Starting phenix.real_space_refine on Fri Feb 14 11:13:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ub8_42078/02_2025/8ub8_42078.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ub8_42078/02_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_42078/02_2025/8ub8_42078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ub8_42078/02_2025/8ub8_42078.map" model { file = "/net/cci-nas-00/data/ceres_data/8ub8_42078/02_2025/8ub8_42078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ub8_42078/02_2025/8ub8_42078.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 143 5.49 5 S 37 5.16 5 C 6036 2.51 5 N 1861 2.21 5 O 2222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10299 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2690 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain: "B" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "C" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 914 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "D" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 893 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 876 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "F" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "G" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 311 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 3} Link IDs: {'rna3p': 13} Chain: "H" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 270 Classifications: {'RNA': 13} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 8} Link IDs: {'rna3p': 12} Chain: "I" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2481 Classifications: {'RNA': 116} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 51, 'rna3p_pyr': 48} Link IDs: {'rna2p': 17, 'rna3p': 98} Chain breaks: 2 Time building chain proxies: 7.12, per 1000 atoms: 0.69 Number of scatterers: 10299 At special positions: 0 Unit cell: (86, 98, 149, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 P 143 15.00 O 2222 8.00 N 1861 7.00 C 6036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 841.1 milliseconds 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 3 sheets defined 75.0% alpha, 3.6% beta 43 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 4.22 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: 3.48 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 1743 1.33 - 1.46: 4503 1.46 - 1.60: 4271 1.60 - 1.74: 241 1.74 - 1.87: 62 Bond restraints: 10820 Sorted by residual: bond pdb=" CA GLN F 64 " pdb=" CB GLN F 64 " ideal model delta sigma weight residual 1.529 1.641 -0.112 1.64e-02 3.72e+03 4.66e+01 bond pdb=" O5' U I 24 " pdb=" C5' U I 24 " ideal model delta sigma weight residual 1.420 1.505 -0.085 1.50e-02 4.44e+03 3.23e+01 bond pdb=" CA ARG E 36 " pdb=" CB ARG E 36 " ideal model delta sigma weight residual 1.529 1.442 0.086 1.64e-02 3.72e+03 2.77e+01 bond pdb=" C PRO F 29 " pdb=" O PRO F 29 " ideal model delta sigma weight residual 1.237 1.190 0.048 1.32e-02 5.74e+03 1.31e+01 bond pdb=" CA ASN C 63 " pdb=" CB ASN C 63 " ideal model delta sigma weight residual 1.536 1.479 0.057 1.58e-02 4.01e+03 1.30e+01 ... (remaining 10815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 13778 2.26 - 4.51: 1349 4.51 - 6.76: 158 6.76 - 9.02: 26 9.02 - 11.27: 5 Bond angle restraints: 15316 Sorted by residual: angle pdb=" N VAL A 170 " pdb=" CA VAL A 170 " pdb=" C VAL A 170 " ideal model delta sigma weight residual 112.96 104.20 8.76 1.00e+00 1.00e+00 7.67e+01 angle pdb=" N ILE F 88 " pdb=" CA ILE F 88 " pdb=" C ILE F 88 " ideal model delta sigma weight residual 113.47 105.05 8.42 1.01e+00 9.80e-01 6.96e+01 angle pdb=" C3' G G 370 " pdb=" O3' G G 370 " pdb=" P G G 371 " ideal model delta sigma weight residual 120.20 108.93 11.27 1.50e+00 4.44e-01 5.65e+01 angle pdb=" C3' G G 372 " pdb=" O3' G G 372 " pdb=" P C G 373 " ideal model delta sigma weight residual 120.20 108.93 11.27 1.50e+00 4.44e-01 5.64e+01 angle pdb=" C3' G G 371 " pdb=" O3' G G 371 " pdb=" P G G 372 " ideal model delta sigma weight residual 120.20 109.25 10.95 1.50e+00 4.44e-01 5.33e+01 ... (remaining 15311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 6022 35.75 - 71.49: 622 71.49 - 107.24: 63 107.24 - 142.98: 2 142.98 - 178.73: 3 Dihedral angle restraints: 6712 sinusoidal: 4101 harmonic: 2611 Sorted by residual: dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual 232.00 53.27 178.73 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U I 3 " pdb=" C1' U I 3 " pdb=" N1 U I 3 " pdb=" C2 U I 3 " ideal model delta sinusoidal sigma weight residual -160.00 -83.65 -76.35 1 1.50e+01 4.44e-03 3.26e+01 dihedral pdb=" CA HIS A 5 " pdb=" C HIS A 5 " pdb=" N ARG A 6 " pdb=" CA ARG A 6 " ideal model delta harmonic sigma weight residual -180.00 -152.74 -27.26 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 6709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1479 0.133 - 0.266: 292 0.266 - 0.399: 30 0.399 - 0.532: 8 0.532 - 0.665: 4 Chirality restraints: 1813 Sorted by residual: chirality pdb=" P G H 117 " pdb=" OP1 G H 117 " pdb=" OP2 G H 117 " pdb=" O5' G H 117 " both_signs ideal model delta sigma weight residual True 2.41 3.08 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" P G G 369 " pdb=" OP1 G G 369 " pdb=" OP2 G G 369 " pdb=" O5' G G 369 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.06e+00 chirality pdb=" P U I 3 " pdb=" OP1 U I 3 " pdb=" OP2 U I 3 " pdb=" O5' U I 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.98e+00 ... (remaining 1810 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 28 " 0.091 2.00e-02 2.50e+03 4.79e-02 4.59e+01 pdb=" CG TYR F 28 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR F 28 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR F 28 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR F 28 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR F 28 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR F 28 " 0.034 2.00e-02 2.50e+03 pdb=" OH TYR F 28 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " 0.080 2.00e-02 2.50e+03 4.06e-02 3.30e+01 pdb=" CG TYR C 28 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 81 " 0.005 2.00e-02 2.50e+03 3.57e-02 3.18e+01 pdb=" CG TRP E 81 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP E 81 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP E 81 " 0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP E 81 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TRP E 81 " 0.038 2.00e-02 2.50e+03 pdb=" CE3 TRP E 81 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 81 " 0.033 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 81 " -0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP E 81 " -0.027 2.00e-02 2.50e+03 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 47 2.49 - 3.09: 7487 3.09 - 3.69: 19014 3.69 - 4.30: 28523 4.30 - 4.90: 41089 Nonbonded interactions: 96160 Sorted by model distance: nonbonded pdb=" O ARG A 6 " pdb=" OD1 ASN A 7 " model vdw 1.887 3.040 nonbonded pdb=" O ASN F 121 " pdb=" NH1 ARG F 122 " model vdw 2.083 3.120 nonbonded pdb=" OE1 GLN D 52 " pdb=" CE2 PHE D 56 " model vdw 2.198 3.340 nonbonded pdb=" OE1 GLU F 108 " pdb=" NH2 ARG F 111 " model vdw 2.285 3.120 nonbonded pdb=" O GLU D 21 " pdb=" OG SER D 25 " model vdw 2.289 3.040 ... (remaining 96155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = (chain 'D' and resid 13 through 121) selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.800 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.710 ------------------------------------------------------------------------------- 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 : 0.898 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: 0.3214 time to fit residues: 80.6520 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 : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 180 PRO Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 91 PRO Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 103 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 306 HIS B 92 HIS D 32 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 92 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.167403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.128466 restraints weight = 13095.922| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.44 r_work: 0.3347 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8425 (m-40) REVERT: A 69 TYR cc_start: 0.5805 (OUTLIER) cc_final: 0.5384 (p90) REVERT: A 72 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7535 (ttpp) REVERT: A 278 LYS cc_start: 0.7377 (mtpt) cc_final: 0.6653 (mmtt) REVERT: B 44 MET cc_start: 0.8983 (mtp) cc_final: 0.8586 (mtp) REVERT: B 108 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7521 (mm-30) REVERT: C 111 ARG cc_start: 0.8527 (ttm-80) cc_final: 0.8159 (ttp80) REVERT: D 62 SER cc_start: 0.8201 (OUTLIER) cc_final: 0.7720 (p) REVERT: D 95 THR cc_start: 0.7597 (p) cc_final: 0.7242 (p) outliers start: 37 outliers final: 14 residues processed: 188 average time/residue: 0.3436 time to fit residues: 82.1817 Evaluate side-chains 167 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 14 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 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 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 = 0.3971 r_free = 0.3971 target = 0.166980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127132 restraints weight = 13282.282| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.50 r_work: 0.3318 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10820 Z= 0.254 Angle : 0.639 10.413 15316 Z= 0.327 Chirality : 0.038 0.190 1813 Planarity : 0.005 0.047 1402 Dihedral : 23.148 179.575 3292 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.44 % Favored : 92.99 % Rotamer: Outliers : 5.07 % Allowed : 18.27 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 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: -0.79 (0.28), residues: 885 helix: 0.34 (0.19), residues: 669 sheet: -3.08 (0.86), residues: 26 loop : -3.08 (0.45), residues: 190 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 0.017 0.002 PHE D 80 TYR 0.018 0.002 TYR D 26 ARG 0.009 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 185 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8839 (m-40) cc_final: 0.8516 (m-40) REVERT: A 67 LEU cc_start: 0.6235 (pp) cc_final: 0.6030 (mp) REVERT: A 278 LYS cc_start: 0.7295 (mtpt) cc_final: 0.6555 (mmtt) REVERT: B 44 MET cc_start: 0.9004 (mtp) cc_final: 0.8713 (mtp) REVERT: B 108 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7402 (mm-30) REVERT: C 111 ARG cc_start: 0.8475 (ttm-80) cc_final: 0.8054 (ttp80) REVERT: D 67 LYS cc_start: 0.7695 (mtmt) cc_final: 0.7250 (mtmt) REVERT: D 95 THR cc_start: 0.7825 (p) cc_final: 0.7488 (p) outliers start: 38 outliers final: 18 residues processed: 172 average time/residue: 0.3346 time to fit residues: 73.4582 Evaluate side-chains 157 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 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 63 ASN 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 Chi-restraints excluded: chain F residue 97 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS A 306 HIS A 313 HIS ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.165219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.125372 restraints weight = 13151.216| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.46 r_work: 0.3298 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10820 Z= 0.311 Angle : 0.648 8.454 15316 Z= 0.329 Chirality : 0.038 0.175 1813 Planarity : 0.005 0.044 1402 Dihedral : 22.975 178.986 3282 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.78 % Favored : 92.66 % Rotamer: Outliers : 4.53 % Allowed : 20.67 % 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 (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: -0.50 (0.28), residues: 885 helix: 0.55 (0.19), residues: 667 sheet: -2.39 (0.90), residues: 26 loop : -3.06 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 318 HIS 0.022 0.001 HIS A 313 PHE 0.018 0.002 PHE D 80 TYR 0.017 0.002 TYR D 26 ARG 0.008 0.001 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 183 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8872 (m-40) cc_final: 0.8524 (m-40) REVERT: A 67 LEU cc_start: 0.6374 (pp) cc_final: 0.6034 (mp) REVERT: A 110 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8278 (mtp180) REVERT: A 278 LYS cc_start: 0.7327 (mtpt) cc_final: 0.6571 (mmtt) REVERT: B 44 MET cc_start: 0.9025 (mtp) cc_final: 0.8737 (mtp) REVERT: B 108 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7384 (mm-30) REVERT: C 111 ARG cc_start: 0.8523 (ttm-80) cc_final: 0.8087 (ttp80) REVERT: D 13 GLN cc_start: 0.4692 (pm20) cc_final: 0.4432 (pm20) REVERT: D 67 LYS cc_start: 0.7821 (mtmt) cc_final: 0.7503 (mtmt) REVERT: D 95 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7596 (p) outliers start: 34 outliers final: 22 residues processed: 171 average time/residue: 0.3220 time to fit residues: 70.7792 Evaluate side-chains 170 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 110 ARG Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 70 optimal weight: 0.0020 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.169217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129194 restraints weight = 13046.202| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.51 r_work: 0.3349 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10820 Z= 0.200 Angle : 0.589 7.105 15316 Z= 0.303 Chirality : 0.035 0.191 1813 Planarity : 0.005 0.053 1402 Dihedral : 22.810 177.782 3282 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.21 % Favored : 93.33 % Rotamer: Outliers : 4.13 % Allowed : 21.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.29), residues: 885 helix: 0.82 (0.20), residues: 668 sheet: -1.77 (0.97), residues: 26 loop : -3.12 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 116 HIS 0.009 0.001 HIS D 38 PHE 0.016 0.002 PHE A 231 TYR 0.016 0.001 TYR A 193 ARG 0.010 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 178 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8592 (mtp85) cc_final: 0.8376 (mtp85) REVERT: A 57 ASN cc_start: 0.8900 (m-40) cc_final: 0.8532 (m-40) REVERT: A 67 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.6067 (mp) REVERT: A 275 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8218 (t) REVERT: A 278 LYS cc_start: 0.7247 (mtpt) cc_final: 0.6527 (mmtt) REVERT: B 44 MET cc_start: 0.8985 (mtp) cc_final: 0.8672 (mtp) REVERT: B 108 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7336 (mm-30) REVERT: C 64 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8144 (tp-100) REVERT: C 111 ARG cc_start: 0.8369 (ttm-80) cc_final: 0.7990 (ttp80) REVERT: D 13 GLN cc_start: 0.4558 (pm20) cc_final: 0.4344 (pm20) REVERT: D 17 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8114 (p) REVERT: D 67 LYS cc_start: 0.7622 (mtmt) cc_final: 0.7351 (mtmt) REVERT: D 95 THR cc_start: 0.7875 (p) cc_final: 0.7556 (p) outliers start: 31 outliers final: 16 residues processed: 165 average time/residue: 0.3285 time to fit residues: 69.6467 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 : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 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 296 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.167851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.127180 restraints weight = 13190.167| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.52 r_work: 0.3314 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3893 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= 0.246 Angle : 0.613 8.519 15316 Z= 0.314 Chirality : 0.036 0.205 1813 Planarity : 0.005 0.057 1402 Dihedral : 22.667 177.248 3278 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.67 % Favored : 92.88 % Rotamer: Outliers : 5.07 % Allowed : 20.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.28), residues: 885 helix: 0.90 (0.20), residues: 662 sheet: -1.20 (1.02), residues: 26 loop : -2.96 (0.44), residues: 197 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 0.017 0.002 PHE D 80 TYR 0.016 0.002 TYR D 26 ARG 0.012 0.001 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 184 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8931 (m-40) cc_final: 0.8564 (m-40) REVERT: A 275 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8277 (t) REVERT: A 278 LYS cc_start: 0.7247 (mtpt) cc_final: 0.6542 (mmtt) REVERT: B 44 MET cc_start: 0.9013 (mtp) cc_final: 0.8750 (mtp) REVERT: B 47 LYS cc_start: 0.8425 (mttp) cc_final: 0.8219 (mttm) REVERT: B 108 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7393 (mm-30) REVERT: C 64 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8190 (tp-100) REVERT: C 111 ARG cc_start: 0.8436 (ttm-80) cc_final: 0.8054 (ttp80) REVERT: D 14 MET cc_start: 0.6609 (tpt) cc_final: 0.6269 (tpt) REVERT: D 62 SER cc_start: 0.7827 (OUTLIER) cc_final: 0.7469 (p) REVERT: D 95 THR cc_start: 0.7921 (OUTLIER) cc_final: 0.7598 (p) REVERT: F 89 GLN cc_start: 0.8011 (pt0) cc_final: 0.7743 (pm20) outliers start: 38 outliers final: 24 residues processed: 167 average time/residue: 0.3207 time to fit residues: 69.3444 Evaluate side-chains 169 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 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 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 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 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 64 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 89 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 65 optimal weight: 0.0770 chunk 35 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.169641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.129306 restraints weight = 13252.623| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.50 r_work: 0.3365 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4120 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= 0.198 Angle : 0.581 6.968 15316 Z= 0.300 Chirality : 0.035 0.210 1813 Planarity : 0.005 0.056 1402 Dihedral : 22.487 176.893 3278 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.99 % Favored : 93.56 % Rotamer: Outliers : 3.60 % Allowed : 21.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.29), residues: 885 helix: 1.07 (0.20), residues: 661 sheet: -0.70 (1.05), residues: 26 loop : -2.93 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 116 HIS 0.008 0.001 HIS A 313 PHE 0.016 0.002 PHE D 80 TYR 0.017 0.001 TYR D 26 ARG 0.011 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 172 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8832 (m-40) cc_final: 0.8468 (m-40) REVERT: A 116 HIS cc_start: 0.8465 (t-90) cc_final: 0.8205 (t70) REVERT: A 275 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8287 (t) REVERT: A 278 LYS cc_start: 0.7218 (mtpt) cc_final: 0.6521 (mmtt) REVERT: B 44 MET cc_start: 0.8975 (mtp) cc_final: 0.8681 (mtp) REVERT: B 108 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7274 (mm-30) REVERT: C 64 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8207 (tp-100) REVERT: C 111 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.7979 (ttp80) REVERT: D 95 THR cc_start: 0.7863 (OUTLIER) cc_final: 0.7410 (p) REVERT: D 98 GLN cc_start: 0.8227 (mt0) cc_final: 0.7762 (mt0) outliers start: 27 outliers final: 18 residues processed: 160 average time/residue: 0.3317 time to fit residues: 68.3720 Evaluate side-chains 162 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 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 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 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 = 0.3993 r_free = 0.3993 target = 0.168724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.128084 restraints weight = 13136.346| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.51 r_work: 0.3329 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4187 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= 0.237 Angle : 0.600 7.178 15316 Z= 0.309 Chirality : 0.035 0.219 1813 Planarity : 0.005 0.056 1402 Dihedral : 22.405 177.531 3277 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.55 % Favored : 92.99 % Rotamer: Outliers : 3.73 % Allowed : 22.00 % Favored : 74.27 % 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: 1.05 (0.20), residues: 662 sheet: -0.34 (1.05), residues: 26 loop : -2.91 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 309 HIS 0.005 0.001 HIS A 313 PHE 0.017 0.002 PHE D 80 TYR 0.019 0.002 TYR D 26 ARG 0.012 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 168 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8840 (m-40) cc_final: 0.8484 (m-40) REVERT: A 116 HIS cc_start: 0.8424 (t-90) cc_final: 0.8110 (t70) REVERT: A 275 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8300 (t) REVERT: B 44 MET cc_start: 0.8977 (mtp) cc_final: 0.8703 (mtp) REVERT: B 77 MET cc_start: 0.9012 (tpt) cc_final: 0.8379 (tpt) REVERT: B 108 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7262 (mm-30) REVERT: C 64 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8218 (tp-100) REVERT: C 111 ARG cc_start: 0.8374 (ttm-80) cc_final: 0.8017 (ttp80) REVERT: D 62 SER cc_start: 0.7921 (OUTLIER) cc_final: 0.7212 (p) REVERT: D 67 LYS cc_start: 0.7725 (mtmt) cc_final: 0.7170 (mtmt) REVERT: D 95 THR cc_start: 0.7931 (OUTLIER) cc_final: 0.7623 (p) outliers start: 28 outliers final: 19 residues processed: 156 average time/residue: 0.3404 time to fit residues: 68.3703 Evaluate side-chains 160 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 97 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.168921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.128268 restraints weight = 13175.676| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.52 r_work: 0.3334 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10820 Z= 0.242 Angle : 0.609 9.169 15316 Z= 0.312 Chirality : 0.036 0.225 1813 Planarity : 0.005 0.056 1402 Dihedral : 22.326 177.959 3277 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.99 % Favored : 93.56 % Rotamer: Outliers : 3.47 % Allowed : 22.53 % Favored : 74.00 % 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: 0.26 (0.29), residues: 885 helix: 1.05 (0.20), residues: 662 sheet: 0.07 (1.07), residues: 26 loop : -2.86 (0.45), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 116 HIS 0.004 0.001 HIS A 27 PHE 0.017 0.002 PHE D 80 TYR 0.020 0.002 TYR D 26 ARG 0.014 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 170 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8898 (m-40) cc_final: 0.8503 (m-40) REVERT: A 116 HIS cc_start: 0.8337 (t-90) cc_final: 0.8029 (t70) REVERT: A 275 SER cc_start: 0.8758 (OUTLIER) cc_final: 0.8282 (t) REVERT: B 44 MET cc_start: 0.8998 (mtp) cc_final: 0.8747 (mtp) REVERT: B 77 MET cc_start: 0.9035 (tpt) cc_final: 0.8478 (tpt) REVERT: B 108 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7145 (mm-30) REVERT: C 64 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8124 (tp-100) REVERT: C 111 ARG cc_start: 0.8375 (ttm-80) cc_final: 0.7960 (ttp80) REVERT: D 62 SER cc_start: 0.7905 (OUTLIER) cc_final: 0.7135 (p) REVERT: D 67 LYS cc_start: 0.7699 (mtmt) cc_final: 0.7120 (mtmt) REVERT: D 95 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7693 (p) outliers start: 26 outliers final: 18 residues processed: 159 average time/residue: 0.3360 time to fit residues: 68.3577 Evaluate side-chains 164 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 185 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 97 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 60 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 0.0970 chunk 100 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 94 optimal weight: 10.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.164899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124709 restraints weight = 13088.009| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.47 r_work: 0.3288 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10820 Z= 0.355 Angle : 0.666 8.623 15316 Z= 0.340 Chirality : 0.038 0.239 1813 Planarity : 0.005 0.051 1402 Dihedral : 22.417 177.979 3275 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.55 % Favored : 92.99 % Rotamer: Outliers : 3.33 % Allowed : 22.40 % Favored : 74.27 % 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: 0.02 (0.28), residues: 885 helix: 0.85 (0.19), residues: 658 sheet: 0.20 (1.06), residues: 26 loop : -2.80 (0.46), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 116 HIS 0.006 0.001 HIS A 313 PHE 0.020 0.002 PHE D 80 TYR 0.027 0.002 TYR D 26 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 170 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8918 (m-40) cc_final: 0.8545 (m-40) REVERT: A 116 HIS cc_start: 0.8380 (t-90) cc_final: 0.8006 (t70) REVERT: A 154 MET cc_start: 0.9059 (mtt) cc_final: 0.8780 (mtt) REVERT: B 44 MET cc_start: 0.9005 (mtp) cc_final: 0.8797 (mtp) REVERT: B 108 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7367 (mm-30) REVERT: C 64 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8176 (tp-100) REVERT: C 111 ARG cc_start: 0.8563 (ttm-80) cc_final: 0.8126 (ttp80) REVERT: D 21 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7420 (mm-30) REVERT: D 62 SER cc_start: 0.7963 (OUTLIER) cc_final: 0.7545 (p) REVERT: D 95 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7656 (p) outliers start: 25 outliers final: 19 residues processed: 160 average time/residue: 0.3207 time to fit residues: 66.2523 Evaluate side-chains 165 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 216 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain 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 62 SER 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 108 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 97 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.167575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127656 restraints weight = 12969.776| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.43 r_work: 0.3322 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10820 Z= 0.266 Angle : 0.622 8.346 15316 Z= 0.318 Chirality : 0.036 0.243 1813 Planarity : 0.005 0.056 1402 Dihedral : 22.339 177.886 3275 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.99 % Favored : 93.45 % Rotamer: Outliers : 3.20 % Allowed : 22.67 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.29), residues: 885 helix: 0.97 (0.20), residues: 658 sheet: 0.35 (1.10), residues: 26 loop : -2.78 (0.46), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 116 HIS 0.004 0.001 HIS A 27 PHE 0.018 0.002 PHE D 80 TYR 0.020 0.002 TYR D 26 ARG 0.014 0.000 ARG F 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5540.24 seconds wall clock time: 99 minutes 0.03 seconds (5940.03 seconds total)