (m-40) cc_final: 0.8591 (m-40) REVERT: A 116 HIS cc_start: 0.7558 (t70) cc_final: 0.7270 (m90) REVERT: A 158 LYS cc_start: 0.8189 (mttp) cc_final: 0.7658 (mmtt) REVERT: A 164 THR cc_start: 0.8656 (m) cc_final: 0.8420 (m) REVERT: A 184 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8616 (tp) REVERT: A 309 TRP cc_start: 0.5544 (m-90) cc_final: 0.5089 (m-10) REVERT: B 1 MET cc_start: 0.8304 (ppp) cc_final: 0.7784 (ppp) REVERT: C 14 MET cc_start: 0.7351 (tpt) cc_final: 0.6894 (ptp) REVERT: C 47 LYS cc_start: 0.9029 (ttpt) cc_final: 0.8699 (mttm) REVERT: C 56 PHE cc_start: 0.9017 (m-80) cc_final: 0.8803 (m-80) REVERT: C 67 LYS cc_start: 0.8405 (mmtm) cc_final: 0.8085 (mmtp) REVERT: D 19 ARG cc_start: 0.7950 (mpt180) cc_final: 0.7430 (mmt-90) REVERT: D 22 ARG cc_start: 0.8223 (mtm-85) cc_final: 0.7968 (mtt-85) REVERT: D 52 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8219 (tm-30) REVERT: D 108 GLU cc_start: 0.7988 (tp30) cc_final: 0.7704 (tp30) REVERT: E 26 TYR cc_start: 0.8583 (t80) cc_final: 0.7516 (t80) REVERT: E 79 ARG cc_start: 0.7877 (mtt90) cc_final: 0.7589 (mtt-85) outliers start: 29 outliers final: 24 residues processed: 196 average time/residue: 0.3017 time to fit residues: 77.4018 Evaluate side-chains 204 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 70 GLU 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 184 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain B residue 4 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 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 66 SER 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 F residue 16 ILE Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10820 Z= 0.296 Angle : 0.683 10.658 15316 Z= 0.346 Chirality : 0.039 0.202 1813 Planarity : 0.006 0.134 1402 Dihedral : 22.090 176.659 3277 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.10 % Favored : 93.33 % Rotamer: Outliers : 3.60 % Allowed : 23.73 % Favored : 72.67 % 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: 0.02 (0.28), residues: 885 helix: 0.75 (0.20), residues: 664 sheet: -1.33 (1.03), residues: 28 loop : -2.22 (0.48), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 309 HIS 0.008 0.001 HIS B 97 PHE 0.031 0.002 PHE B 80 TYR 0.016 0.002 TYR C 28 ARG 0.010 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 210 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8757 (mp0) cc_final: 0.8417 (tm-30) REVERT: A 116 HIS cc_start: 0.7554 (t70) cc_final: 0.7192 (m90) REVERT: A 158 LYS cc_start: 0.8209 (mttp) cc_final: 0.7717 (mmtt) REVERT: A 164 THR cc_start: 0.8706 (m) cc_final: 0.8474 (m) REVERT: A 309 TRP cc_start: 0.5655 (m-90) cc_final: 0.5146 (m-10) REVERT: B 1 MET cc_start: 0.8421 (ppp) cc_final: 0.7875 (ppp) REVERT: C 14 MET cc_start: 0.7385 (tpt) cc_final: 0.6944 (ptp) REVERT: C 47 LYS cc_start: 0.8970 (ttpt) cc_final: 0.8631 (mttm) REVERT: C 56 PHE cc_start: 0.9054 (m-80) cc_final: 0.8844 (m-80) REVERT: C 67 LYS cc_start: 0.8344 (mmtm) cc_final: 0.8009 (mmtp) REVERT: D 22 ARG cc_start: 0.8285 (mtm-85) cc_final: 0.7956 (mtt-85) REVERT: D 37 LYS cc_start: 0.7923 (mmtm) cc_final: 0.7558 (ptmm) REVERT: D 52 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8587 (tm-30) REVERT: D 108 GLU cc_start: 0.8016 (tp30) cc_final: 0.7716 (tp30) REVERT: E 26 TYR cc_start: 0.8766 (t80) cc_final: 0.7991 (t80) REVERT: E 79 ARG cc_start: 0.7976 (mtt90) cc_final: 0.7670 (mtt-85) outliers start: 27 outliers final: 21 residues processed: 201 average time/residue: 0.3037 time to fit residues: 80.2460 Evaluate side-chains 200 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 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 4 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 92 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 52 GLN 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 F residue 16 ILE Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** ** D 32 GLN ** 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 = 0.4096 r_free = 0.4096 target = 0.156017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.121664 restraints weight = 16207.328| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.91 r_work: 0.3462 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10820 Z= 0.233 Angle : 0.657 10.867 15316 Z= 0.332 Chirality : 0.038 0.192 1813 Planarity : 0.006 0.132 1402 Dihedral : 22.065 175.532 3274 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.88 % Favored : 93.56 % Rotamer: Outliers : 2.93 % Allowed : 24.80 % Favored : 72.27 % 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: 0.10 (0.29), residues: 885 helix: 0.79 (0.19), residues: 667 sheet: -1.38 (1.02), residues: 28 loop : -2.15 (0.49), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 309 HIS 0.008 0.001 HIS B 97 PHE 0.028 0.002 PHE B 80 TYR 0.015 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: 2552.06 seconds wall clock time: 47 minutes 32.15 seconds (2852.15 seconds total)