Starting phenix.real_space_refine on Sat Aug 23 05:57:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ub8_42078/08_2025/8ub8_42078.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ub8_42078/08_2025/8ub8_42078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ub8_42078/08_2025/8ub8_42078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ub8_42078/08_2025/8ub8_42078.map" model { file = "/net/cci-nas-00/data/ceres_data/8ub8_42078/08_2025/8ub8_42078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ub8_42078/08_2025/8ub8_42078.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.84, per 1000 atoms: 0.28 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: 1.12 Conformation dependent library (CDL) restraints added in 304.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 1.47 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: 2.16 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 1743 1.33 - 1.46: 4503 1.46 - 1.60: 4271 1.60 - 1.74: 241 1.74 - 1.87: 62 Bond restraints: 10820 Sorted by residual: bond pdb=" CA GLN F 64 " pdb=" CB GLN F 64 " ideal model delta sigma weight residual 1.529 1.641 -0.112 1.64e-02 3.72e+03 4.66e+01 bond pdb=" O5' U I 24 " pdb=" C5' U I 24 " ideal model delta sigma weight residual 1.420 1.505 -0.085 1.50e-02 4.44e+03 3.23e+01 bond pdb=" CA ARG E 36 " pdb=" CB ARG E 36 " ideal model delta sigma weight residual 1.529 1.442 0.086 1.64e-02 3.72e+03 2.77e+01 bond pdb=" C PRO F 29 " pdb=" O PRO F 29 " ideal model delta sigma weight residual 1.237 1.190 0.048 1.32e-02 5.74e+03 1.31e+01 bond pdb=" CA ASN C 63 " pdb=" CB ASN C 63 " ideal model delta sigma weight residual 1.536 1.479 0.057 1.58e-02 4.01e+03 1.30e+01 ... (remaining 10815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 13778 2.26 - 4.51: 1349 4.51 - 6.76: 158 6.76 - 9.02: 26 9.02 - 11.27: 5 Bond angle restraints: 15316 Sorted by residual: angle pdb=" N VAL A 170 " pdb=" CA VAL A 170 " pdb=" C VAL A 170 " ideal model delta sigma weight residual 112.96 104.20 8.76 1.00e+00 1.00e+00 7.67e+01 angle pdb=" N ILE F 88 " pdb=" CA ILE F 88 " pdb=" C ILE F 88 " ideal model delta sigma weight residual 113.47 105.05 8.42 1.01e+00 9.80e-01 6.96e+01 angle pdb=" C3' G G 370 " pdb=" O3' G G 370 " pdb=" P G G 371 " ideal model delta sigma weight residual 120.20 108.93 11.27 1.50e+00 4.44e-01 5.65e+01 angle pdb=" C3' G G 372 " pdb=" O3' G G 372 " pdb=" P C G 373 " ideal model delta sigma weight residual 120.20 108.93 11.27 1.50e+00 4.44e-01 5.64e+01 angle pdb=" C3' G G 371 " pdb=" O3' G G 371 " pdb=" P G G 372 " ideal model delta sigma weight residual 120.20 109.25 10.95 1.50e+00 4.44e-01 5.33e+01 ... (remaining 15311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 6022 35.75 - 71.49: 622 71.49 - 107.24: 63 107.24 - 142.98: 2 142.98 - 178.73: 3 Dihedral angle restraints: 6712 sinusoidal: 4101 harmonic: 2611 Sorted by residual: dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual 232.00 53.27 178.73 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U I 3 " pdb=" C1' U I 3 " pdb=" N1 U I 3 " pdb=" C2 U I 3 " ideal model delta sinusoidal sigma weight residual -160.00 -83.65 -76.35 1 1.50e+01 4.44e-03 3.26e+01 dihedral pdb=" CA HIS A 5 " pdb=" C HIS A 5 " pdb=" N ARG A 6 " pdb=" CA ARG A 6 " ideal model delta harmonic sigma weight residual -180.00 -152.74 -27.26 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 6709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1479 0.133 - 0.266: 292 0.266 - 0.399: 30 0.399 - 0.532: 8 0.532 - 0.665: 4 Chirality restraints: 1813 Sorted by residual: chirality pdb=" P G H 117 " pdb=" OP1 G H 117 " pdb=" OP2 G H 117 " pdb=" O5' G H 117 " both_signs ideal model delta sigma weight residual True 2.41 3.08 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" P G G 369 " pdb=" OP1 G G 369 " pdb=" OP2 G G 369 " pdb=" O5' G G 369 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.06e+00 chirality pdb=" P U I 3 " pdb=" OP1 U I 3 " pdb=" OP2 U I 3 " pdb=" O5' U I 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.98e+00 ... (remaining 1810 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 28 " 0.091 2.00e-02 2.50e+03 4.79e-02 4.59e+01 pdb=" CG TYR F 28 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR F 28 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR F 28 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR F 28 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR F 28 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR F 28 " 0.034 2.00e-02 2.50e+03 pdb=" OH TYR F 28 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " 0.080 2.00e-02 2.50e+03 4.06e-02 3.30e+01 pdb=" CG TYR C 28 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 81 " 0.005 2.00e-02 2.50e+03 3.57e-02 3.18e+01 pdb=" CG TRP E 81 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP E 81 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP E 81 " 0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP E 81 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TRP E 81 " 0.038 2.00e-02 2.50e+03 pdb=" CE3 TRP E 81 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 81 " 0.033 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 81 " -0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP E 81 " -0.027 2.00e-02 2.50e+03 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 47 2.49 - 3.09: 7487 3.09 - 3.69: 19014 3.69 - 4.30: 28523 4.30 - 4.90: 41089 Nonbonded interactions: 96160 Sorted by model distance: nonbonded pdb=" O ARG A 6 " pdb=" OD1 ASN A 7 " model vdw 1.887 3.040 nonbonded pdb=" O ASN F 121 " pdb=" NH1 ARG F 122 " model vdw 2.083 3.120 nonbonded pdb=" OE1 GLN D 52 " pdb=" CE2 PHE D 56 " model vdw 2.198 3.340 nonbonded pdb=" OE1 GLU F 108 " pdb=" NH2 ARG F 111 " model vdw 2.285 3.120 nonbonded pdb=" O GLU D 21 " pdb=" OG SER D 25 " model vdw 2.289 3.040 ... (remaining 96155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = (chain 'D' and resid 13 through 121) selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.240 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.112 10820 Z= 0.656 Angle : 1.426 11.275 15316 Z= 0.910 Chirality : 0.109 0.665 1813 Planarity : 0.013 0.124 1402 Dihedral : 23.559 178.728 5028 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 27.19 Ramachandran Plot: Outliers : 2.26 % Allowed : 8.70 % Favored : 89.04 % Rotamer: Outliers : 6.27 % Allowed : 16.53 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.036 0.004 ARG A 127 TYR 0.091 0.014 TYR F 28 PHE 0.062 0.012 PHE E 84 TRP 0.072 0.013 TRP E 81 HIS 0.026 0.005 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.01074 (10820) covalent geometry : angle 1.42638 (15316) hydrogen bonds : bond 0.19784 ( 593) hydrogen bonds : angle 9.02641 ( 1599) *********************** 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 : 0.322 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: 0.1574 time to fit residues: 39.3001 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 : 0.382 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS B 92 HIS D 32 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.171320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.132586 restraints weight = 13427.717| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.47 r_work: 0.3404 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10820 Z= 0.173 Angle : 0.685 7.433 15316 Z= 0.355 Chirality : 0.040 0.230 1813 Planarity : 0.006 0.056 1402 Dihedral : 23.474 177.660 3313 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.68 % Allowed : 5.99 % Favored : 93.33 % Rotamer: Outliers : 4.00 % Allowed : 18.40 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.26), residues: 885 helix: -0.30 (0.18), residues: 671 sheet: -3.84 (0.73), residues: 26 loop : -3.41 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 111 TYR 0.015 0.002 TYR D 26 PHE 0.020 0.002 PHE D 56 TRP 0.012 0.002 TRP C 81 HIS 0.009 0.001 HIS C 38 Details of bonding type rmsd covalent geometry : bond 0.00382 (10820) covalent geometry : angle 0.68506 (15316) hydrogen bonds : bond 0.04980 ( 593) hydrogen bonds : angle 4.58128 ( 1599) *********************** 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 192 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8371 (m-40) REVERT: A 130 ARG cc_start: 0.7865 (mmt-90) cc_final: 0.7554 (mmt90) REVERT: A 278 LYS cc_start: 0.7434 (mtpt) cc_final: 0.6648 (mmtt) REVERT: B 44 MET cc_start: 0.9025 (mtp) cc_final: 0.8636 (mtp) REVERT: B 108 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7644 (mm-30) REVERT: C 57 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.8954 (mm) REVERT: C 111 ARG cc_start: 0.8380 (ttm-80) cc_final: 0.8164 (ttp80) REVERT: D 62 SER cc_start: 0.8102 (OUTLIER) cc_final: 0.7758 (p) REVERT: D 95 THR cc_start: 0.7515 (p) cc_final: 0.7160 (p) outliers start: 30 outliers final: 13 residues processed: 181 average time/residue: 0.1668 time to fit residues: 38.1089 Evaluate side-chains 166 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 70 GLU Chi-restraints excluded: chain A residue 97 ILE 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 57 ILE 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 62 SER Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 101 THR 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 71 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 20 optimal weight: 0.0970 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.169486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129609 restraints weight = 13254.236| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.47 r_work: 0.3348 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10820 Z= 0.171 Angle : 0.628 7.998 15316 Z= 0.323 Chirality : 0.037 0.183 1813 Planarity : 0.005 0.045 1402 Dihedral : 23.093 179.432 3288 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.33 % Favored : 93.11 % Rotamer: Outliers : 4.00 % Allowed : 18.67 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.28), residues: 885 helix: 0.42 (0.19), residues: 665 sheet: -3.00 (0.86), residues: 26 loop : -2.99 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 111 TYR 0.018 0.002 TYR D 26 PHE 0.019 0.002 PHE D 56 TRP 0.008 0.001 TRP C 81 HIS 0.006 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00380 (10820) covalent geometry : angle 0.62834 (15316) hydrogen bonds : bond 0.04643 ( 593) hydrogen bonds : angle 4.30910 ( 1599) *********************** 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 172 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8703 (m-40) cc_final: 0.8378 (m-40) REVERT: A 130 ARG cc_start: 0.7831 (mmt-90) cc_final: 0.7567 (mmt90) REVERT: A 278 LYS cc_start: 0.7375 (mtpt) cc_final: 0.6615 (mmtt) REVERT: B 44 MET cc_start: 0.8978 (mtp) cc_final: 0.8697 (mtp) REVERT: B 108 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7425 (mm-30) REVERT: D 14 MET cc_start: 0.7377 (tpp) cc_final: 0.7059 (tpt) REVERT: D 67 LYS cc_start: 0.7773 (mtmt) cc_final: 0.7475 (mtmt) REVERT: D 95 THR cc_start: 0.7722 (p) cc_final: 0.7387 (p) outliers start: 30 outliers final: 15 residues processed: 164 average time/residue: 0.1625 time to fit residues: 34.2169 Evaluate side-chains 154 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 103 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 ILE 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 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 50 LEU 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 88 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 58 optimal weight: 0.2980 chunk 61 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.169112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.129175 restraints weight = 13206.286| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.50 r_work: 0.3347 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3536 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= 0.146 Angle : 0.587 7.021 15316 Z= 0.302 Chirality : 0.036 0.173 1813 Planarity : 0.005 0.046 1402 Dihedral : 22.843 177.637 3280 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.99 % Favored : 93.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.29), residues: 885 helix: 0.78 (0.20), residues: 668 sheet: -2.47 (0.91), residues: 26 loop : -3.13 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 111 TYR 0.013 0.001 TYR D 26 PHE 0.015 0.002 PHE A 231 TRP 0.009 0.001 TRP A 318 HIS 0.012 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00317 (10820) covalent geometry : angle 0.58664 (15316) hydrogen bonds : bond 0.04297 ( 593) hydrogen bonds : angle 4.08722 ( 1599) *********************** 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 181 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8804 (m-40) cc_final: 0.8466 (m-40) REVERT: A 110 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8217 (mtp180) REVERT: A 278 LYS cc_start: 0.7288 (mtpt) cc_final: 0.6566 (mmtt) REVERT: B 44 MET cc_start: 0.9001 (mtp) cc_final: 0.8651 (mtp) REVERT: B 108 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7348 (mm-30) REVERT: C 111 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.8050 (ttp80) REVERT: D 13 GLN cc_start: 0.4336 (pm20) cc_final: 0.4115 (pm20) REVERT: D 67 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7414 (mtmt) REVERT: D 95 THR cc_start: 0.7909 (p) cc_final: 0.7589 (p) outliers start: 32 outliers final: 18 residues processed: 170 average time/residue: 0.1513 time to fit residues: 33.1071 Evaluate side-chains 158 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 103 LEU Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 275 SER 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 16 optimal weight: 0.8980 chunk 97 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 HIS A 313 HIS ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.167726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.127532 restraints weight = 13111.722| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.48 r_work: 0.3321 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10820 Z= 0.172 Angle : 0.609 7.182 15316 Z= 0.313 Chirality : 0.036 0.195 1813 Planarity : 0.005 0.042 1402 Dihedral : 22.677 176.909 3280 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.78 % Favored : 92.77 % Rotamer: Outliers : 4.80 % Allowed : 20.67 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.29), residues: 885 helix: 0.89 (0.20), residues: 665 sheet: -1.78 (0.97), residues: 26 loop : -3.03 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 111 TYR 0.015 0.002 TYR A 193 PHE 0.017 0.002 PHE D 80 TRP 0.016 0.001 TRP D 116 HIS 0.010 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00387 (10820) covalent geometry : angle 0.60880 (15316) hydrogen bonds : bond 0.04427 ( 593) hydrogen bonds : angle 4.13479 ( 1599) *********************** 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 185 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8864 (m-40) cc_final: 0.8521 (m-40) REVERT: A 110 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8217 (mtp180) REVERT: A 275 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8293 (t) REVERT: A 278 LYS cc_start: 0.7267 (mtpt) cc_final: 0.6550 (mmtt) REVERT: B 14 MET cc_start: 0.9166 (mtt) cc_final: 0.8921 (mtt) REVERT: B 44 MET cc_start: 0.8987 (mtp) cc_final: 0.8731 (mtp) REVERT: B 108 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7402 (mm-30) REVERT: D 67 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7502 (mtmt) REVERT: D 95 THR cc_start: 0.7863 (OUTLIER) cc_final: 0.7568 (p) outliers start: 36 outliers final: 20 residues processed: 173 average time/residue: 0.1576 time to fit residues: 34.9170 Evaluate side-chains 164 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 110 ARG 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 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 D residue 19 ARG Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 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 80 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 0.0030 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 313 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.170584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130490 restraints weight = 13306.956| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.52 r_work: 0.3375 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10820 Z= 0.142 Angle : 0.587 7.822 15316 Z= 0.304 Chirality : 0.036 0.202 1813 Planarity : 0.005 0.045 1402 Dihedral : 22.556 177.463 3279 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.99 % Favored : 93.56 % Rotamer: Outliers : 4.00 % Allowed : 21.07 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.29), residues: 885 helix: 1.01 (0.20), residues: 668 sheet: -1.14 (1.02), residues: 26 loop : -3.04 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 111 TYR 0.016 0.001 TYR D 26 PHE 0.015 0.002 PHE D 80 TRP 0.013 0.001 TRP D 116 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00315 (10820) covalent geometry : angle 0.58713 (15316) hydrogen bonds : bond 0.04279 ( 593) hydrogen bonds : angle 4.05565 ( 1599) *********************** 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 174 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8761 (m-40) cc_final: 0.8409 (m-40) REVERT: A 116 HIS cc_start: 0.8501 (t-90) cc_final: 0.8265 (t70) REVERT: A 275 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8263 (t) REVERT: A 278 LYS cc_start: 0.7238 (mtpt) cc_final: 0.6536 (mmtt) REVERT: B 14 MET cc_start: 0.9138 (mtt) cc_final: 0.8901 (mtt) REVERT: B 44 MET cc_start: 0.8932 (mtp) cc_final: 0.8656 (mtp) REVERT: B 108 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7267 (mm-30) REVERT: C 64 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8162 (tp-100) REVERT: C 111 ARG cc_start: 0.8392 (ttm-80) cc_final: 0.8134 (ttp80) REVERT: D 95 THR cc_start: 0.7759 (OUTLIER) cc_final: 0.7446 (p) outliers start: 30 outliers final: 17 residues processed: 164 average time/residue: 0.1577 time to fit residues: 33.0750 Evaluate side-chains 159 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 256 ARG Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 89 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 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 F 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.170170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.129661 restraints weight = 13182.746| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.48 r_work: 0.3367 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10820 Z= 0.163 Angle : 0.596 7.012 15316 Z= 0.306 Chirality : 0.035 0.216 1813 Planarity : 0.005 0.042 1402 Dihedral : 22.420 178.239 3275 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.21 % Favored : 93.33 % Rotamer: Outliers : 3.33 % Allowed : 21.87 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.29), residues: 885 helix: 1.08 (0.20), residues: 662 sheet: -0.68 (1.02), residues: 26 loop : -2.92 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 111 TYR 0.017 0.002 TYR D 26 PHE 0.017 0.002 PHE D 80 TRP 0.014 0.001 TRP D 116 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00370 (10820) covalent geometry : angle 0.59614 (15316) hydrogen bonds : bond 0.04332 ( 593) hydrogen bonds : angle 4.08725 ( 1599) *********************** 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 169 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8680 (m-40) cc_final: 0.8346 (m-40) REVERT: A 116 HIS cc_start: 0.8439 (t-90) cc_final: 0.8141 (t70) REVERT: A 275 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8365 (t) REVERT: B 14 MET cc_start: 0.9149 (mtt) cc_final: 0.8908 (mtt) REVERT: B 44 MET cc_start: 0.8942 (mtp) cc_final: 0.8716 (mtp) REVERT: B 108 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7159 (mm-30) REVERT: C 64 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8202 (tp-100) REVERT: D 95 THR cc_start: 0.7781 (OUTLIER) cc_final: 0.7466 (p) outliers start: 25 outliers final: 17 residues processed: 159 average time/residue: 0.1569 time to fit residues: 32.0355 Evaluate side-chains 161 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 271 LEU Chi-restraints excluded: chain A residue 275 SER 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 D residue 19 ARG Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 97 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 89 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 79 optimal weight: 0.0470 chunk 46 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 overall best weight: 0.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.168365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.127782 restraints weight = 13190.770| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.48 r_work: 0.3328 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10820 Z= 0.176 Angle : 0.608 6.919 15316 Z= 0.311 Chirality : 0.036 0.222 1813 Planarity : 0.005 0.047 1402 Dihedral : 22.364 178.412 3275 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.33 % Favored : 93.22 % Rotamer: Outliers : 3.47 % Allowed : 21.47 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.29), residues: 885 helix: 1.09 (0.20), residues: 661 sheet: -0.33 (1.03), residues: 26 loop : -2.94 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 111 TYR 0.018 0.002 TYR D 26 PHE 0.017 0.002 PHE D 80 TRP 0.015 0.001 TRP D 116 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00401 (10820) covalent geometry : angle 0.60805 (15316) hydrogen bonds : bond 0.04389 ( 593) hydrogen bonds : angle 4.08710 ( 1599) *********************** 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 168 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8859 (m-40) cc_final: 0.8495 (m-40) REVERT: A 116 HIS cc_start: 0.8365 (t-90) cc_final: 0.8067 (t70) REVERT: B 5 GLU cc_start: 0.8252 (pp20) cc_final: 0.7974 (pp20) REVERT: B 14 MET cc_start: 0.9195 (mtt) cc_final: 0.8967 (mtt) REVERT: B 44 MET cc_start: 0.8994 (mtp) cc_final: 0.8749 (mtp) REVERT: B 108 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7193 (mm-30) REVERT: C 64 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8154 (tp-100) REVERT: D 95 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7596 (p) outliers start: 26 outliers final: 18 residues processed: 160 average time/residue: 0.1532 time to fit residues: 31.5833 Evaluate side-chains 158 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 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 19 ARG Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.168789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.128182 restraints weight = 13084.307| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.49 r_work: 0.3335 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10820 Z= 0.167 Angle : 0.608 8.105 15316 Z= 0.312 Chirality : 0.036 0.225 1813 Planarity : 0.005 0.048 1402 Dihedral : 22.330 178.397 3275 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.10 % Favored : 93.45 % Rotamer: Outliers : 3.07 % Allowed : 21.87 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.28), residues: 885 helix: 1.07 (0.20), residues: 663 sheet: -0.16 (1.04), residues: 26 loop : -3.05 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 111 TYR 0.013 0.002 TYR C 28 PHE 0.016 0.002 PHE D 80 TRP 0.008 0.001 TRP A 309 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00379 (10820) covalent geometry : angle 0.60811 (15316) hydrogen bonds : bond 0.04368 ( 593) hydrogen bonds : angle 4.07984 ( 1599) *********************** 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 161 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8842 (m-40) cc_final: 0.8478 (m-40) REVERT: A 116 HIS cc_start: 0.8347 (t-90) cc_final: 0.8066 (t70) REVERT: A 275 SER cc_start: 0.8811 (OUTLIER) cc_final: 0.8340 (t) REVERT: B 5 GLU cc_start: 0.8261 (pp20) cc_final: 0.7979 (pp20) REVERT: B 14 MET cc_start: 0.9181 (mtt) cc_final: 0.8952 (mtt) REVERT: B 44 MET cc_start: 0.8977 (mtp) cc_final: 0.8729 (mtp) REVERT: B 77 MET cc_start: 0.9043 (tpt) cc_final: 0.8413 (tpt) REVERT: B 108 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7145 (mm-30) REVERT: C 64 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8157 (tp-100) REVERT: D 95 THR cc_start: 0.7913 (OUTLIER) cc_final: 0.7586 (p) outliers start: 23 outliers final: 18 residues processed: 151 average time/residue: 0.1573 time to fit residues: 30.5655 Evaluate side-chains 157 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 58 optimal weight: 0.5980 chunk 15 optimal weight: 0.0980 chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 0.0970 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 95 optimal weight: 10.0000 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.172602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132982 restraints weight = 13009.336| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.47 r_work: 0.3407 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10820 Z= 0.127 Angle : 0.573 7.209 15316 Z= 0.294 Chirality : 0.034 0.228 1813 Planarity : 0.005 0.059 1402 Dihedral : 22.182 178.937 3275 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.88 % Favored : 93.67 % Rotamer: Outliers : 2.53 % Allowed : 22.53 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.29), residues: 885 helix: 1.29 (0.20), residues: 663 sheet: 0.18 (1.08), residues: 26 loop : -3.02 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 111 TYR 0.014 0.001 TYR A 193 PHE 0.015 0.002 PHE A 231 TRP 0.012 0.001 TRP D 116 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00278 (10820) covalent geometry : angle 0.57278 (15316) hydrogen bonds : bond 0.04244 ( 593) hydrogen bonds : angle 3.96789 ( 1599) ********************** 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 155 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8681 (m-40) cc_final: 0.8356 (m-40) REVERT: A 116 HIS cc_start: 0.8225 (t-90) cc_final: 0.7990 (t70) REVERT: A 275 SER cc_start: 0.8803 (OUTLIER) cc_final: 0.8304 (t) REVERT: B 14 MET cc_start: 0.9126 (mtt) cc_final: 0.8914 (mtt) REVERT: B 44 MET cc_start: 0.8867 (mtp) cc_final: 0.8627 (mtp) REVERT: C 64 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8273 (tp-100) REVERT: D 95 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7580 (p) REVERT: E 103 GLN cc_start: 0.8017 (tp-100) cc_final: 0.7376 (tp-100) REVERT: F 90 LYS cc_start: 0.6872 (mmtt) cc_final: 0.6653 (mmtt) outliers start: 19 outliers final: 14 residues processed: 146 average time/residue: 0.1613 time to fit residues: 30.0193 Evaluate side-chains 147 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 48 optimal weight: 0.3980 chunk 34 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.171647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.131432 restraints weight = 13151.857| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.49 r_work: 0.3376 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4712 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= 0.143 Angle : 0.591 9.039 15316 Z= 0.303 Chirality : 0.035 0.227 1813 Planarity : 0.005 0.059 1402 Dihedral : 22.147 179.253 3275 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.99 % Favored : 93.67 % Rotamer: Outliers : 2.93 % Allowed : 21.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.29), residues: 885 helix: 1.29 (0.20), residues: 663 sheet: 0.39 (1.09), residues: 26 loop : -2.95 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 111 TYR 0.017 0.001 TYR D 26 PHE 0.016 0.002 PHE A 231 TRP 0.013 0.001 TRP D 116 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00319 (10820) covalent geometry : angle 0.59108 (15316) hydrogen bonds : bond 0.04269 ( 593) hydrogen bonds : angle 4.04009 ( 1599) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2780.62 seconds wall clock time: 48 minutes 48.32 seconds (2928.32 seconds total)