Starting phenix.real_space_refine on Sat Nov 16 02:05:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ub8_42078/11_2024/8ub8_42078.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ub8_42078/11_2024/8ub8_42078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ub8_42078/11_2024/8ub8_42078.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ub8_42078/11_2024/8ub8_42078.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ub8_42078/11_2024/8ub8_42078.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ub8_42078/11_2024/8ub8_42078.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 143 5.49 5 S 37 5.16 5 C 6036 2.51 5 N 1861 2.21 5 O 2222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-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: 6.69, per 1000 atoms: 0.65 Number of scatterers: 10299 At special positions: 0 Unit cell: (86, 98, 149, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 P 143 15.00 O 2222 8.00 N 1861 7.00 C 6036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 807.4 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: 44 helices and 3 sheets defined 75.0% alpha, 3.6% beta 43 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 4.27 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 14 through 27 removed outlier: 3.560A pdb=" N ASP A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 40 removed outlier: 3.857A pdb=" N GLU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.532A pdb=" N LEU A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 94 removed outlier: 3.957A pdb=" N ILE A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 98 Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.574A pdb=" N ILE A 146 " --> pdb=" O PHE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 183 through 203 removed outlier: 3.588A pdb=" N ALA A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 241 Processing helix chain 'A' and resid 273 through 289 Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.842A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 324 Processing helix chain 'B' and resid 10 through 32 removed outlier: 3.682A pdb=" N ARG B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 38 through 50 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 65 through 88 Processing helix chain 'B' and resid 95 through 122 Processing helix chain 'C' and resid 11 through 34 removed outlier: 3.657A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 51 through 62 removed outlier: 3.514A pdb=" N LEU C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 88 removed outlier: 3.592A pdb=" N LEU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 122 Processing helix chain 'D' and resid 14 through 34 removed outlier: 3.720A pdb=" N ARG D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 51 through 62 removed outlier: 3.590A pdb=" N LEU D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 removed outlier: 3.874A pdb=" N LEU D 68 " --> pdb=" O GLN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 121 removed outlier: 3.810A pdb=" N GLN D 103 " --> pdb=" O VAL D 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 34 removed outlier: 3.697A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Proline residue: E 29 - end of helix Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 51 through 62 removed outlier: 3.519A pdb=" N LEU E 55 " --> pdb=" O GLY E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 86 Processing helix chain 'E' and resid 95 through 121 Processing helix chain 'F' and resid 14 through 28 removed outlier: 3.605A pdb=" N GLU F 18 " --> pdb=" O MET F 14 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 64 through 87 removed outlier: 3.631A pdb=" N GLY F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 93 Proline residue: F 91 - end of helix No H-bonds generated for 'chain 'F' and resid 88 through 93' Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.118A pdb=" N LEU F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 213 removed outlier: 3.929A pdb=" N HIS A 248 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 260 484 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 109 hydrogen bonds 174 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 1743 1.33 - 1.46: 4503 1.46 - 1.60: 4271 1.60 - 1.74: 241 1.74 - 1.87: 62 Bond restraints: 10820 Sorted by residual: bond pdb=" CA GLN F 64 " pdb=" CB GLN F 64 " ideal model delta sigma weight residual 1.529 1.641 -0.112 1.64e-02 3.72e+03 4.66e+01 bond pdb=" O5' U I 24 " pdb=" C5' U I 24 " ideal model delta sigma weight residual 1.420 1.505 -0.085 1.50e-02 4.44e+03 3.23e+01 bond pdb=" CA ARG E 36 " pdb=" CB ARG E 36 " ideal model delta sigma weight residual 1.529 1.442 0.086 1.64e-02 3.72e+03 2.77e+01 bond pdb=" C PRO F 29 " pdb=" O PRO F 29 " ideal model delta sigma weight residual 1.237 1.190 0.048 1.32e-02 5.74e+03 1.31e+01 bond pdb=" CA ASN C 63 " pdb=" CB ASN C 63 " ideal model delta sigma weight residual 1.536 1.479 0.057 1.58e-02 4.01e+03 1.30e+01 ... (remaining 10815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 13778 2.26 - 4.51: 1349 4.51 - 6.76: 158 6.76 - 9.02: 26 9.02 - 11.27: 5 Bond angle restraints: 15316 Sorted by residual: angle pdb=" N VAL A 170 " pdb=" CA VAL A 170 " pdb=" C VAL A 170 " ideal model delta sigma weight residual 112.96 104.20 8.76 1.00e+00 1.00e+00 7.67e+01 angle pdb=" N ILE F 88 " pdb=" CA ILE F 88 " pdb=" C ILE F 88 " ideal model delta sigma weight residual 113.47 105.05 8.42 1.01e+00 9.80e-01 6.96e+01 angle pdb=" C3' G G 370 " pdb=" O3' G G 370 " pdb=" P G G 371 " ideal model delta sigma weight residual 120.20 108.93 11.27 1.50e+00 4.44e-01 5.65e+01 angle pdb=" C3' G G 372 " pdb=" O3' G G 372 " pdb=" P C G 373 " ideal model delta sigma weight residual 120.20 108.93 11.27 1.50e+00 4.44e-01 5.64e+01 angle pdb=" C3' G G 371 " pdb=" O3' G G 371 " pdb=" P G G 372 " ideal model delta sigma weight residual 120.20 109.25 10.95 1.50e+00 4.44e-01 5.33e+01 ... (remaining 15311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 6022 35.75 - 71.49: 622 71.49 - 107.24: 63 107.24 - 142.98: 2 142.98 - 178.73: 3 Dihedral angle restraints: 6712 sinusoidal: 4101 harmonic: 2611 Sorted by residual: dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual 232.00 53.27 178.73 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U I 3 " pdb=" C1' U I 3 " pdb=" N1 U I 3 " pdb=" C2 U I 3 " ideal model delta sinusoidal sigma weight residual -160.00 -83.65 -76.35 1 1.50e+01 4.44e-03 3.26e+01 dihedral pdb=" CA HIS A 5 " pdb=" C HIS A 5 " pdb=" N ARG A 6 " pdb=" CA ARG A 6 " ideal model delta harmonic sigma weight residual -180.00 -152.74 -27.26 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 6709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1479 0.133 - 0.266: 292 0.266 - 0.399: 30 0.399 - 0.532: 8 0.532 - 0.665: 4 Chirality restraints: 1813 Sorted by residual: chirality pdb=" P G H 117 " pdb=" OP1 G H 117 " pdb=" OP2 G H 117 " pdb=" O5' G H 117 " both_signs ideal model delta sigma weight residual True 2.41 3.08 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" P G G 369 " pdb=" OP1 G G 369 " pdb=" OP2 G G 369 " pdb=" O5' G G 369 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.06e+00 chirality pdb=" P U I 3 " pdb=" OP1 U I 3 " pdb=" OP2 U I 3 " pdb=" O5' U I 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.98e+00 ... (remaining 1810 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 28 " 0.091 2.00e-02 2.50e+03 4.79e-02 4.59e+01 pdb=" CG TYR F 28 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR F 28 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR F 28 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR F 28 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR F 28 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR F 28 " 0.034 2.00e-02 2.50e+03 pdb=" OH TYR F 28 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " 0.080 2.00e-02 2.50e+03 4.06e-02 3.30e+01 pdb=" CG TYR C 28 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 81 " 0.005 2.00e-02 2.50e+03 3.57e-02 3.18e+01 pdb=" CG TRP E 81 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP E 81 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP E 81 " 0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP E 81 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TRP E 81 " 0.038 2.00e-02 2.50e+03 pdb=" CE3 TRP E 81 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 81 " 0.033 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 81 " -0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP E 81 " -0.027 2.00e-02 2.50e+03 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 47 2.49 - 3.09: 7487 3.09 - 3.69: 19014 3.69 - 4.30: 28523 4.30 - 4.90: 41089 Nonbonded interactions: 96160 Sorted by model distance: nonbonded pdb=" O ARG A 6 " pdb=" OD1 ASN A 7 " model vdw 1.887 3.040 nonbonded pdb=" O ASN F 121 " pdb=" NH1 ARG F 122 " model vdw 2.083 3.120 nonbonded pdb=" OE1 GLN D 52 " pdb=" CE2 PHE D 56 " model vdw 2.198 3.340 nonbonded pdb=" OE1 GLU F 108 " pdb=" NH2 ARG F 111 " model vdw 2.285 3.120 nonbonded pdb=" O GLU D 21 " pdb=" OG SER D 25 " model vdw 2.289 3.040 ... (remaining 96155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = (chain 'D' and resid 13 through 121) selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.750 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.112 10820 Z= 0.672 Angle : 1.426 11.275 15316 Z= 0.910 Chirality : 0.109 0.665 1813 Planarity : 0.013 0.124 1402 Dihedral : 23.559 178.728 5028 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 27.19 Ramachandran Plot: Outliers : 2.26 % Allowed : 8.70 % Favored : 89.04 % Rotamer: Outliers : 6.27 % Allowed : 16.53 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.22), residues: 885 helix: -2.01 (0.16), residues: 656 sheet: -4.26 (0.80), residues: 26 loop : -4.02 (0.35), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.013 TRP E 81 HIS 0.026 0.005 HIS A 88 PHE 0.062 0.012 PHE E 84 TYR 0.091 0.014 TYR F 28 ARG 0.036 0.004 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.5413 (OUTLIER) cc_final: 0.5071 (p90) REVERT: A 111 PRO cc_start: 0.7939 (Cg_exo) cc_final: 0.7738 (Cg_endo) REVERT: A 112 ASP cc_start: 0.8570 (m-30) cc_final: 0.8269 (t0) REVERT: A 309 TRP cc_start: 0.6882 (m100) cc_final: 0.6657 (m100) REVERT: B 77 MET cc_start: 0.8180 (tpt) cc_final: 0.7837 (tpt) REVERT: C 91 PRO cc_start: 0.8287 (OUTLIER) cc_final: 0.7904 (Cg_endo) REVERT: D 18 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7220 (tp30) REVERT: D 26 TYR cc_start: 0.8019 (t80) cc_final: 0.7809 (t80) REVERT: D 95 THR cc_start: 0.7279 (p) cc_final: 0.7070 (p) REVERT: E 63 ASN cc_start: 0.7839 (t0) cc_final: 0.6734 (p0) outliers start: 47 outliers final: 16 residues processed: 195 average time/residue: 0.3209 time to fit residues: 80.1365 Evaluate side-chains 164 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 180 PRO Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 91 PRO Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 103 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 306 HIS B 92 HIS D 32 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 92 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10820 Z= 0.262 Angle : 0.703 8.659 15316 Z= 0.362 Chirality : 0.041 0.233 1813 Planarity : 0.006 0.043 1402 Dihedral : 23.588 177.237 3313 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.33 % Favored : 93.11 % Rotamer: Outliers : 4.93 % Allowed : 17.07 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.26), residues: 885 helix: -0.38 (0.18), residues: 670 sheet: -3.85 (0.72), residues: 26 loop : -3.42 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 81 HIS 0.012 0.001 HIS C 38 PHE 0.019 0.002 PHE D 56 TYR 0.016 0.002 TYR A 152 ARG 0.005 0.001 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8480 (m-40) REVERT: A 69 TYR cc_start: 0.5058 (OUTLIER) cc_final: 0.4827 (p90) REVERT: A 80 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7023 (mp0) REVERT: A 125 GLU cc_start: 0.7514 (tp30) cc_final: 0.7162 (mm-30) REVERT: A 278 LYS cc_start: 0.6289 (mtpt) cc_final: 0.6037 (mmtt) REVERT: B 44 MET cc_start: 0.8413 (mtp) cc_final: 0.8005 (mtp) REVERT: B 108 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7348 (mm-30) REVERT: C 111 ARG cc_start: 0.7841 (ttm-80) cc_final: 0.7090 (ttp80) REVERT: D 14 MET cc_start: 0.5840 (ttt) cc_final: 0.5542 (ttm) REVERT: D 26 TYR cc_start: 0.8159 (t80) cc_final: 0.7888 (t80) outliers start: 37 outliers final: 14 residues processed: 188 average time/residue: 0.3484 time to fit residues: 83.0162 Evaluate side-chains 167 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 14 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS A 313 HIS ** 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: 0.7035 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10820 Z= 0.295 Angle : 0.662 9.862 15316 Z= 0.338 Chirality : 0.039 0.191 1813 Planarity : 0.005 0.046 1402 Dihedral : 23.176 179.362 3291 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.78 % Favored : 92.66 % Rotamer: Outliers : 5.20 % Allowed : 18.67 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.28), residues: 885 helix: 0.26 (0.19), residues: 667 sheet: -3.14 (0.85), residues: 26 loop : -3.13 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 116 HIS 0.006 0.001 HIS A 27 PHE 0.018 0.002 PHE D 80 TYR 0.016 0.002 TYR A 152 ARG 0.008 0.001 ARG F 111 *********************** 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 188 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7963 (t-100) cc_final: 0.7360 (t60) REVERT: A 54 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7974 (mttt) REVERT: A 80 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7067 (mp0) REVERT: A 125 GLU cc_start: 0.7517 (tp30) cc_final: 0.7245 (mm-30) REVERT: A 278 LYS cc_start: 0.6285 (mtpt) cc_final: 0.5989 (mmtt) REVERT: B 44 MET cc_start: 0.8413 (mtp) cc_final: 0.8119 (mtp) REVERT: B 89 GLN cc_start: 0.6932 (mm-40) cc_final: 0.6675 (tp40) REVERT: B 108 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7216 (mm-30) REVERT: D 14 MET cc_start: 0.5671 (ttt) cc_final: 0.5448 (tpp) REVERT: D 18 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7552 (mt-10) REVERT: D 26 TYR cc_start: 0.8200 (t80) cc_final: 0.7970 (t80) REVERT: D 67 LYS cc_start: 0.6868 (mtmt) cc_final: 0.6636 (mtmt) outliers start: 39 outliers final: 18 residues processed: 174 average time/residue: 0.3339 time to fit residues: 74.4684 Evaluate side-chains 161 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 HIS A 313 HIS ** 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: 0.7020 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10820 Z= 0.233 Angle : 0.620 8.405 15316 Z= 0.316 Chirality : 0.037 0.175 1813 Planarity : 0.005 0.046 1402 Dihedral : 22.928 179.544 3282 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.21 % Favored : 93.22 % Rotamer: Outliers : 4.27 % Allowed : 20.27 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.28), residues: 885 helix: 0.58 (0.20), residues: 671 sheet: -2.43 (0.89), residues: 26 loop : -3.08 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.007 0.001 HIS A 313 PHE 0.017 0.002 PHE D 80 TYR 0.014 0.002 TYR A 152 ARG 0.009 0.000 ARG F 111 *********************** 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 182 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7962 (t-100) cc_final: 0.7325 (t60) REVERT: A 80 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7076 (mp0) REVERT: A 125 GLU cc_start: 0.7417 (tp30) cc_final: 0.7181 (mm-30) REVERT: A 278 LYS cc_start: 0.6320 (mtpt) cc_final: 0.6028 (mmtt) REVERT: B 44 MET cc_start: 0.8400 (mtp) cc_final: 0.8064 (mtp) REVERT: B 108 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7086 (mm-30) REVERT: D 17 VAL cc_start: 0.7219 (p) cc_final: 0.6989 (p) REVERT: D 67 LYS cc_start: 0.6980 (mtmt) cc_final: 0.6724 (mtmt) REVERT: D 89 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7181 (mm-40) outliers start: 32 outliers final: 22 residues processed: 172 average time/residue: 0.3231 time to fit residues: 71.3867 Evaluate side-chains 163 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10820 Z= 0.237 Angle : 0.607 7.197 15316 Z= 0.312 Chirality : 0.036 0.190 1813 Planarity : 0.005 0.051 1402 Dihedral : 22.814 179.216 3282 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.44 % Favored : 93.11 % Rotamer: Outliers : 4.27 % Allowed : 19.60 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.28), residues: 885 helix: 0.76 (0.20), residues: 668 sheet: -1.88 (0.95), residues: 26 loop : -3.09 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 116 HIS 0.005 0.001 HIS A 313 PHE 0.016 0.002 PHE A 231 TYR 0.017 0.002 TYR A 193 ARG 0.011 0.000 ARG F 111 *********************** 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 179 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7954 (t-100) cc_final: 0.7295 (t60) REVERT: A 80 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7042 (mp0) REVERT: A 275 SER cc_start: 0.7408 (OUTLIER) cc_final: 0.7180 (t) REVERT: A 278 LYS cc_start: 0.6343 (mtpt) cc_final: 0.6064 (mmtt) REVERT: B 42 ARG cc_start: 0.7535 (ttp-170) cc_final: 0.7275 (ttp-170) REVERT: B 44 MET cc_start: 0.8375 (mtp) cc_final: 0.8054 (mtp) REVERT: B 108 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7115 (mm-30) REVERT: C 111 ARG cc_start: 0.7758 (ttm-80) cc_final: 0.7051 (ttp80) REVERT: D 17 VAL cc_start: 0.7295 (OUTLIER) cc_final: 0.6979 (p) REVERT: D 21 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7061 (mt-10) REVERT: D 26 TYR cc_start: 0.8194 (t80) cc_final: 0.7920 (t80) REVERT: D 67 LYS cc_start: 0.7036 (mtmt) cc_final: 0.6745 (mtmt) REVERT: D 89 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7471 (mm-40) outliers start: 32 outliers final: 21 residues processed: 169 average time/residue: 0.3350 time to fit residues: 72.4108 Evaluate side-chains 166 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.1980 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 313 HIS ** 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: 0.7011 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10820 Z= 0.205 Angle : 0.590 7.050 15316 Z= 0.304 Chirality : 0.035 0.203 1813 Planarity : 0.005 0.058 1402 Dihedral : 22.690 179.763 3282 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.21 % Favored : 93.33 % Rotamer: Outliers : 4.80 % Allowed : 19.73 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.29), residues: 885 helix: 0.88 (0.20), residues: 668 sheet: -1.35 (0.99), residues: 26 loop : -3.07 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 116 HIS 0.018 0.001 HIS A 313 PHE 0.016 0.002 PHE D 80 TYR 0.014 0.001 TYR A 193 ARG 0.010 0.000 ARG F 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7946 (t-100) cc_final: 0.7272 (t60) REVERT: A 80 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7064 (mp0) REVERT: A 275 SER cc_start: 0.7413 (OUTLIER) cc_final: 0.7182 (t) REVERT: A 278 LYS cc_start: 0.6326 (mtpt) cc_final: 0.6054 (mmtt) REVERT: B 44 MET cc_start: 0.8365 (mtp) cc_final: 0.8039 (mtp) REVERT: B 108 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7105 (mm-30) REVERT: C 64 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7675 (tp-100) REVERT: C 111 ARG cc_start: 0.7758 (ttm-80) cc_final: 0.7047 (ttp80) REVERT: D 21 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6991 (mt-10) REVERT: D 26 TYR cc_start: 0.8205 (t80) cc_final: 0.7945 (t80) REVERT: D 67 LYS cc_start: 0.7058 (mtmt) cc_final: 0.6793 (mtmt) outliers start: 36 outliers final: 25 residues processed: 169 average time/residue: 0.3307 time to fit residues: 72.2030 Evaluate side-chains 165 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 36 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10820 Z= 0.252 Angle : 0.604 7.077 15316 Z= 0.310 Chirality : 0.036 0.217 1813 Planarity : 0.005 0.055 1402 Dihedral : 22.564 179.892 3278 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.33 % Favored : 93.22 % Rotamer: Outliers : 4.53 % Allowed : 20.13 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.29), residues: 885 helix: 0.94 (0.20), residues: 661 sheet: -0.91 (1.02), residues: 26 loop : -2.97 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 116 HIS 0.012 0.001 HIS A 313 PHE 0.018 0.002 PHE D 80 TYR 0.015 0.002 TYR C 28 ARG 0.010 0.000 ARG F 111 *********************** 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 170 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7965 (t-100) cc_final: 0.7280 (t60) REVERT: A 80 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7036 (mp0) REVERT: B 42 ARG cc_start: 0.7543 (ttp-170) cc_final: 0.7316 (ttp-170) REVERT: B 44 MET cc_start: 0.8349 (mtp) cc_final: 0.8047 (mtp) REVERT: B 108 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7072 (mm-30) REVERT: C 64 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7676 (tp-100) REVERT: C 111 ARG cc_start: 0.7806 (ttm-80) cc_final: 0.7120 (ttp80) REVERT: D 21 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7018 (mt-10) REVERT: D 26 TYR cc_start: 0.8217 (t80) cc_final: 0.7979 (t80) REVERT: D 67 LYS cc_start: 0.7076 (mtmt) cc_final: 0.6836 (mtmt) REVERT: D 89 GLN cc_start: 0.8058 (tp40) cc_final: 0.7858 (mm-40) outliers start: 34 outliers final: 25 residues processed: 158 average time/residue: 0.3165 time to fit residues: 64.3014 Evaluate side-chains 161 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 36 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10820 Z= 0.232 Angle : 0.590 6.951 15316 Z= 0.303 Chirality : 0.035 0.224 1813 Planarity : 0.005 0.056 1402 Dihedral : 22.447 179.808 3278 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.33 % Favored : 93.22 % Rotamer: Outliers : 3.87 % Allowed : 20.27 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.29), residues: 885 helix: 1.01 (0.20), residues: 662 sheet: -0.53 (1.04), residues: 26 loop : -2.90 (0.45), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 116 HIS 0.008 0.001 HIS A 116 PHE 0.017 0.002 PHE D 80 TYR 0.015 0.002 TYR C 28 ARG 0.010 0.000 ARG F 111 *********************** 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 163 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7959 (t-100) cc_final: 0.7260 (t60) REVERT: A 80 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7047 (mp0) REVERT: B 44 MET cc_start: 0.8348 (mtp) cc_final: 0.8052 (mtp) REVERT: B 108 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7044 (mm-30) REVERT: C 64 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7723 (tp-100) REVERT: C 111 ARG cc_start: 0.7677 (ttm-80) cc_final: 0.6994 (ttp80) REVERT: D 21 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6795 (mt-10) REVERT: D 26 TYR cc_start: 0.8156 (t80) cc_final: 0.7864 (t80) REVERT: D 67 LYS cc_start: 0.7074 (mtmt) cc_final: 0.6867 (mtmt) outliers start: 29 outliers final: 23 residues processed: 153 average time/residue: 0.3205 time to fit residues: 63.1336 Evaluate side-chains 155 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 36 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 54 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 58 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10820 Z= 0.241 Angle : 0.600 7.432 15316 Z= 0.307 Chirality : 0.036 0.230 1813 Planarity : 0.005 0.056 1402 Dihedral : 22.377 179.775 3277 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.99 % Favored : 93.45 % Rotamer: Outliers : 3.47 % Allowed : 21.07 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.29), residues: 885 helix: 1.04 (0.20), residues: 661 sheet: -0.23 (1.05), residues: 26 loop : -2.87 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 309 HIS 0.007 0.001 HIS A 116 PHE 0.017 0.002 PHE D 80 TYR 0.015 0.002 TYR C 28 ARG 0.013 0.001 ARG F 111 *********************** 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 159 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7962 (t-100) cc_final: 0.7255 (t60) REVERT: A 42 ASP cc_start: 0.8164 (p0) cc_final: 0.7915 (p0) REVERT: A 80 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7048 (mp0) REVERT: B 42 ARG cc_start: 0.7563 (ttp-170) cc_final: 0.7227 (ttp-170) REVERT: B 44 MET cc_start: 0.8343 (mtp) cc_final: 0.8047 (mtp) REVERT: B 108 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7045 (mm-30) REVERT: C 64 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7722 (tp-100) REVERT: C 111 ARG cc_start: 0.7717 (ttm-80) cc_final: 0.7056 (ttp80) REVERT: D 21 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6801 (mt-10) REVERT: D 26 TYR cc_start: 0.8162 (t80) cc_final: 0.7866 (t80) REVERT: D 68 LEU cc_start: 0.8387 (mt) cc_final: 0.8135 (tp) outliers start: 26 outliers final: 21 residues processed: 147 average time/residue: 0.3226 time to fit residues: 60.9694 Evaluate side-chains 153 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 63 optimal weight: 0.0870 chunk 85 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10820 Z= 0.208 Angle : 0.589 7.116 15316 Z= 0.302 Chirality : 0.035 0.233 1813 Planarity : 0.005 0.056 1402 Dihedral : 22.288 179.421 3275 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.10 % Favored : 93.33 % Rotamer: Outliers : 2.93 % Allowed : 21.47 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.29), residues: 885 helix: 1.13 (0.20), residues: 661 sheet: 0.03 (1.08), residues: 26 loop : -2.86 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 116 HIS 0.011 0.001 HIS D 38 PHE 0.016 0.002 PHE D 80 TYR 0.013 0.001 TYR C 28 ARG 0.014 0.001 ARG F 111 ********************** 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 157 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 TRP cc_start: 0.7926 (t-100) cc_final: 0.7213 (t60) REVERT: A 42 ASP cc_start: 0.8113 (p0) cc_final: 0.7847 (p0) REVERT: A 154 MET cc_start: 0.8015 (mtt) cc_final: 0.7686 (mtt) REVERT: A 275 SER cc_start: 0.7522 (OUTLIER) cc_final: 0.7303 (t) REVERT: B 42 ARG cc_start: 0.7586 (ttp-170) cc_final: 0.7296 (ttp-170) REVERT: B 44 MET cc_start: 0.8344 (mtp) cc_final: 0.8027 (mtp) REVERT: B 77 MET cc_start: 0.8189 (tpt) cc_final: 0.7666 (tpt) REVERT: B 108 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7047 (mm-30) REVERT: C 111 ARG cc_start: 0.7697 (ttm-80) cc_final: 0.6981 (ttp80) REVERT: D 21 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6677 (mt-10) REVERT: D 26 TYR cc_start: 0.8159 (t80) cc_final: 0.7869 (t80) REVERT: D 68 LEU cc_start: 0.8296 (mt) cc_final: 0.8041 (tp) outliers start: 22 outliers final: 18 residues processed: 149 average time/residue: 0.3468 time to fit residues: 65.9346 Evaluate side-chains 152 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 0.0870 chunk 10 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN C 92 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.172336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133173 restraints weight = 12801.745| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.43 r_work: 0.3398 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10820 Z= 0.177 Angle : 0.568 7.117 15316 Z= 0.292 Chirality : 0.034 0.237 1813 Planarity : 0.005 0.057 1402 Dihedral : 22.156 178.935 3275 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.76 % Favored : 93.79 % Rotamer: Outliers : 2.67 % Allowed : 22.13 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.29), residues: 885 helix: 1.26 (0.20), residues: 663 sheet: 0.28 (1.09), residues: 26 loop : -2.88 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 116 HIS 0.007 0.001 HIS C 92 PHE 0.015 0.002 PHE A 231 TYR 0.012 0.001 TYR D 26 ARG 0.015 0.000 ARG F 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2523.63 seconds wall clock time: 46 minutes 56.82 seconds (2816.82 seconds total)