Starting phenix.real_space_refine on Thu Jul 2 22:13:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dsd_30831/07_2026/7dsd_30831.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsd_30831/07_2026/7dsd_30831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dsd_30831/07_2026/7dsd_30831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsd_30831/07_2026/7dsd_30831.map" model { file = "/net/cci-nas-00/data/ceres_data/7dsd_30831/07_2026/7dsd_30831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsd_30831/07_2026/7dsd_30831.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7dsd_30831/07_2026/7dsd_30831.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dsd_30831/07_2026/7dsd_30831.cif" } resolution = 2.9 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= -0.001 sd= 0.045 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: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 6874 2.51 5 N 1694 2.21 5 O 1883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10542 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1492 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 1.72, per 1000 atoms: 0.16 Number of scatterers: 10542 At special positions: 0 Unit cell: (112.554, 111.54, 92.274, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 1883 8.00 N 1694 7.00 C 6874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 159 " distance=2.03 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 139 " " NAG B1001 " - " ASN B 139 " " NAG C1001 " - " ASN C 139 " " NAG D1001 " - " ASN D 139 " " NAG E1001 " - " ASN E 139 " " NAG F1001 " - " ASN F 139 " " NAG G1001 " - " ASN G 139 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 329.1 milliseconds 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2590 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 70.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 8 through 15 Processing helix chain 'A' and resid 25 through 36 Processing helix chain 'A' and resid 47 through 70 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 73 through 83 removed outlier: 3.626A pdb=" N LEU A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.766A pdb=" N ALA A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 128 Processing helix chain 'A' and resid 146 through 156 removed outlier: 4.023A pdb=" N LYS A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 204 removed outlier: 3.590A pdb=" N ALA A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 15 Processing helix chain 'B' and resid 25 through 36 Processing helix chain 'B' and resid 47 through 70 Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 73 through 83 removed outlier: 3.626A pdb=" N LEU B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 83 " --> pdb=" O GLU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 107 Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.767A pdb=" N ALA B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 146 through 156 removed outlier: 4.023A pdb=" N LYS B 156 " --> pdb=" O LYS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 204 removed outlier: 3.590A pdb=" N ALA B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 15 Processing helix chain 'C' and resid 25 through 36 Processing helix chain 'C' and resid 47 through 70 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 73 through 83 removed outlier: 3.627A pdb=" N LEU C 77 " --> pdb=" O ASN C 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 107 Processing helix chain 'C' and resid 107 through 120 removed outlier: 3.766A pdb=" N ALA C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 128 Processing helix chain 'C' and resid 146 through 156 removed outlier: 4.023A pdb=" N LYS C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 204 removed outlier: 3.590A pdb=" N ALA C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 15 Processing helix chain 'D' and resid 25 through 36 Processing helix chain 'D' and resid 47 through 70 Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 73 through 83 removed outlier: 3.626A pdb=" N LEU D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 83 " --> pdb=" O GLU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 107 Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.767A pdb=" N ALA D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 146 through 156 removed outlier: 4.023A pdb=" N LYS D 156 " --> pdb=" O LYS D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 204 removed outlier: 3.590A pdb=" N ALA D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 15 Processing helix chain 'E' and resid 25 through 36 Processing helix chain 'E' and resid 47 through 70 Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 73 through 83 removed outlier: 3.626A pdb=" N LEU E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG E 83 " --> pdb=" O GLU E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 107 Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.767A pdb=" N ALA E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 146 through 156 removed outlier: 4.023A pdb=" N LYS E 156 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 204 removed outlier: 3.589A pdb=" N ALA E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 15 Processing helix chain 'F' and resid 25 through 36 Processing helix chain 'F' and resid 47 through 70 Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 73 through 83 removed outlier: 3.626A pdb=" N LEU F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG F 83 " --> pdb=" O GLU F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 107 Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.767A pdb=" N ALA F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 146 through 156 removed outlier: 4.023A pdb=" N LYS F 156 " --> pdb=" O LYS F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 204 removed outlier: 3.589A pdb=" N ALA F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 15 Processing helix chain 'G' and resid 25 through 36 Processing helix chain 'G' and resid 47 through 70 Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 73 through 83 removed outlier: 3.627A pdb=" N LEU G 77 " --> pdb=" O ASN G 73 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG G 83 " --> pdb=" O GLU G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 107 Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.767A pdb=" N ALA G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 128 Processing helix chain 'G' and resid 146 through 156 removed outlier: 4.023A pdb=" N LYS G 156 " --> pdb=" O LYS G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 204 removed outlier: 3.590A pdb=" N ALA G 174 " --> pdb=" O SER G 170 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3231 1.34 - 1.46: 2370 1.46 - 1.58: 5039 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 10780 Sorted by residual: bond pdb=" C1 NAG F1001 " pdb=" O5 NAG F1001 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C1 NAG C1001 " pdb=" O5 NAG C1001 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C1 NAG A1001 " pdb=" O5 NAG A1001 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG D1001 " pdb=" O5 NAG D1001 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 ... (remaining 10775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 13820 1.15 - 2.30: 565 2.30 - 3.45: 175 3.45 - 4.60: 56 4.60 - 5.75: 21 Bond angle restraints: 14637 Sorted by residual: angle pdb=" N ALA B 93 " pdb=" CA ALA B 93 " pdb=" C ALA B 93 " ideal model delta sigma weight residual 110.44 115.35 -4.91 1.20e+00 6.94e-01 1.68e+01 angle pdb=" N ALA E 93 " pdb=" CA ALA E 93 " pdb=" C ALA E 93 " ideal model delta sigma weight residual 110.44 115.34 -4.90 1.20e+00 6.94e-01 1.66e+01 angle pdb=" N ALA A 93 " pdb=" CA ALA A 93 " pdb=" C ALA A 93 " ideal model delta sigma weight residual 110.44 115.33 -4.89 1.20e+00 6.94e-01 1.66e+01 angle pdb=" N ALA F 93 " pdb=" CA ALA F 93 " pdb=" C ALA F 93 " ideal model delta sigma weight residual 110.44 115.31 -4.87 1.20e+00 6.94e-01 1.65e+01 angle pdb=" N ALA C 93 " pdb=" CA ALA C 93 " pdb=" C ALA C 93 " ideal model delta sigma weight residual 110.44 115.31 -4.87 1.20e+00 6.94e-01 1.65e+01 ... (remaining 14632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.45: 5793 11.45 - 22.91: 430 22.91 - 34.36: 91 34.36 - 45.81: 35 45.81 - 57.27: 56 Dihedral angle restraints: 6405 sinusoidal: 2429 harmonic: 3976 Sorted by residual: dihedral pdb=" CA ALA B 93 " pdb=" C ALA B 93 " pdb=" N VAL B 94 " pdb=" CA VAL B 94 " ideal model delta harmonic sigma weight residual 180.00 155.27 24.73 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ALA E 93 " pdb=" C ALA E 93 " pdb=" N VAL E 94 " pdb=" CA VAL E 94 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA ALA A 93 " pdb=" C ALA A 93 " pdb=" N VAL A 94 " pdb=" CA VAL A 94 " ideal model delta harmonic sigma weight residual 180.00 155.29 24.71 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 6402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 892 0.024 - 0.048: 496 0.048 - 0.073: 180 0.073 - 0.097: 82 0.097 - 0.121: 58 Chirality restraints: 1708 Sorted by residual: chirality pdb=" CA PRO C 60 " pdb=" N PRO C 60 " pdb=" C PRO C 60 " pdb=" CB PRO C 60 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.66e-01 chirality pdb=" CA PRO B 60 " pdb=" N PRO B 60 " pdb=" C PRO B 60 " pdb=" CB PRO B 60 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA PRO D 60 " pdb=" N PRO D 60 " pdb=" C PRO D 60 " pdb=" CB PRO D 60 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.55e-01 ... (remaining 1705 not shown) Planarity restraints: 1813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 59 " 0.027 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO E 60 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 60 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 60 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 59 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO G 60 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 59 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 60 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " -0.023 5.00e-02 4.00e+02 ... (remaining 1810 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3381 2.84 - 3.36: 10475 3.36 - 3.87: 16450 3.87 - 4.39: 18303 4.39 - 4.90: 31894 Nonbonded interactions: 80503 Sorted by model distance: nonbonded pdb=" OH TYR G 68 " pdb=" OG1 THR G 103 " model vdw 2.326 3.040 nonbonded pdb=" OH TYR A 68 " pdb=" OG1 THR A 103 " model vdw 2.326 3.040 nonbonded pdb=" OH TYR E 68 " pdb=" OG1 THR E 103 " model vdw 2.326 3.040 nonbonded pdb=" OH TYR B 68 " pdb=" OG1 THR B 103 " model vdw 2.326 3.040 nonbonded pdb=" OH TYR F 68 " pdb=" OG1 THR F 103 " model vdw 2.327 3.040 ... (remaining 80498 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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=1.00 max=1.00 mean=1.00 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: 1.640 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.880 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.010 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:9.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 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 : 0.004 0.038 10801 Z= 0.192 Angle : 0.647 5.746 14686 Z= 0.386 Chirality : 0.039 0.121 1708 Planarity : 0.004 0.040 1806 Dihedral : 10.511 57.267 3773 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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 are not related in a simple way. whole: -1.06 (0.23), residues: 1309 helix: 0.09 (0.16), residues: 931 sheet: None (None), residues: 0 loop : -2.62 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.007 0.001 TYR E 34 PHE 0.008 0.001 PHE G 63 TRP 0.005 0.001 TRP G 81 HIS 0.001 0.000 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (10780) covalent geometry : angle 0.63641 / 0.38 (14637) SS BOND : bond 0.00223 / 0.16 ( 14) SS BOND : angle 0.88321 / 0.69 ( 28) hydrogen bonds : bond 0.11927 / 7.48 ( 645) hydrogen bonds : angle 4.93159 / 3.60 ( 1935) link_NAG-ASN : bond 0.00559 / 0.34 ( 7) link_NAG-ASN : angle 3.10861 / 2.27 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7741 (mmm) cc_final: 0.7531 (mmp) REVERT: A 71 ASN cc_start: 0.8868 (t0) cc_final: 0.8270 (t0) REVERT: A 74 ILE cc_start: 0.8273 (pt) cc_final: 0.8051 (tp) REVERT: A 96 ARG cc_start: 0.7451 (mtp180) cc_final: 0.7189 (mmt180) REVERT: A 120 ASP cc_start: 0.8254 (t70) cc_final: 0.7622 (t0) REVERT: A 133 ASP cc_start: 0.9094 (t0) cc_final: 0.8852 (t0) REVERT: A 142 TYR cc_start: 0.8896 (m-80) cc_final: 0.8629 (m-80) REVERT: A 152 LYS cc_start: 0.9271 (mttt) cc_final: 0.8975 (mppt) REVERT: A 167 GLU cc_start: 0.8757 (mp0) cc_final: 0.8319 (pm20) REVERT: B 26 MET cc_start: 0.7740 (mmm) cc_final: 0.7363 (mmp) REVERT: B 71 ASN cc_start: 0.8670 (t0) cc_final: 0.8256 (t0) REVERT: B 81 TRP cc_start: 0.6649 (m100) cc_final: 0.6435 (t60) REVERT: B 96 ARG cc_start: 0.7419 (mtp180) cc_final: 0.7117 (mtt180) REVERT: B 105 ARG cc_start: 0.8551 (mpt180) cc_final: 0.8318 (mmt-90) REVERT: B 120 ASP cc_start: 0.8198 (t70) cc_final: 0.7423 (t70) REVERT: B 142 TYR cc_start: 0.8859 (m-80) cc_final: 0.8654 (m-80) REVERT: B 164 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8524 (pp20) REVERT: B 165 GLU cc_start: 0.8827 (mp0) cc_final: 0.8486 (mp0) REVERT: B 167 GLU cc_start: 0.8707 (mp0) cc_final: 0.8286 (pm20) REVERT: C 26 MET cc_start: 0.7933 (mmm) cc_final: 0.7681 (mmp) REVERT: C 71 ASN cc_start: 0.8836 (t0) cc_final: 0.8348 (t0) REVERT: C 74 ILE cc_start: 0.8232 (pt) cc_final: 0.7995 (tp) REVERT: C 82 LYS cc_start: 0.8921 (tttt) cc_final: 0.8706 (tppt) REVERT: C 96 ARG cc_start: 0.7553 (mtp180) cc_final: 0.7286 (mtt180) REVERT: C 120 ASP cc_start: 0.8174 (t70) cc_final: 0.7622 (t0) REVERT: C 133 ASP cc_start: 0.9083 (t0) cc_final: 0.8861 (t0) REVERT: C 142 TYR cc_start: 0.8896 (m-80) cc_final: 0.8477 (m-80) REVERT: C 165 GLU cc_start: 0.8851 (mp0) cc_final: 0.8068 (mp0) REVERT: C 167 GLU cc_start: 0.8709 (mp0) cc_final: 0.8393 (pm20) REVERT: D 26 MET cc_start: 0.7920 (mmm) cc_final: 0.7655 (mmp) REVERT: D 71 ASN cc_start: 0.8776 (t0) cc_final: 0.8249 (t0) REVERT: D 74 ILE cc_start: 0.8285 (pt) cc_final: 0.8068 (tp) REVERT: D 96 ARG cc_start: 0.7312 (mtp180) cc_final: 0.7055 (mmt180) REVERT: D 120 ASP cc_start: 0.8235 (t70) cc_final: 0.7863 (t0) REVERT: D 133 ASP cc_start: 0.9152 (t0) cc_final: 0.8903 (t0) REVERT: D 152 LYS cc_start: 0.9211 (mttt) cc_final: 0.8863 (mppt) REVERT: D 167 GLU cc_start: 0.8730 (mp0) cc_final: 0.8435 (pm20) REVERT: E 26 MET cc_start: 0.7733 (mmm) cc_final: 0.7519 (mmp) REVERT: E 71 ASN cc_start: 0.8864 (t0) cc_final: 0.8250 (t0) REVERT: E 74 ILE cc_start: 0.8268 (pt) cc_final: 0.8043 (tp) REVERT: E 82 LYS cc_start: 0.9007 (tttt) cc_final: 0.8753 (tppt) REVERT: E 96 ARG cc_start: 0.7391 (mtp180) cc_final: 0.7092 (mmt180) REVERT: E 120 ASP cc_start: 0.8217 (t70) cc_final: 0.7606 (t0) REVERT: E 165 GLU cc_start: 0.8813 (mp0) cc_final: 0.8246 (mp0) REVERT: E 167 GLU cc_start: 0.8748 (mp0) cc_final: 0.8379 (pm20) REVERT: F 26 MET cc_start: 0.7754 (mmm) cc_final: 0.7306 (mmp) REVERT: F 71 ASN cc_start: 0.8925 (t0) cc_final: 0.8438 (t0) REVERT: F 96 ARG cc_start: 0.7498 (mtp180) cc_final: 0.7203 (mmt180) REVERT: F 105 ARG cc_start: 0.8644 (mpt180) cc_final: 0.8398 (mmt-90) REVERT: F 119 MET cc_start: 0.8683 (mmm) cc_final: 0.8357 (mmt) REVERT: F 120 ASP cc_start: 0.8188 (t70) cc_final: 0.7686 (t0) REVERT: F 165 GLU cc_start: 0.8839 (mp0) cc_final: 0.8298 (mp0) REVERT: F 167 GLU cc_start: 0.8704 (mp0) cc_final: 0.8206 (pm20) REVERT: G 26 MET cc_start: 0.7721 (mmm) cc_final: 0.7462 (mmp) REVERT: G 71 ASN cc_start: 0.8730 (t0) cc_final: 0.8091 (t0) REVERT: G 81 TRP cc_start: 0.6714 (m100) cc_final: 0.6439 (t60) REVERT: G 96 ARG cc_start: 0.7582 (mtp180) cc_final: 0.7325 (mmt180) REVERT: G 119 MET cc_start: 0.8640 (mmm) cc_final: 0.8227 (mmp) REVERT: G 120 ASP cc_start: 0.8218 (t70) cc_final: 0.7654 (t0) REVERT: G 133 ASP cc_start: 0.9138 (t0) cc_final: 0.8838 (t0) REVERT: G 152 LYS cc_start: 0.9208 (mttt) cc_final: 0.8896 (mttp) REVERT: G 164 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8691 (pp20) REVERT: G 165 GLU cc_start: 0.8889 (mp0) cc_final: 0.8345 (mp0) REVERT: G 167 GLU cc_start: 0.8748 (mp0) cc_final: 0.8381 (pm20) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 0.6808 time to fit residues: 283.4058 Evaluate side-chains 369 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 0.0470 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.0570 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.0020 chunk 55 optimal weight: 0.6980 overall best weight: 0.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN A 154 GLN B 71 ASN B 104 GLN B 154 GLN ** C 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN D 71 ASN D 104 GLN D 154 GLN ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN E 154 GLN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 GLN F 154 GLN ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 154 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.115055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.078684 restraints weight = 19109.887| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.27 r_work: 0.2798 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10801 Z= 0.126 Angle : 0.605 5.579 14686 Z= 0.307 Chirality : 0.039 0.137 1708 Planarity : 0.005 0.038 1806 Dihedral : 4.150 19.631 1442 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.20 % Allowed : 16.77 % Favored : 82.03 % 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 are not related in a simple way. whole: 0.54 (0.24), residues: 1309 helix: 1.42 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -2.50 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 83 TYR 0.012 0.001 TYR A 47 PHE 0.005 0.001 PHE E 137 TRP 0.004 0.001 TRP D 62 HIS 0.000 0.000 HIS E 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10780) covalent geometry : angle 0.60263 / 0.31 (14637) SS BOND : bond 0.00229 / 0.16 ( 14) SS BOND : angle 0.32322 / 0.26 ( 28) hydrogen bonds : bond 0.03748 / 2.45 ( 645) hydrogen bonds : angle 3.21253 / 2.29 ( 1935) link_NAG-ASN : bond 0.00082 / 0.04 ( 7) link_NAG-ASN : angle 1.56122 / 1.13 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 380 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7930 (mmm) cc_final: 0.7601 (mmp) REVERT: A 71 ASN cc_start: 0.8918 (t0) cc_final: 0.8534 (t0) REVERT: A 81 TRP cc_start: 0.7143 (t-100) cc_final: 0.6240 (t60) REVERT: A 83 ARG cc_start: 0.7402 (ttm-80) cc_final: 0.7151 (mtm110) REVERT: A 96 ARG cc_start: 0.7506 (mtp180) cc_final: 0.7301 (mtt180) REVERT: A 122 LYS cc_start: 0.8789 (mttm) cc_final: 0.8541 (mttm) REVERT: A 152 LYS cc_start: 0.9432 (mttt) cc_final: 0.9216 (mppt) REVERT: A 167 GLU cc_start: 0.8862 (mp0) cc_final: 0.8478 (pm20) REVERT: A 169 ILE cc_start: 0.9263 (mt) cc_final: 0.8990 (tt) REVERT: B 26 MET cc_start: 0.7862 (mmm) cc_final: 0.7575 (mmp) REVERT: B 71 ASN cc_start: 0.8876 (OUTLIER) cc_final: 0.8293 (t0) REVERT: B 79 GLU cc_start: 0.9214 (tp30) cc_final: 0.8883 (tp30) REVERT: B 81 TRP cc_start: 0.6689 (m100) cc_final: 0.6462 (t60) REVERT: B 82 LYS cc_start: 0.9051 (tptt) cc_final: 0.8737 (tmmt) REVERT: B 96 ARG cc_start: 0.7496 (mtp180) cc_final: 0.7177 (mtt180) REVERT: B 142 TYR cc_start: 0.8945 (m-80) cc_final: 0.8261 (m-10) REVERT: B 167 GLU cc_start: 0.8918 (mp0) cc_final: 0.8532 (pm20) REVERT: C 26 MET cc_start: 0.7961 (mmm) cc_final: 0.7650 (mmp) REVERT: C 40 THR cc_start: 0.9109 (t) cc_final: 0.8549 (p) REVERT: C 71 ASN cc_start: 0.9007 (t0) cc_final: 0.8668 (t0) REVERT: C 74 ILE cc_start: 0.8453 (pt) cc_final: 0.8192 (tp) REVERT: C 81 TRP cc_start: 0.6887 (t-100) cc_final: 0.5986 (t60) REVERT: C 96 ARG cc_start: 0.7392 (mtp180) cc_final: 0.7124 (mtt-85) REVERT: C 142 TYR cc_start: 0.9034 (m-80) cc_final: 0.8466 (m-80) REVERT: C 152 LYS cc_start: 0.9370 (mttt) cc_final: 0.9148 (mppt) REVERT: C 167 GLU cc_start: 0.8910 (mp0) cc_final: 0.8460 (pm20) REVERT: D 26 MET cc_start: 0.8025 (mmm) cc_final: 0.7715 (mmp) REVERT: D 68 TYR cc_start: 0.8602 (m-80) cc_final: 0.8224 (m-80) REVERT: D 71 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8248 (t0) REVERT: D 81 TRP cc_start: 0.7400 (OUTLIER) cc_final: 0.6356 (t60) REVERT: D 96 ARG cc_start: 0.7419 (mtp180) cc_final: 0.7166 (mmt180) REVERT: D 152 LYS cc_start: 0.9364 (mttt) cc_final: 0.9117 (mppt) REVERT: D 167 GLU cc_start: 0.9027 (mp0) cc_final: 0.8671 (pm20) REVERT: E 26 MET cc_start: 0.7930 (mmm) cc_final: 0.7644 (mmp) REVERT: E 71 ASN cc_start: 0.9076 (t0) cc_final: 0.8665 (t0) REVERT: E 81 TRP cc_start: 0.7279 (t-100) cc_final: 0.6308 (t60) REVERT: E 96 ARG cc_start: 0.7377 (mtp180) cc_final: 0.7092 (mmt180) REVERT: E 167 GLU cc_start: 0.8966 (mp0) cc_final: 0.8557 (pm20) REVERT: F 26 MET cc_start: 0.8024 (mmm) cc_final: 0.7573 (mmp) REVERT: F 40 THR cc_start: 0.9070 (t) cc_final: 0.8471 (p) REVERT: F 71 ASN cc_start: 0.8917 (t0) cc_final: 0.8448 (t0) REVERT: F 96 ARG cc_start: 0.7271 (mtp180) cc_final: 0.7056 (mmt180) REVERT: F 105 ARG cc_start: 0.9055 (mpt180) cc_final: 0.8843 (mmt-90) REVERT: F 136 GLU cc_start: 0.8820 (pm20) cc_final: 0.8619 (pm20) REVERT: F 142 TYR cc_start: 0.8901 (m-80) cc_final: 0.8103 (m-80) REVERT: F 148 LYS cc_start: 0.9349 (mmpt) cc_final: 0.8945 (mmpt) REVERT: F 152 LYS cc_start: 0.9382 (mttt) cc_final: 0.9027 (mppt) REVERT: F 167 GLU cc_start: 0.8818 (mp0) cc_final: 0.8396 (pm20) REVERT: G 26 MET cc_start: 0.7992 (mmm) cc_final: 0.7662 (mmp) REVERT: G 71 ASN cc_start: 0.8909 (t0) cc_final: 0.8346 (t0) REVERT: G 73 ASN cc_start: 0.8720 (m-40) cc_final: 0.8411 (m-40) REVERT: G 81 TRP cc_start: 0.6731 (m100) cc_final: 0.6492 (t60) REVERT: G 96 ARG cc_start: 0.7567 (mtp180) cc_final: 0.7347 (mmt180) REVERT: G 105 ARG cc_start: 0.8955 (mmt90) cc_final: 0.8623 (mmt-90) REVERT: G 119 MET cc_start: 0.9018 (mmm) cc_final: 0.8811 (mmp) REVERT: G 136 GLU cc_start: 0.8794 (pm20) cc_final: 0.8547 (pm20) REVERT: G 142 TYR cc_start: 0.8806 (m-10) cc_final: 0.8495 (m-10) REVERT: G 148 LYS cc_start: 0.9335 (mmpt) cc_final: 0.8863 (mmpt) REVERT: G 152 LYS cc_start: 0.9390 (mttt) cc_final: 0.9015 (mtmm) REVERT: G 167 GLU cc_start: 0.9018 (mp0) cc_final: 0.8596 (pm20) outliers start: 13 outliers final: 5 residues processed: 382 average time/residue: 0.6602 time to fit residues: 266.6755 Evaluate side-chains 377 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 369 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain D residue 71 ASN Chi-restraints excluded: chain D residue 81 TRP Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain G residue 35 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 58 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 110 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN B 71 ASN B 104 GLN D 104 GLN E 104 GLN G 71 ASN G 104 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.113126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.076310 restraints weight = 19368.678| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.32 r_work: 0.2766 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10801 Z= 0.134 Angle : 0.613 5.566 14686 Z= 0.310 Chirality : 0.040 0.134 1708 Planarity : 0.005 0.039 1806 Dihedral : 4.107 18.979 1442 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.49 % Allowed : 19.26 % Favored : 78.25 % 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 are not related in a simple way. whole: 1.25 (0.24), residues: 1309 helix: 1.82 (0.18), residues: 924 sheet: None (None), residues: 0 loop : -1.71 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 83 TYR 0.012 0.001 TYR B 34 PHE 0.005 0.001 PHE G 189 TRP 0.004 0.001 TRP E 187 HIS 0.001 0.000 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.13 (10780) covalent geometry : angle 0.61143 / 0.31 (14637) SS BOND : bond 0.00262 / 0.18 ( 14) SS BOND : angle 0.47508 / 0.37 ( 28) hydrogen bonds : bond 0.04044 / 2.61 ( 645) hydrogen bonds : angle 3.08926 / 2.20 ( 1935) link_NAG-ASN : bond 0.00099 / 0.05 ( 7) link_NAG-ASN : angle 1.34829 / 0.98 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 384 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8070 (mmm) cc_final: 0.7780 (mmp) REVERT: A 71 ASN cc_start: 0.8920 (t0) cc_final: 0.8483 (t0) REVERT: A 81 TRP cc_start: 0.7173 (t-100) cc_final: 0.6369 (t60) REVERT: A 96 ARG cc_start: 0.7501 (mtp180) cc_final: 0.7292 (mtt-85) REVERT: A 167 GLU cc_start: 0.8886 (mp0) cc_final: 0.8542 (pm20) REVERT: B 26 MET cc_start: 0.7982 (mmm) cc_final: 0.7628 (mmp) REVERT: B 71 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8357 (t0) REVERT: B 96 ARG cc_start: 0.7469 (mtp180) cc_final: 0.7145 (mtt180) REVERT: B 142 TYR cc_start: 0.8889 (m-80) cc_final: 0.8358 (m-10) REVERT: B 143 GLN cc_start: 0.8471 (mm110) cc_final: 0.8267 (mm110) REVERT: B 165 GLU cc_start: 0.8632 (mp0) cc_final: 0.8154 (mp0) REVERT: B 167 GLU cc_start: 0.8897 (mp0) cc_final: 0.8516 (pm20) REVERT: C 26 MET cc_start: 0.8083 (mmm) cc_final: 0.7768 (mmp) REVERT: C 40 THR cc_start: 0.9189 (t) cc_final: 0.8663 (p) REVERT: C 71 ASN cc_start: 0.8995 (t0) cc_final: 0.8761 (t0) REVERT: C 74 ILE cc_start: 0.8463 (pt) cc_final: 0.8198 (tp) REVERT: C 81 TRP cc_start: 0.6965 (t-100) cc_final: 0.6034 (t60) REVERT: C 96 ARG cc_start: 0.7468 (mtp180) cc_final: 0.7221 (mmt180) REVERT: C 142 TYR cc_start: 0.8973 (m-80) cc_final: 0.8496 (m-10) REVERT: C 167 GLU cc_start: 0.8923 (mp0) cc_final: 0.8537 (pm20) REVERT: C 179 ARG cc_start: 0.8745 (ttm110) cc_final: 0.8494 (ttp-110) REVERT: D 26 MET cc_start: 0.8078 (mmm) cc_final: 0.7791 (mmp) REVERT: D 68 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: D 71 ASN cc_start: 0.8950 (t0) cc_final: 0.8626 (t0) REVERT: D 81 TRP cc_start: 0.7383 (t-100) cc_final: 0.6465 (t60) REVERT: D 96 ARG cc_start: 0.7403 (mtp180) cc_final: 0.7165 (mmt180) REVERT: D 143 GLN cc_start: 0.8553 (mm110) cc_final: 0.8305 (mm110) REVERT: D 167 GLU cc_start: 0.9010 (mp0) cc_final: 0.8666 (pm20) REVERT: E 26 MET cc_start: 0.8059 (mmm) cc_final: 0.7769 (mmp) REVERT: E 71 ASN cc_start: 0.9075 (t0) cc_final: 0.8747 (t0) REVERT: E 81 TRP cc_start: 0.7355 (t-100) cc_final: 0.6554 (t60) REVERT: E 96 ARG cc_start: 0.7406 (mtp180) cc_final: 0.7126 (mmt180) REVERT: E 122 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8235 (mttp) REVERT: E 143 GLN cc_start: 0.8548 (mm110) cc_final: 0.8312 (mm110) REVERT: E 148 LYS cc_start: 0.9309 (mmpt) cc_final: 0.8948 (mmpt) REVERT: E 149 GLU cc_start: 0.9265 (pm20) cc_final: 0.9017 (pm20) REVERT: E 152 LYS cc_start: 0.9368 (mttt) cc_final: 0.9010 (mtmm) REVERT: E 167 GLU cc_start: 0.8999 (mp0) cc_final: 0.8689 (pm20) REVERT: F 71 ASN cc_start: 0.8900 (t0) cc_final: 0.8641 (t0) REVERT: F 81 TRP cc_start: 0.7050 (t-100) cc_final: 0.6078 (t60) REVERT: F 96 ARG cc_start: 0.7297 (mtp180) cc_final: 0.7075 (mmt180) REVERT: F 105 ARG cc_start: 0.9057 (mpt180) cc_final: 0.8841 (mmt-90) REVERT: F 119 MET cc_start: 0.9187 (mmt) cc_final: 0.8949 (mmp) REVERT: F 122 LYS cc_start: 0.8781 (mttm) cc_final: 0.8567 (mttp) REVERT: F 136 GLU cc_start: 0.8847 (pm20) cc_final: 0.8629 (pm20) REVERT: F 142 TYR cc_start: 0.8892 (m-80) cc_final: 0.8118 (m-80) REVERT: F 148 LYS cc_start: 0.9285 (mmpt) cc_final: 0.9040 (mmpt) REVERT: F 152 LYS cc_start: 0.9342 (mttt) cc_final: 0.9016 (mppt) REVERT: F 167 GLU cc_start: 0.8830 (mp0) cc_final: 0.8469 (pm20) REVERT: F 179 ARG cc_start: 0.8755 (ttm110) cc_final: 0.8398 (ttp-110) REVERT: G 26 MET cc_start: 0.8163 (mmm) cc_final: 0.7852 (mmp) REVERT: G 71 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8211 (t0) REVERT: G 77 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8305 (mm) REVERT: G 96 ARG cc_start: 0.7515 (mtp180) cc_final: 0.7308 (mmt180) REVERT: G 105 ARG cc_start: 0.8965 (mmt90) cc_final: 0.8696 (mmt-90) REVERT: G 136 GLU cc_start: 0.8874 (pm20) cc_final: 0.8643 (pm20) REVERT: G 142 TYR cc_start: 0.8820 (m-10) cc_final: 0.8593 (m-10) REVERT: G 143 GLN cc_start: 0.8567 (mm110) cc_final: 0.8358 (mm110) REVERT: G 149 GLU cc_start: 0.9394 (mp0) cc_final: 0.9187 (pm20) REVERT: G 152 LYS cc_start: 0.9353 (mttt) cc_final: 0.9048 (mtmm) REVERT: G 167 GLU cc_start: 0.8972 (mp0) cc_final: 0.8665 (pm20) outliers start: 27 outliers final: 10 residues processed: 390 average time/residue: 0.6575 time to fit residues: 270.9212 Evaluate side-chains 390 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 375 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 71 ASN Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 71 ASN Chi-restraints excluded: chain G residue 77 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 40 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 19 optimal weight: 40.0000 chunk 122 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN B 104 GLN C 104 GLN D 104 GLN E 104 GLN ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.112363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.075730 restraints weight = 19506.293| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.33 r_work: 0.2761 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10801 Z= 0.134 Angle : 0.620 5.477 14686 Z= 0.313 Chirality : 0.040 0.130 1708 Planarity : 0.004 0.042 1806 Dihedral : 4.084 17.949 1442 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.32 % Allowed : 20.46 % Favored : 76.22 % 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 are not related in a simple way. whole: 1.59 (0.25), residues: 1309 helix: 1.99 (0.18), residues: 924 sheet: None (None), residues: 0 loop : -1.32 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 83 TYR 0.012 0.001 TYR C 34 PHE 0.005 0.001 PHE G 189 TRP 0.025 0.001 TRP B 81 HIS 0.001 0.000 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.13 (10780) covalent geometry : angle 0.61717 / 0.31 (14637) SS BOND : bond 0.00254 / 0.17 ( 14) SS BOND : angle 0.43686 / 0.35 ( 28) hydrogen bonds : bond 0.04015 / 2.62 ( 645) hydrogen bonds : angle 3.05244 / 2.17 ( 1935) link_NAG-ASN : bond 0.00098 / 0.06 ( 7) link_NAG-ASN : angle 1.83219 / 1.35 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 387 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8161 (mmm) cc_final: 0.7875 (mmp) REVERT: A 71 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8533 (t0) REVERT: A 79 GLU cc_start: 0.9224 (tp30) cc_final: 0.8709 (tp30) REVERT: A 81 TRP cc_start: 0.7225 (t-100) cc_final: 0.6452 (t60) REVERT: A 83 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7275 (ttm110) REVERT: A 96 ARG cc_start: 0.7507 (mtp180) cc_final: 0.7272 (mmt180) REVERT: A 142 TYR cc_start: 0.8926 (m-80) cc_final: 0.8661 (m-10) REVERT: A 152 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8967 (mtmm) REVERT: A 167 GLU cc_start: 0.8893 (mp0) cc_final: 0.8614 (pm20) REVERT: A 169 ILE cc_start: 0.9258 (mt) cc_final: 0.8964 (tt) REVERT: B 26 MET cc_start: 0.8075 (mmm) cc_final: 0.7725 (mmp) REVERT: B 96 ARG cc_start: 0.7459 (mtp180) cc_final: 0.7141 (mtt180) REVERT: B 142 TYR cc_start: 0.9041 (m-80) cc_final: 0.8501 (m-10) REVERT: B 143 GLN cc_start: 0.8685 (mm110) cc_final: 0.8432 (mm110) REVERT: B 148 LYS cc_start: 0.9260 (mmpt) cc_final: 0.9054 (mmpt) REVERT: B 152 LYS cc_start: 0.9339 (mttt) cc_final: 0.9103 (mtmm) REVERT: B 167 GLU cc_start: 0.8914 (mp0) cc_final: 0.8580 (pm20) REVERT: C 26 MET cc_start: 0.8158 (mmm) cc_final: 0.7798 (mmp) REVERT: C 40 THR cc_start: 0.9131 (t) cc_final: 0.8567 (p) REVERT: C 71 ASN cc_start: 0.8996 (t0) cc_final: 0.8786 (t0) REVERT: C 74 ILE cc_start: 0.8472 (pt) cc_final: 0.8242 (tp) REVERT: C 81 TRP cc_start: 0.6966 (t-100) cc_final: 0.6165 (t60) REVERT: C 96 ARG cc_start: 0.7456 (mtp180) cc_final: 0.7232 (mmt180) REVERT: C 142 TYR cc_start: 0.8926 (m-80) cc_final: 0.8505 (m-10) REVERT: C 152 LYS cc_start: 0.9328 (mttt) cc_final: 0.9119 (mtmm) REVERT: C 167 GLU cc_start: 0.8911 (mp0) cc_final: 0.8609 (pm20) REVERT: D 26 MET cc_start: 0.8113 (mmm) cc_final: 0.7820 (mmp) REVERT: D 38 GLU cc_start: 0.8759 (tp30) cc_final: 0.8554 (tp30) REVERT: D 68 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: D 71 ASN cc_start: 0.8886 (t0) cc_final: 0.8445 (t0) REVERT: D 77 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8153 (mm) REVERT: D 81 TRP cc_start: 0.7389 (t-100) cc_final: 0.6583 (t60) REVERT: D 96 ARG cc_start: 0.7412 (mtp180) cc_final: 0.7173 (mmt180) REVERT: D 104 GLN cc_start: 0.8722 (mt0) cc_final: 0.8447 (mt0) REVERT: D 143 GLN cc_start: 0.8742 (mm110) cc_final: 0.8423 (mm110) REVERT: D 152 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8989 (mppt) REVERT: D 167 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8704 (pm20) REVERT: E 26 MET cc_start: 0.8139 (mmm) cc_final: 0.7886 (mmp) REVERT: E 68 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: E 71 ASN cc_start: 0.9105 (t0) cc_final: 0.8753 (t0) REVERT: E 81 TRP cc_start: 0.7261 (t-100) cc_final: 0.6576 (t60) REVERT: E 96 ARG cc_start: 0.7351 (mtp180) cc_final: 0.7112 (mmt180) REVERT: E 143 GLN cc_start: 0.8713 (mm110) cc_final: 0.8389 (mm110) REVERT: E 148 LYS cc_start: 0.9271 (mmpt) cc_final: 0.8968 (mmpt) REVERT: E 149 GLU cc_start: 0.9287 (pm20) cc_final: 0.9049 (pm20) REVERT: E 152 LYS cc_start: 0.9366 (mttt) cc_final: 0.9040 (mtmm) REVERT: E 167 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8747 (pm20) REVERT: F 71 ASN cc_start: 0.8914 (t0) cc_final: 0.8679 (t0) REVERT: F 77 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8367 (mm) REVERT: F 81 TRP cc_start: 0.7033 (t-100) cc_final: 0.6215 (t60) REVERT: F 96 ARG cc_start: 0.7360 (mtp180) cc_final: 0.7134 (mmt180) REVERT: F 105 ARG cc_start: 0.9077 (mpt180) cc_final: 0.8858 (mmt-90) REVERT: F 122 LYS cc_start: 0.8894 (mttm) cc_final: 0.8681 (mttp) REVERT: F 136 GLU cc_start: 0.8925 (pm20) cc_final: 0.8713 (pm20) REVERT: F 142 TYR cc_start: 0.8916 (m-80) cc_final: 0.8180 (m-80) REVERT: F 152 LYS cc_start: 0.9358 (mttt) cc_final: 0.9117 (mtmm) REVERT: F 167 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8547 (pm20) REVERT: F 179 ARG cc_start: 0.8815 (ttm110) cc_final: 0.8540 (ttp-110) REVERT: G 26 MET cc_start: 0.8208 (mmm) cc_final: 0.7938 (mmp) REVERT: G 68 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.8181 (t80) REVERT: G 71 ASN cc_start: 0.8954 (t0) cc_final: 0.8317 (t0) REVERT: G 73 ASN cc_start: 0.8809 (m-40) cc_final: 0.7873 (m-40) REVERT: G 105 ARG cc_start: 0.9006 (mmt90) cc_final: 0.8734 (mmt-90) REVERT: G 143 GLN cc_start: 0.8731 (mm110) cc_final: 0.8519 (mm110) REVERT: G 148 LYS cc_start: 0.9319 (mmpt) cc_final: 0.9102 (mmpt) REVERT: G 152 LYS cc_start: 0.9351 (mttt) cc_final: 0.9061 (mtmm) REVERT: G 167 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8700 (pm20) outliers start: 36 outliers final: 14 residues processed: 401 average time/residue: 0.6264 time to fit residues: 265.8639 Evaluate side-chains 401 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 375 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 167 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 73 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 50.0000 chunk 107 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN C 104 GLN E 104 GLN ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.109481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.072622 restraints weight = 19637.660| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.34 r_work: 0.2700 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10801 Z= 0.182 Angle : 0.664 5.750 14686 Z= 0.336 Chirality : 0.041 0.125 1708 Planarity : 0.005 0.044 1806 Dihedral : 4.099 17.698 1442 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.78 % Allowed : 21.38 % Favored : 74.84 % 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 are not related in a simple way. whole: 1.59 (0.24), residues: 1309 helix: 1.98 (0.18), residues: 924 sheet: None (None), residues: 0 loop : -1.31 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 179 TYR 0.013 0.001 TYR B 34 PHE 0.006 0.001 PHE C 189 TRP 0.025 0.001 TRP B 81 HIS 0.001 0.000 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.18 (10780) covalent geometry : angle 0.65836 / 0.34 (14637) SS BOND : bond 0.00321 / 0.22 ( 14) SS BOND : angle 0.67729 / 0.51 ( 28) hydrogen bonds : bond 0.04795 / 3.16 ( 645) hydrogen bonds : angle 3.16538 / 2.26 ( 1935) link_NAG-ASN : bond 0.00061 / 0.04 ( 7) link_NAG-ASN : angle 2.27486 / 1.65 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 372 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8071 (mmm) cc_final: 0.7774 (mmp) REVERT: A 32 GLN cc_start: 0.9118 (tp40) cc_final: 0.8539 (tm-30) REVERT: A 40 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8689 (p) REVERT: A 71 ASN cc_start: 0.9011 (t0) cc_final: 0.8436 (t0) REVERT: A 79 GLU cc_start: 0.9292 (tp30) cc_final: 0.8933 (tp30) REVERT: A 81 TRP cc_start: 0.7259 (t-100) cc_final: 0.6423 (t60) REVERT: A 143 GLN cc_start: 0.8495 (mm110) cc_final: 0.8243 (mm110) REVERT: A 152 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8984 (mtmm) REVERT: A 167 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8664 (pm20) REVERT: B 26 MET cc_start: 0.8178 (mmm) cc_final: 0.7874 (mmp) REVERT: B 71 ASN cc_start: 0.8773 (t0) cc_final: 0.8461 (t0) REVERT: B 96 ARG cc_start: 0.7453 (mtp180) cc_final: 0.7117 (mmt180) REVERT: B 142 TYR cc_start: 0.9117 (m-80) cc_final: 0.8461 (m-80) REVERT: B 143 GLN cc_start: 0.8786 (mm110) cc_final: 0.8478 (mm110) REVERT: B 152 LYS cc_start: 0.9368 (mttt) cc_final: 0.9141 (mtmm) REVERT: B 167 GLU cc_start: 0.8955 (mp0) cc_final: 0.8619 (pm20) REVERT: C 26 MET cc_start: 0.8212 (mmm) cc_final: 0.7880 (mmp) REVERT: C 40 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8577 (p) REVERT: C 71 ASN cc_start: 0.8994 (t0) cc_final: 0.8717 (t0) REVERT: C 74 ILE cc_start: 0.8491 (pt) cc_final: 0.8225 (tp) REVERT: C 81 TRP cc_start: 0.7164 (t-100) cc_final: 0.6399 (t60) REVERT: C 96 ARG cc_start: 0.7479 (mtp180) cc_final: 0.7255 (mmt180) REVERT: C 122 LYS cc_start: 0.9001 (mttp) cc_final: 0.8580 (mttp) REVERT: C 142 TYR cc_start: 0.8951 (m-80) cc_final: 0.8496 (m-10) REVERT: C 148 LYS cc_start: 0.9296 (mmpt) cc_final: 0.9087 (mmpt) REVERT: C 152 LYS cc_start: 0.9309 (mttt) cc_final: 0.9074 (mppt) REVERT: C 167 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8650 (pm20) REVERT: D 26 MET cc_start: 0.8168 (mmm) cc_final: 0.7882 (mmp) REVERT: D 38 GLU cc_start: 0.8861 (tp30) cc_final: 0.8579 (tp30) REVERT: D 40 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8604 (p) REVERT: D 71 ASN cc_start: 0.8927 (t0) cc_final: 0.8533 (t0) REVERT: D 77 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8151 (mm) REVERT: D 81 TRP cc_start: 0.7492 (t-100) cc_final: 0.6737 (t60) REVERT: D 96 ARG cc_start: 0.7432 (mtp180) cc_final: 0.7204 (mmt180) REVERT: D 143 GLN cc_start: 0.8883 (mm110) cc_final: 0.8599 (mm110) REVERT: D 167 GLU cc_start: 0.9049 (mp0) cc_final: 0.8733 (pm20) REVERT: E 26 MET cc_start: 0.8210 (mmm) cc_final: 0.7871 (mmp) REVERT: E 40 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8710 (p) REVERT: E 71 ASN cc_start: 0.9082 (t0) cc_final: 0.8675 (t0) REVERT: E 81 TRP cc_start: 0.7283 (t-100) cc_final: 0.6641 (t60) REVERT: E 96 ARG cc_start: 0.7466 (mtp180) cc_final: 0.7197 (mtt180) REVERT: E 143 GLN cc_start: 0.8787 (mm110) cc_final: 0.8432 (mm110) REVERT: E 148 LYS cc_start: 0.9234 (mmpt) cc_final: 0.8842 (mmpt) REVERT: E 149 GLU cc_start: 0.9284 (pm20) cc_final: 0.9024 (pm20) REVERT: E 152 LYS cc_start: 0.9390 (mttt) cc_final: 0.9037 (mtmm) REVERT: E 165 GLU cc_start: 0.8611 (mp0) cc_final: 0.8022 (mp0) REVERT: E 167 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8774 (pm20) REVERT: F 71 ASN cc_start: 0.8913 (t0) cc_final: 0.8636 (t0) REVERT: F 77 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8394 (mm) REVERT: F 81 TRP cc_start: 0.7136 (t-100) cc_final: 0.6341 (t60) REVERT: F 96 ARG cc_start: 0.7497 (mtp180) cc_final: 0.7261 (mmt180) REVERT: F 105 ARG cc_start: 0.9085 (mpt180) cc_final: 0.8872 (mmt-90) REVERT: F 136 GLU cc_start: 0.8966 (pm20) cc_final: 0.8745 (pm20) REVERT: F 142 TYR cc_start: 0.8967 (m-80) cc_final: 0.8136 (m-80) REVERT: F 148 LYS cc_start: 0.9326 (mmpt) cc_final: 0.8810 (mmpt) REVERT: F 152 LYS cc_start: 0.9366 (mttt) cc_final: 0.9023 (mppt) REVERT: F 167 GLU cc_start: 0.8910 (mp0) cc_final: 0.8565 (pm20) REVERT: F 179 ARG cc_start: 0.8855 (ttm110) cc_final: 0.8594 (ttp-110) REVERT: G 26 MET cc_start: 0.8275 (mmm) cc_final: 0.8033 (mmp) REVERT: G 71 ASN cc_start: 0.8882 (t0) cc_final: 0.8298 (t0) REVERT: G 73 ASN cc_start: 0.8700 (m110) cc_final: 0.8443 (m-40) REVERT: G 105 ARG cc_start: 0.9002 (mmt90) cc_final: 0.8725 (mmt-90) REVERT: G 143 GLN cc_start: 0.8874 (mm110) cc_final: 0.8588 (mm110) REVERT: G 165 GLU cc_start: 0.8816 (mp0) cc_final: 0.8548 (mp0) REVERT: G 167 GLU cc_start: 0.9008 (mp0) cc_final: 0.8729 (pm20) outliers start: 41 outliers final: 16 residues processed: 387 average time/residue: 0.6623 time to fit residues: 271.0209 Evaluate side-chains 392 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 366 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 185 CYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 199 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 90 optimal weight: 0.0970 chunk 59 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN B 104 GLN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 GLN E 104 GLN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.112401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.076025 restraints weight = 19597.153| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.33 r_work: 0.2767 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10801 Z= 0.136 Angle : 0.669 6.487 14686 Z= 0.337 Chirality : 0.039 0.130 1708 Planarity : 0.005 0.044 1806 Dihedral : 3.965 16.569 1442 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.32 % Allowed : 22.58 % Favored : 74.10 % 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 are not related in a simple way. whole: 1.77 (0.25), residues: 1309 helix: 2.20 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.42 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 179 TYR 0.015 0.001 TYR A 142 PHE 0.004 0.001 PHE G 189 TRP 0.028 0.001 TRP G 81 HIS 0.000 0.000 HIS F 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (10780) covalent geometry : angle 0.66480 / 0.34 (14637) SS BOND : bond 0.00227 / 0.16 ( 14) SS BOND : angle 0.40788 / 0.33 ( 28) hydrogen bonds : bond 0.03770 / 2.47 ( 645) hydrogen bonds : angle 2.96844 / 2.12 ( 1935) link_NAG-ASN : bond 0.00123 / 0.08 ( 7) link_NAG-ASN : angle 2.10043 / 1.54 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 379 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8091 (mmm) cc_final: 0.7779 (mmp) REVERT: A 40 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8701 (p) REVERT: A 71 ASN cc_start: 0.8996 (t160) cc_final: 0.8538 (t0) REVERT: A 81 TRP cc_start: 0.7230 (t-100) cc_final: 0.6344 (t60) REVERT: A 82 LYS cc_start: 0.8786 (pptt) cc_final: 0.8577 (pptt) REVERT: A 96 ARG cc_start: 0.7452 (ptp-110) cc_final: 0.7200 (pmm-80) REVERT: A 143 GLN cc_start: 0.8618 (mm110) cc_final: 0.8345 (mm110) REVERT: A 152 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8993 (mtmm) REVERT: A 167 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8682 (pm20) REVERT: A 169 ILE cc_start: 0.9248 (mt) cc_final: 0.8947 (tt) REVERT: A 199 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8865 (tt) REVERT: B 26 MET cc_start: 0.8141 (mmm) cc_final: 0.7765 (mmp) REVERT: B 68 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8169 (t80) REVERT: B 96 ARG cc_start: 0.7357 (mtp180) cc_final: 0.7001 (mmt180) REVERT: B 142 TYR cc_start: 0.9102 (m-80) cc_final: 0.8570 (m-10) REVERT: B 143 GLN cc_start: 0.8912 (mm110) cc_final: 0.8593 (mm110) REVERT: B 148 LYS cc_start: 0.9271 (mmpt) cc_final: 0.8868 (mmpt) REVERT: B 152 LYS cc_start: 0.9315 (mttt) cc_final: 0.8985 (mtmm) REVERT: B 167 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8613 (pm20) REVERT: C 26 MET cc_start: 0.8125 (mmm) cc_final: 0.7818 (mmp) REVERT: C 40 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8430 (p) REVERT: C 71 ASN cc_start: 0.8901 (t0) cc_final: 0.8567 (t0) REVERT: C 74 ILE cc_start: 0.8456 (pt) cc_final: 0.8168 (tp) REVERT: C 81 TRP cc_start: 0.7175 (t-100) cc_final: 0.6432 (t60) REVERT: C 167 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8670 (pm20) REVERT: C 199 LEU cc_start: 0.8969 (tp) cc_final: 0.8768 (tt) REVERT: D 26 MET cc_start: 0.8151 (mmm) cc_final: 0.7844 (mmp) REVERT: D 38 GLU cc_start: 0.8838 (tp30) cc_final: 0.8533 (tp30) REVERT: D 40 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8652 (p) REVERT: D 68 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.8188 (m-80) REVERT: D 71 ASN cc_start: 0.8864 (t0) cc_final: 0.8474 (t0) REVERT: D 77 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8124 (mm) REVERT: D 81 TRP cc_start: 0.7455 (t-100) cc_final: 0.6767 (t60) REVERT: D 82 LYS cc_start: 0.8839 (pptt) cc_final: 0.8628 (pptt) REVERT: D 167 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8726 (pm20) REVERT: E 26 MET cc_start: 0.8226 (mmm) cc_final: 0.7855 (mmp) REVERT: E 40 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8657 (p) REVERT: E 68 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: E 71 ASN cc_start: 0.9020 (t0) cc_final: 0.8589 (t0) REVERT: E 81 TRP cc_start: 0.7242 (t-100) cc_final: 0.6582 (t60) REVERT: E 143 GLN cc_start: 0.8791 (mm110) cc_final: 0.8398 (mm110) REVERT: E 167 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8796 (pm20) REVERT: F 71 ASN cc_start: 0.8883 (t0) cc_final: 0.8608 (t0) REVERT: F 77 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8330 (mm) REVERT: F 81 TRP cc_start: 0.7129 (t-100) cc_final: 0.6259 (t60) REVERT: F 105 ARG cc_start: 0.9075 (mpt180) cc_final: 0.8862 (mmt-90) REVERT: F 142 TYR cc_start: 0.8882 (m-80) cc_final: 0.8393 (m-80) REVERT: F 152 LYS cc_start: 0.9342 (mttt) cc_final: 0.9122 (mtmm) REVERT: F 167 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8533 (pm20) REVERT: G 26 MET cc_start: 0.8220 (mmm) cc_final: 0.7995 (mmp) REVERT: G 71 ASN cc_start: 0.8873 (t0) cc_final: 0.8319 (t0) REVERT: G 73 ASN cc_start: 0.8590 (m110) cc_final: 0.8381 (m-40) REVERT: G 102 MET cc_start: 0.9167 (ttm) cc_final: 0.8958 (ttp) REVERT: G 105 ARG cc_start: 0.9013 (mmt90) cc_final: 0.8733 (mmt-90) REVERT: G 122 LYS cc_start: 0.8864 (mttm) cc_final: 0.8477 (mttm) REVERT: G 143 GLN cc_start: 0.8935 (mm110) cc_final: 0.8632 (mm110) REVERT: G 148 LYS cc_start: 0.9305 (mmpt) cc_final: 0.8698 (mmpt) REVERT: G 152 LYS cc_start: 0.9328 (mttt) cc_final: 0.8967 (mtmm) REVERT: G 167 GLU cc_start: 0.9006 (mp0) cc_final: 0.8757 (pm20) outliers start: 36 outliers final: 9 residues processed: 392 average time/residue: 0.6544 time to fit residues: 271.4241 Evaluate side-chains 396 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 370 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 68 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 114 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 79 optimal weight: 0.0370 chunk 97 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 71 ASN B 104 GLN C 104 GLN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 GLN E 104 GLN G 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.109404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.072544 restraints weight = 19803.897| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.40 r_work: 0.2714 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10801 Z= 0.197 Angle : 0.736 7.175 14686 Z= 0.373 Chirality : 0.042 0.127 1708 Planarity : 0.005 0.048 1806 Dihedral : 3.977 19.124 1442 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.23 % Allowed : 23.96 % Favored : 72.81 % 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 are not related in a simple way. whole: 1.62 (0.24), residues: 1309 helix: 2.06 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.39 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 83 TYR 0.016 0.001 TYR B 34 PHE 0.007 0.001 PHE C 189 TRP 0.032 0.001 TRP B 81 HIS 0.001 0.000 HIS G 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.20 (10780) covalent geometry : angle 0.73130 / 0.37 (14637) SS BOND : bond 0.00374 / 0.25 ( 14) SS BOND : angle 0.67685 / 0.51 ( 28) hydrogen bonds : bond 0.04985 / 3.29 ( 645) hydrogen bonds : angle 3.19272 / 2.28 ( 1935) link_NAG-ASN : bond 0.00092 / 0.06 ( 7) link_NAG-ASN : angle 2.25184 / 1.64 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 366 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8263 (mmm) cc_final: 0.7956 (mmp) REVERT: A 40 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8656 (p) REVERT: A 71 ASN cc_start: 0.8953 (t0) cc_final: 0.8521 (t0) REVERT: A 81 TRP cc_start: 0.7341 (t-100) cc_final: 0.6392 (t60) REVERT: A 122 LYS cc_start: 0.8992 (mttm) cc_final: 0.8761 (mtmt) REVERT: A 143 GLN cc_start: 0.8697 (mm110) cc_final: 0.8422 (mm110) REVERT: A 167 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8723 (pm20) REVERT: A 199 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8832 (tt) REVERT: B 26 MET cc_start: 0.8254 (mmm) cc_final: 0.7993 (mmp) REVERT: B 68 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.8076 (t80) REVERT: B 91 ASP cc_start: 0.7758 (p0) cc_final: 0.7504 (p0) REVERT: B 96 ARG cc_start: 0.7416 (mtp180) cc_final: 0.7105 (mmt180) REVERT: B 142 TYR cc_start: 0.9135 (m-80) cc_final: 0.8517 (m-80) REVERT: B 143 GLN cc_start: 0.8958 (mm110) cc_final: 0.8652 (mm110) REVERT: B 148 LYS cc_start: 0.9289 (mmpt) cc_final: 0.9032 (mmpt) REVERT: B 152 LYS cc_start: 0.9397 (mttt) cc_final: 0.9075 (mtmm) REVERT: B 167 GLU cc_start: 0.8938 (mp0) cc_final: 0.8630 (pm20) REVERT: B 179 ARG cc_start: 0.8842 (ttm110) cc_final: 0.8524 (ttp-110) REVERT: C 26 MET cc_start: 0.8270 (mmm) cc_final: 0.7963 (mmp) REVERT: C 40 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8595 (p) REVERT: C 71 ASN cc_start: 0.8898 (t0) cc_final: 0.8578 (t0) REVERT: C 74 ILE cc_start: 0.8545 (pt) cc_final: 0.8272 (tp) REVERT: C 81 TRP cc_start: 0.7212 (t-100) cc_final: 0.6516 (t60) REVERT: C 83 ARG cc_start: 0.7890 (ttm-80) cc_final: 0.7677 (mtm110) REVERT: C 96 ARG cc_start: 0.7470 (ptt-90) cc_final: 0.7122 (pmm-80) REVERT: C 122 LYS cc_start: 0.9014 (mttp) cc_final: 0.8603 (mttp) REVERT: C 152 LYS cc_start: 0.9186 (mppt) cc_final: 0.8656 (mtmm) REVERT: C 167 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8746 (pm20) REVERT: C 199 LEU cc_start: 0.9041 (tp) cc_final: 0.8831 (tt) REVERT: D 26 MET cc_start: 0.8270 (mmm) cc_final: 0.7957 (mmp) REVERT: D 38 GLU cc_start: 0.8886 (tp30) cc_final: 0.8558 (tp30) REVERT: D 40 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8677 (p) REVERT: D 71 ASN cc_start: 0.8910 (t0) cc_final: 0.8397 (t0) REVERT: D 77 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8115 (mm) REVERT: D 81 TRP cc_start: 0.7446 (t-100) cc_final: 0.6716 (t60) REVERT: D 91 ASP cc_start: 0.7671 (p0) cc_final: 0.7392 (p0) REVERT: D 164 GLU cc_start: 0.8665 (pm20) cc_final: 0.8440 (pm20) REVERT: D 167 GLU cc_start: 0.9039 (mp0) cc_final: 0.8729 (pm20) REVERT: E 26 MET cc_start: 0.8293 (mmm) cc_final: 0.7940 (mmp) REVERT: E 40 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8715 (p) REVERT: E 68 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8540 (m-80) REVERT: E 71 ASN cc_start: 0.9024 (t0) cc_final: 0.8588 (t0) REVERT: E 81 TRP cc_start: 0.7327 (t-100) cc_final: 0.6676 (t60) REVERT: E 95 LEU cc_start: 0.8188 (mt) cc_final: 0.7959 (pp) REVERT: E 122 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8454 (mtmp) REVERT: E 143 GLN cc_start: 0.8887 (mm110) cc_final: 0.8520 (mm110) REVERT: E 148 LYS cc_start: 0.9241 (mmpt) cc_final: 0.8773 (mmpt) REVERT: E 149 GLU cc_start: 0.9252 (pm20) cc_final: 0.8981 (pm20) REVERT: E 152 LYS cc_start: 0.9413 (mttt) cc_final: 0.9074 (mtmm) REVERT: E 167 GLU cc_start: 0.8973 (mp0) cc_final: 0.8748 (pm20) REVERT: E 199 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8884 (tt) REVERT: F 71 ASN cc_start: 0.8911 (t0) cc_final: 0.8603 (t0) REVERT: F 77 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8353 (mm) REVERT: F 81 TRP cc_start: 0.7244 (t-100) cc_final: 0.6349 (t60) REVERT: F 91 ASP cc_start: 0.8130 (p0) cc_final: 0.7889 (p0) REVERT: F 105 ARG cc_start: 0.9097 (mpt180) cc_final: 0.8887 (mmt-90) REVERT: F 142 TYR cc_start: 0.9116 (m-80) cc_final: 0.8508 (m-80) REVERT: F 148 LYS cc_start: 0.9325 (mmpt) cc_final: 0.9121 (mmpt) REVERT: F 152 LYS cc_start: 0.9370 (mttt) cc_final: 0.9143 (mtmm) REVERT: F 164 GLU cc_start: 0.8626 (pm20) cc_final: 0.8377 (pm20) REVERT: F 167 GLU cc_start: 0.8899 (mp0) cc_final: 0.8602 (pm20) REVERT: F 179 ARG cc_start: 0.8922 (ttm110) cc_final: 0.8615 (ttp-110) REVERT: G 26 MET cc_start: 0.8342 (mmm) cc_final: 0.8042 (mmp) REVERT: G 71 ASN cc_start: 0.8868 (t0) cc_final: 0.8273 (t0) REVERT: G 73 ASN cc_start: 0.8660 (m110) cc_final: 0.8390 (m-40) REVERT: G 122 LYS cc_start: 0.8968 (mttm) cc_final: 0.8645 (mtmm) REVERT: G 143 GLN cc_start: 0.8977 (mm110) cc_final: 0.8671 (mm110) REVERT: G 167 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8765 (pm20) outliers start: 35 outliers final: 11 residues processed: 377 average time/residue: 0.6372 time to fit residues: 254.3859 Evaluate side-chains 387 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 362 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain G residue 167 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 chunk 117 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 0 optimal weight: 80.0000 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 GLN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 GLN E 104 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.111284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.075126 restraints weight = 19555.094| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.37 r_work: 0.2766 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10801 Z= 0.155 Angle : 0.760 7.129 14686 Z= 0.384 Chirality : 0.040 0.116 1708 Planarity : 0.005 0.083 1806 Dihedral : 3.897 16.834 1442 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.49 % Allowed : 26.27 % Favored : 71.24 % 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 are not related in a simple way. whole: 1.68 (0.24), residues: 1309 helix: 2.14 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.47 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 83 TYR 0.018 0.001 TYR A 142 PHE 0.004 0.001 PHE G 189 TRP 0.032 0.001 TRP B 81 HIS 0.001 0.000 HIS E 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (10780) covalent geometry : angle 0.75709 / 0.38 (14637) SS BOND : bond 0.00287 / 0.19 ( 14) SS BOND : angle 0.40299 / 0.32 ( 28) hydrogen bonds : bond 0.04097 / 2.69 ( 645) hydrogen bonds : angle 3.01841 / 2.16 ( 1935) link_NAG-ASN : bond 0.00115 / 0.07 ( 7) link_NAG-ASN : angle 2.05412 / 1.51 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 368 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.8241 (mmm) cc_final: 0.7910 (mmp) REVERT: A 40 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8699 (p) REVERT: A 71 ASN cc_start: 0.8952 (t0) cc_final: 0.8578 (t0) REVERT: A 81 TRP cc_start: 0.7333 (t-100) cc_final: 0.6449 (t60) REVERT: A 82 LYS cc_start: 0.8771 (pptt) cc_final: 0.8462 (pptt) REVERT: A 96 ARG cc_start: 0.7576 (ptp-110) cc_final: 0.7353 (mtm110) REVERT: A 143 GLN cc_start: 0.8714 (mm110) cc_final: 0.8409 (mm110) REVERT: A 167 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8705 (pm20) REVERT: A 199 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8874 (tt) REVERT: B 26 MET cc_start: 0.8171 (mmm) cc_final: 0.7813 (mmp) REVERT: B 68 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.8040 (t80) REVERT: B 91 ASP cc_start: 0.7718 (p0) cc_final: 0.7440 (p0) REVERT: B 96 ARG cc_start: 0.7284 (mtp180) cc_final: 0.6944 (mmt180) REVERT: B 142 TYR cc_start: 0.9141 (m-80) cc_final: 0.8564 (m-10) REVERT: B 143 GLN cc_start: 0.8968 (mm110) cc_final: 0.8628 (mm110) REVERT: B 152 LYS cc_start: 0.9368 (mttt) cc_final: 0.9124 (mtmm) REVERT: B 167 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8610 (pm20) REVERT: B 179 ARG cc_start: 0.8807 (ttm110) cc_final: 0.8539 (ttp-110) REVERT: C 26 MET cc_start: 0.8200 (mmm) cc_final: 0.7902 (mmp) REVERT: C 40 THR cc_start: 0.9114 (OUTLIER) cc_final: 0.8568 (p) REVERT: C 71 ASN cc_start: 0.8856 (t0) cc_final: 0.8555 (t0) REVERT: C 74 ILE cc_start: 0.8524 (pt) cc_final: 0.8202 (tp) REVERT: C 81 TRP cc_start: 0.7211 (t-100) cc_final: 0.6488 (t60) REVERT: C 96 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.7153 (mtt90) REVERT: C 122 LYS cc_start: 0.8976 (mttp) cc_final: 0.8558 (mttp) REVERT: C 149 GLU cc_start: 0.9215 (pm20) cc_final: 0.8899 (pm20) REVERT: C 152 LYS cc_start: 0.9168 (mppt) cc_final: 0.8703 (mppt) REVERT: C 164 GLU cc_start: 0.8779 (pm20) cc_final: 0.8501 (pm20) REVERT: C 167 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8746 (pm20) REVERT: C 199 LEU cc_start: 0.9034 (tp) cc_final: 0.8829 (tt) REVERT: D 26 MET cc_start: 0.8247 (mmm) cc_final: 0.7933 (mmp) REVERT: D 38 GLU cc_start: 0.8874 (tp30) cc_final: 0.8565 (tp30) REVERT: D 40 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8660 (p) REVERT: D 71 ASN cc_start: 0.8843 (t0) cc_final: 0.8410 (t0) REVERT: D 77 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8111 (mm) REVERT: D 81 TRP cc_start: 0.7404 (t-100) cc_final: 0.6642 (t60) REVERT: D 143 GLN cc_start: 0.9055 (mm110) cc_final: 0.8669 (mm110) REVERT: D 167 GLU cc_start: 0.9006 (mp0) cc_final: 0.8722 (pm20) REVERT: E 26 MET cc_start: 0.8258 (mmm) cc_final: 0.7895 (mmp) REVERT: E 40 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8655 (p) REVERT: E 68 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.8256 (m-80) REVERT: E 71 ASN cc_start: 0.9001 (t0) cc_final: 0.8602 (t0) REVERT: E 81 TRP cc_start: 0.7284 (t-100) cc_final: 0.6546 (t60) REVERT: E 95 LEU cc_start: 0.8281 (mt) cc_final: 0.8015 (pp) REVERT: E 143 GLN cc_start: 0.8987 (mm110) cc_final: 0.8665 (mm110) REVERT: E 148 LYS cc_start: 0.9225 (mmpt) cc_final: 0.8779 (mmpt) REVERT: E 149 GLU cc_start: 0.9248 (pm20) cc_final: 0.8963 (pm20) REVERT: E 152 LYS cc_start: 0.9399 (mttt) cc_final: 0.9061 (mtmm) REVERT: E 167 GLU cc_start: 0.8971 (mp0) cc_final: 0.8739 (pm20) REVERT: E 199 LEU cc_start: 0.9104 (tp) cc_final: 0.8858 (tt) REVERT: F 71 ASN cc_start: 0.8884 (t0) cc_final: 0.8585 (t0) REVERT: F 77 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8322 (mm) REVERT: F 81 TRP cc_start: 0.7234 (t-100) cc_final: 0.6262 (t60) REVERT: F 91 ASP cc_start: 0.8008 (p0) cc_final: 0.7730 (p0) REVERT: F 96 ARG cc_start: 0.7389 (mtp180) cc_final: 0.7151 (mmt180) REVERT: F 105 ARG cc_start: 0.9087 (mpt180) cc_final: 0.8878 (mmt-90) REVERT: F 122 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8574 (mttp) REVERT: F 142 TYR cc_start: 0.9073 (m-80) cc_final: 0.8496 (m-80) REVERT: F 152 LYS cc_start: 0.9352 (mttt) cc_final: 0.9120 (mtmm) REVERT: F 167 GLU cc_start: 0.8886 (mp0) cc_final: 0.8589 (pm20) REVERT: G 26 MET cc_start: 0.8322 (mmm) cc_final: 0.7999 (mmp) REVERT: G 71 ASN cc_start: 0.8861 (t0) cc_final: 0.8280 (t0) REVERT: G 73 ASN cc_start: 0.8631 (m110) cc_final: 0.8314 (m-40) REVERT: G 143 GLN cc_start: 0.9010 (mm110) cc_final: 0.8732 (mm110) REVERT: G 167 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8763 (pm20) outliers start: 27 outliers final: 12 residues processed: 377 average time/residue: 0.6489 time to fit residues: 258.6432 Evaluate side-chains 390 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 363 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 185 CYS Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain G residue 133 ASP Chi-restraints excluded: chain G residue 167 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 15 optimal weight: 0.0470 chunk 58 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 71 ASN B 104 GLN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.111683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.075705 restraints weight = 19819.614| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.39 r_work: 0.2775 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10801 Z= 0.154 Angle : 0.794 7.699 14686 Z= 0.398 Chirality : 0.040 0.118 1708 Planarity : 0.005 0.045 1806 Dihedral : 3.822 17.165 1442 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.58 % Allowed : 26.08 % Favored : 71.34 % 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 are not related in a simple way. whole: 1.74 (0.24), residues: 1309 helix: 2.17 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.41 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 83 TYR 0.017 0.001 TYR A 142 PHE 0.004 0.001 PHE B 124 TRP 0.034 0.001 TRP G 81 HIS 0.000 0.000 HIS D 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.15 (10780) covalent geometry : angle 0.79132 / 0.40 (14637) SS BOND : bond 0.00263 / 0.18 ( 14) SS BOND : angle 0.36756 / 0.30 ( 28) hydrogen bonds : bond 0.03887 / 2.55 ( 645) hydrogen bonds : angle 2.96779 / 2.13 ( 1935) link_NAG-ASN : bond 0.00176 / 0.11 ( 7) link_NAG-ASN : angle 1.97372 / 1.45 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 368 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8744 (p) REVERT: A 71 ASN cc_start: 0.8933 (t0) cc_final: 0.8573 (t0) REVERT: A 81 TRP cc_start: 0.7316 (t-100) cc_final: 0.6441 (t60) REVERT: A 82 LYS cc_start: 0.8764 (pptt) cc_final: 0.8478 (pptt) REVERT: A 143 GLN cc_start: 0.8758 (mm110) cc_final: 0.8438 (mm110) REVERT: A 167 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8710 (pm20) REVERT: A 169 ILE cc_start: 0.9290 (mt) cc_final: 0.9038 (tt) REVERT: A 199 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8878 (tt) REVERT: B 26 MET cc_start: 0.8190 (mmm) cc_final: 0.7989 (mmp) REVERT: B 68 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8045 (t80) REVERT: B 91 ASP cc_start: 0.7716 (p0) cc_final: 0.7451 (p0) REVERT: B 96 ARG cc_start: 0.7276 (mtp180) cc_final: 0.6962 (mmt180) REVERT: B 142 TYR cc_start: 0.9105 (m-80) cc_final: 0.8583 (m-10) REVERT: B 143 GLN cc_start: 0.8986 (mm110) cc_final: 0.8636 (mm110) REVERT: B 152 LYS cc_start: 0.9386 (mttt) cc_final: 0.9149 (mtmm) REVERT: B 167 GLU cc_start: 0.8873 (mp0) cc_final: 0.8632 (pm20) REVERT: B 179 ARG cc_start: 0.8829 (ttm110) cc_final: 0.8554 (ttp-110) REVERT: C 26 MET cc_start: 0.8221 (mmm) cc_final: 0.7926 (mmp) REVERT: C 40 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8603 (p) REVERT: C 71 ASN cc_start: 0.8855 (t0) cc_final: 0.8586 (t0) REVERT: C 73 ASN cc_start: 0.8802 (m-40) cc_final: 0.8468 (m110) REVERT: C 74 ILE cc_start: 0.8539 (pt) cc_final: 0.8202 (tp) REVERT: C 81 TRP cc_start: 0.7225 (t-100) cc_final: 0.6541 (t60) REVERT: C 122 LYS cc_start: 0.8990 (mttp) cc_final: 0.8547 (mttp) REVERT: C 167 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8745 (pm20) REVERT: C 201 ARG cc_start: 0.8375 (ttt90) cc_final: 0.8141 (ttt90) REVERT: D 26 MET cc_start: 0.8298 (mmm) cc_final: 0.7804 (mmp) REVERT: D 38 GLU cc_start: 0.8880 (tp30) cc_final: 0.8565 (tp30) REVERT: D 40 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8698 (p) REVERT: D 68 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.8074 (m-80) REVERT: D 71 ASN cc_start: 0.8836 (t0) cc_final: 0.8455 (t0) REVERT: D 77 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8118 (mm) REVERT: D 81 TRP cc_start: 0.7371 (t-100) cc_final: 0.6613 (t60) REVERT: D 143 GLN cc_start: 0.9094 (mm110) cc_final: 0.8732 (mm110) REVERT: D 149 GLU cc_start: 0.9219 (pm20) cc_final: 0.8959 (pm20) REVERT: D 152 LYS cc_start: 0.9186 (mtmm) cc_final: 0.8570 (mtmm) REVERT: D 167 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8722 (pm20) REVERT: E 40 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8690 (p) REVERT: E 68 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.8270 (m-80) REVERT: E 71 ASN cc_start: 0.9018 (t0) cc_final: 0.8608 (t0) REVERT: E 81 TRP cc_start: 0.7295 (t-100) cc_final: 0.6555 (t60) REVERT: E 95 LEU cc_start: 0.8293 (mt) cc_final: 0.7995 (pp) REVERT: E 122 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8474 (mtmp) REVERT: E 143 GLN cc_start: 0.9023 (mm110) cc_final: 0.8704 (mm110) REVERT: E 148 LYS cc_start: 0.9217 (mmpt) cc_final: 0.8789 (mmpt) REVERT: E 149 GLU cc_start: 0.9227 (pm20) cc_final: 0.8935 (pm20) REVERT: E 152 LYS cc_start: 0.9393 (mttt) cc_final: 0.9040 (mtmm) REVERT: E 167 GLU cc_start: 0.8942 (mp0) cc_final: 0.8736 (pm20) REVERT: E 199 LEU cc_start: 0.9149 (tp) cc_final: 0.8907 (tt) REVERT: F 71 ASN cc_start: 0.8845 (t0) cc_final: 0.8559 (t0) REVERT: F 77 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8305 (mm) REVERT: F 81 TRP cc_start: 0.7221 (t-100) cc_final: 0.6317 (t60) REVERT: F 91 ASP cc_start: 0.7986 (p0) cc_final: 0.7718 (p0) REVERT: F 96 ARG cc_start: 0.7374 (mtp180) cc_final: 0.7148 (mmt180) REVERT: F 105 ARG cc_start: 0.9088 (mpt180) cc_final: 0.8881 (mmt-90) REVERT: F 122 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8619 (mttp) REVERT: F 142 TYR cc_start: 0.9068 (m-80) cc_final: 0.8509 (m-10) REVERT: F 152 LYS cc_start: 0.9363 (mttt) cc_final: 0.9128 (mtmm) REVERT: F 167 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8616 (pm20) REVERT: G 26 MET cc_start: 0.8345 (mmm) cc_final: 0.8042 (mmp) REVERT: G 71 ASN cc_start: 0.8866 (t0) cc_final: 0.8188 (t0) REVERT: G 73 ASN cc_start: 0.8612 (m110) cc_final: 0.8326 (m-40) REVERT: G 82 LYS cc_start: 0.8766 (pptt) cc_final: 0.8525 (tptt) REVERT: G 83 ARG cc_start: 0.8059 (ptp-110) cc_final: 0.7683 (mtm110) REVERT: G 122 LYS cc_start: 0.8911 (mttm) cc_final: 0.8519 (mttm) REVERT: G 136 GLU cc_start: 0.8871 (pm20) cc_final: 0.8633 (pm20) REVERT: G 143 GLN cc_start: 0.9068 (mm110) cc_final: 0.8794 (mm110) REVERT: G 167 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8763 (pm20) outliers start: 28 outliers final: 10 residues processed: 378 average time/residue: 0.6693 time to fit residues: 267.8066 Evaluate side-chains 387 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 360 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain G residue 167 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 0.0980 chunk 114 optimal weight: 50.0000 chunk 109 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 50.0000 chunk 19 optimal weight: 50.0000 chunk 62 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.111918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.075722 restraints weight = 19590.013| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.38 r_work: 0.2780 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10801 Z= 0.159 Angle : 0.828 8.394 14686 Z= 0.415 Chirality : 0.040 0.115 1708 Planarity : 0.005 0.049 1806 Dihedral : 3.807 17.797 1442 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.58 % Allowed : 26.73 % Favored : 70.69 % 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 are not related in a simple way. whole: 1.75 (0.24), residues: 1309 helix: 2.17 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.38 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 83 TYR 0.018 0.001 TYR A 142 PHE 0.006 0.001 PHE D 163 TRP 0.036 0.001 TRP G 81 HIS 0.001 0.000 HIS D 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.16 (10780) covalent geometry : angle 0.82644 / 0.42 (14637) SS BOND : bond 0.00260 / 0.18 ( 14) SS BOND : angle 0.39756 / 0.32 ( 28) hydrogen bonds : bond 0.03779 / 2.47 ( 645) hydrogen bonds : angle 2.97735 / 2.14 ( 1935) link_NAG-ASN : bond 0.00167 / 0.10 ( 7) link_NAG-ASN : angle 1.90311 / 1.40 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2618 Ramachandran restraints generated. 1309 Oldfield, 0 Emsley, 1309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 363 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8795 (p) REVERT: A 71 ASN cc_start: 0.8931 (t0) cc_final: 0.8578 (t0) REVERT: A 81 TRP cc_start: 0.7324 (t-100) cc_final: 0.6419 (t60) REVERT: A 95 LEU cc_start: 0.8230 (mt) cc_final: 0.8008 (pp) REVERT: A 143 GLN cc_start: 0.8820 (mm110) cc_final: 0.8501 (mm110) REVERT: A 152 LYS cc_start: 0.9235 (mtmm) cc_final: 0.8679 (mptp) REVERT: A 167 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8716 (pm20) REVERT: A 169 ILE cc_start: 0.9272 (mt) cc_final: 0.9024 (tt) REVERT: B 26 MET cc_start: 0.8235 (mmm) cc_final: 0.7854 (mmp) REVERT: B 68 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.8031 (t80) REVERT: B 91 ASP cc_start: 0.7508 (p0) cc_final: 0.7265 (p0) REVERT: B 142 TYR cc_start: 0.9070 (m-80) cc_final: 0.8604 (m-10) REVERT: B 143 GLN cc_start: 0.9038 (mm110) cc_final: 0.8701 (mm110) REVERT: B 152 LYS cc_start: 0.9385 (mttt) cc_final: 0.9147 (mtmm) REVERT: B 167 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8643 (pm20) REVERT: C 26 MET cc_start: 0.8313 (mmm) cc_final: 0.7933 (mmp) REVERT: C 40 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8578 (p) REVERT: C 71 ASN cc_start: 0.8817 (t0) cc_final: 0.8558 (t0) REVERT: C 73 ASN cc_start: 0.8811 (m-40) cc_final: 0.8523 (m110) REVERT: C 74 ILE cc_start: 0.8564 (pt) cc_final: 0.8221 (tp) REVERT: C 81 TRP cc_start: 0.7159 (t-100) cc_final: 0.6545 (t60) REVERT: C 96 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7188 (mtm110) REVERT: C 122 LYS cc_start: 0.9001 (mttp) cc_final: 0.8738 (mtmm) REVERT: C 152 LYS cc_start: 0.9198 (mtmm) cc_final: 0.8816 (mtmm) REVERT: C 167 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8771 (pm20) REVERT: C 201 ARG cc_start: 0.8402 (ttt90) cc_final: 0.8190 (ttt90) REVERT: D 26 MET cc_start: 0.8402 (mmm) cc_final: 0.8085 (mmp) REVERT: D 38 GLU cc_start: 0.8899 (tp30) cc_final: 0.8567 (tp30) REVERT: D 40 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8706 (p) REVERT: D 68 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.8135 (m-80) REVERT: D 71 ASN cc_start: 0.8819 (t0) cc_final: 0.8445 (t0) REVERT: D 77 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8166 (mm) REVERT: D 81 TRP cc_start: 0.7365 (t-100) cc_final: 0.6607 (t60) REVERT: D 143 GLN cc_start: 0.9106 (mm110) cc_final: 0.8742 (mm110) REVERT: D 167 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8721 (pm20) REVERT: E 40 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8701 (p) REVERT: E 68 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8240 (m-80) REVERT: E 71 ASN cc_start: 0.9010 (t0) cc_final: 0.8587 (t0) REVERT: E 81 TRP cc_start: 0.7281 (t-100) cc_final: 0.6547 (t60) REVERT: E 95 LEU cc_start: 0.8294 (mt) cc_final: 0.7954 (pp) REVERT: E 122 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8446 (mtmp) REVERT: E 143 GLN cc_start: 0.9027 (mm110) cc_final: 0.8702 (mm110) REVERT: E 148 LYS cc_start: 0.9214 (mmpt) cc_final: 0.8799 (mmpt) REVERT: E 149 GLU cc_start: 0.9218 (pm20) cc_final: 0.8921 (pm20) REVERT: E 152 LYS cc_start: 0.9398 (mttt) cc_final: 0.9048 (mtmm) REVERT: E 167 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8745 (pm20) REVERT: E 199 LEU cc_start: 0.9152 (tp) cc_final: 0.8914 (tt) REVERT: F 71 ASN cc_start: 0.8864 (t0) cc_final: 0.8575 (t0) REVERT: F 77 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8291 (mm) REVERT: F 81 TRP cc_start: 0.7234 (t-100) cc_final: 0.6357 (t60) REVERT: F 91 ASP cc_start: 0.7934 (p0) cc_final: 0.7638 (p0) REVERT: F 96 ARG cc_start: 0.7377 (mtp180) cc_final: 0.7142 (mmt180) REVERT: F 105 ARG cc_start: 0.9097 (mpt180) cc_final: 0.8896 (mmt-90) REVERT: F 122 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8623 (mttp) REVERT: F 142 TYR cc_start: 0.9059 (m-80) cc_final: 0.8546 (m-10) REVERT: F 152 LYS cc_start: 0.9367 (mttt) cc_final: 0.9053 (mtmm) REVERT: F 167 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8625 (pm20) REVERT: G 71 ASN cc_start: 0.8858 (t0) cc_final: 0.8437 (t0) REVERT: G 73 ASN cc_start: 0.8548 (m110) cc_final: 0.8194 (m-40) REVERT: G 136 GLU cc_start: 0.8881 (pm20) cc_final: 0.8655 (pm20) REVERT: G 143 GLN cc_start: 0.9073 (mm110) cc_final: 0.8820 (mm110) REVERT: G 167 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8778 (pm20) REVERT: G 199 LEU cc_start: 0.9160 (tp) cc_final: 0.8835 (tt) outliers start: 28 outliers final: 10 residues processed: 372 average time/residue: 0.7019 time to fit residues: 276.4649 Evaluate side-chains 386 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 357 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain G residue 26 MET Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 167 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 57 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 19 optimal weight: 50.0000 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.111881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.075870 restraints weight = 19785.489| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.37 r_work: 0.2788 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10801 Z= 0.161 Angle : 0.837 8.278 14686 Z= 0.420 Chirality : 0.040 0.115 1708 Planarity : 0.006 0.083 1806 Dihedral : 3.846 18.243 1442 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.76 % Allowed : 26.73 % Favored : 70.51 % 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 are not related in a simple way. whole: 1.77 (0.24), residues: 1309 helix: 2.18 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.35 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 83 TYR 0.019 0.001 TYR A 142 PHE 0.004 0.001 PHE B 124 TRP 0.036 0.001 TRP G 81 HIS 0.000 0.000 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.16 (10780) covalent geometry : angle 0.83457 / 0.42 (14637) SS BOND : bond 0.00255 / 0.17 ( 14) SS BOND : angle 0.37639 / 0.31 ( 28) hydrogen bonds : bond 0.03748 / 2.45 ( 645) hydrogen bonds : angle 2.97498 / 2.13 ( 1935) link_NAG-ASN : bond 0.00202 / 0.12 ( 7) link_NAG-ASN : angle 1.92816 / 1.42 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4863.96 seconds wall clock time: 83 minutes 12.22 seconds (4992.22 seconds total)