Starting phenix.real_space_refine on Mon Jul 28 18:29:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dsd_30831/07_2025/7dsd_30831.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsd_30831/07_2025/7dsd_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_2025/7dsd_30831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsd_30831/07_2025/7dsd_30831.map" model { file = "/net/cci-nas-00/data/ceres_data/7dsd_30831/07_2025/7dsd_30831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsd_30831/07_2025/7dsd_30831.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 3.80, per 1000 atoms: 0.36 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 C 41 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 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: 2.76 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.88 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: 2.45 Time building geometry restraints manager: 3.24 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: 5912 11.45 - 22.91: 430 22.91 - 34.36: 119 34.36 - 45.81: 35 45.81 - 57.27: 56 Dihedral angle restraints: 6552 sinusoidal: 2576 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 6549 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 1.050 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 22.520 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 : 10.556 57.267 3920 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (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 TRP 0.005 0.001 TRP G 81 HIS 0.001 0.000 HIS B 166 PHE 0.008 0.001 PHE G 63 TYR 0.007 0.001 TYR E 34 ARG 0.003 0.000 ARG A 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 7) link_NAG-ASN : angle 3.10861 ( 21) hydrogen bonds : bond 0.11927 ( 645) hydrogen bonds : angle 4.93159 ( 1935) SS BOND : bond 0.00223 ( 14) SS BOND : angle 0.88321 ( 28) covalent geometry : bond 0.00438 (10780) covalent geometry : angle 0.63641 (14637) *********************** 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 : 1.354 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: 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: 0.6434 (t60) REVERT: B 96 ARG cc_start: 0.7419 (mtp180) cc_final: 0.7116 (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: 0.8233 (pt) cc_final: 0.7995 (tp) REVERT: C 82 LYS cc_start: 0.8921 (tttt) cc_final: 0.8717 (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: 0.8754 (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 74 ILE cc_start: 0.8202 (pt) cc_final: 0.8001 (tp) 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: 0.6438 (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: 1.5952 time to fit residues: 664.1899 Evaluate side-chains 370 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 34 optimal weight: 0.0870 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 77 optimal weight: 0.0570 chunk 120 optimal weight: 0.0970 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3595 r_free = 0.3595 target = 0.114990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.078701 restraints weight = 18954.925| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.28 r_work: 0.2801 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10801 Z= 0.126 Angle : 0.605 5.585 14686 Z= 0.306 Chirality : 0.039 0.138 1708 Planarity : 0.005 0.038 1806 Dihedral : 4.121 19.606 1589 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.57 % Allowed : 16.22 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.24), residues: 1309 helix: 1.41 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -2.52 (0.28), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 62 HIS 0.001 0.000 HIS E 166 PHE 0.006 0.001 PHE E 137 TYR 0.012 0.001 TYR A 47 ARG 0.008 0.000 ARG E 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00127 ( 7) link_NAG-ASN : angle 1.66159 ( 21) hydrogen bonds : bond 0.03680 ( 645) hydrogen bonds : angle 3.19984 ( 1935) SS BOND : bond 0.00238 ( 14) SS BOND : angle 0.34008 ( 28) covalent geometry : bond 0.00291 (10780) covalent geometry : angle 0.60240 (14637) *********************** 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 396 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 379 time to evaluate : 1.617 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: A 26 MET cc_start: 0.7934 (mmm) cc_final: 0.7606 (mmp) REVERT: A 71 ASN cc_start: 0.8918 (t0) cc_final: 0.8503 (t0) REVERT: A 81 TRP cc_start: 0.7133 (t-100) cc_final: 0.6275 (t60) REVERT: A 122 LYS cc_start: 0.8778 (mttm) cc_final: 0.8511 (mttm) REVERT: A 152 LYS cc_start: 0.9431 (mttt) cc_final: 0.9215 (mppt) REVERT: A 167 GLU cc_start: 0.8890 (mp0) cc_final: 0.8502 (pm20) REVERT: A 169 ILE cc_start: 0.9261 (mt) cc_final: 0.8997 (tt) REVERT: B 71 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.8292 (t0) REVERT: B 79 GLU cc_start: 0.9198 (tp30) cc_final: 0.8992 (tp30) REVERT: B 81 TRP cc_start: 0.6697 (m100) cc_final: 0.6464 (t60) REVERT: B 82 LYS cc_start: 0.9056 (tptt) cc_final: 0.8741 (tmmt) REVERT: B 96 ARG cc_start: 0.7488 (mtp180) cc_final: 0.7172 (mtt180) REVERT: B 142 TYR cc_start: 0.8945 (m-80) cc_final: 0.8263 (m-10) REVERT: B 165 GLU cc_start: 0.8989 (mp0) cc_final: 0.8215 (mp0) REVERT: B 167 GLU cc_start: 0.8940 (mp0) cc_final: 0.8552 (pm20) REVERT: C 26 MET cc_start: 0.7955 (mmm) cc_final: 0.7645 (mmp) REVERT: C 40 THR cc_start: 0.9112 (t) cc_final: 0.8548 (p) REVERT: C 71 ASN cc_start: 0.9005 (t0) cc_final: 0.8666 (t0) REVERT: C 81 TRP cc_start: 0.6896 (t-100) cc_final: 0.5994 (t60) REVERT: C 96 ARG cc_start: 0.7384 (mtp180) cc_final: 0.7122 (mtt-85) REVERT: C 142 TYR cc_start: 0.9035 (m-80) cc_final: 0.8467 (m-80) REVERT: C 152 LYS cc_start: 0.9360 (mttt) cc_final: 0.9140 (mppt) REVERT: C 164 GLU cc_start: 0.8356 (pp20) cc_final: 0.8093 (pp20) REVERT: C 167 GLU cc_start: 0.8939 (mp0) cc_final: 0.8486 (pm20) REVERT: D 26 MET cc_start: 0.8034 (mmm) cc_final: 0.7723 (mmp) REVERT: D 68 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.8218 (m-80) REVERT: D 71 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8247 (t0) REVERT: D 81 TRP cc_start: 0.7425 (OUTLIER) cc_final: 0.6374 (t60) REVERT: D 96 ARG cc_start: 0.7415 (mtp180) cc_final: 0.7163 (mmt180) REVERT: D 152 LYS cc_start: 0.9366 (mttt) cc_final: 0.9126 (mppt) REVERT: D 167 GLU cc_start: 0.9041 (mp0) cc_final: 0.8673 (pm20) REVERT: E 26 MET cc_start: 0.7928 (mmm) cc_final: 0.7641 (mmp) REVERT: E 71 ASN cc_start: 0.9075 (t0) cc_final: 0.8665 (t0) REVERT: E 81 TRP cc_start: 0.7287 (t-100) cc_final: 0.6390 (t60) REVERT: E 96 ARG cc_start: 0.7367 (mtp180) cc_final: 0.7089 (mmt180) REVERT: E 167 GLU cc_start: 0.8988 (mp0) cc_final: 0.8579 (pm20) REVERT: F 26 MET cc_start: 0.8018 (mmm) cc_final: 0.7575 (mmp) REVERT: F 40 THR cc_start: 0.9075 (t) cc_final: 0.8467 (p) REVERT: F 71 ASN cc_start: 0.8916 (t0) cc_final: 0.8441 (t0) REVERT: F 74 ILE cc_start: 0.8430 (pt) cc_final: 0.8219 (tp) REVERT: F 81 TRP cc_start: 0.6966 (t-100) cc_final: 0.6088 (t60) REVERT: F 96 ARG cc_start: 0.7268 (mtp180) cc_final: 0.7058 (mmt180) REVERT: F 105 ARG cc_start: 0.9058 (mpt180) cc_final: 0.8845 (mmt-90) REVERT: F 136 GLU cc_start: 0.8829 (pm20) cc_final: 0.8627 (pm20) REVERT: F 142 TYR cc_start: 0.8881 (m-80) cc_final: 0.8089 (m-80) REVERT: F 148 LYS cc_start: 0.9345 (mmpt) cc_final: 0.8969 (mmpt) REVERT: F 152 LYS cc_start: 0.9378 (mttt) cc_final: 0.9034 (mppt) REVERT: F 167 GLU cc_start: 0.8850 (mp0) cc_final: 0.8430 (pm20) REVERT: G 26 MET cc_start: 0.8034 (mmm) cc_final: 0.7709 (mmp) REVERT: G 71 ASN cc_start: 0.8909 (t0) cc_final: 0.8349 (t0) REVERT: G 73 ASN cc_start: 0.8736 (m-40) cc_final: 0.8421 (m-40) REVERT: G 81 TRP cc_start: 0.6754 (m100) cc_final: 0.6496 (t60) REVERT: G 96 ARG cc_start: 0.7571 (mtp180) cc_final: 0.7345 (mmt180) REVERT: G 105 ARG cc_start: 0.8959 (mmt90) cc_final: 0.8628 (mmt-90) REVERT: G 119 MET cc_start: 0.9016 (mmm) cc_final: 0.8808 (mmp) REVERT: G 136 GLU cc_start: 0.8808 (pm20) cc_final: 0.8557 (pm20) REVERT: G 142 TYR cc_start: 0.8813 (m-10) cc_final: 0.8513 (m-10) REVERT: G 148 LYS cc_start: 0.9340 (mmpt) cc_final: 0.8892 (mmpt) REVERT: G 152 LYS cc_start: 0.9388 (mttt) cc_final: 0.9015 (mtmm) REVERT: G 167 GLU cc_start: 0.9030 (mp0) cc_final: 0.8606 (pm20) outliers start: 17 outliers final: 8 residues processed: 381 average time/residue: 2.1078 time to fit residues: 846.7238 Evaluate side-chains 381 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 369 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 26 MET 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 D residue 68 TYR 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 2 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 115 optimal weight: 0.0370 chunk 72 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN B 104 GLN D 104 GLN E 104 GLN G 71 ASN G 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.114159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.077364 restraints weight = 19387.099| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.35 r_work: 0.2788 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10801 Z= 0.127 Angle : 0.606 5.531 14686 Z= 0.307 Chirality : 0.039 0.133 1708 Planarity : 0.004 0.039 1806 Dihedral : 4.040 18.763 1589 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.84 % Allowed : 20.18 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1309 helix: 1.86 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.58 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 81 HIS 0.001 0.000 HIS C 166 PHE 0.005 0.001 PHE B 137 TYR 0.010 0.001 TYR B 34 ARG 0.008 0.001 ARG B 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 7) link_NAG-ASN : angle 1.32275 ( 21) hydrogen bonds : bond 0.03738 ( 645) hydrogen bonds : angle 3.03761 ( 1935) SS BOND : bond 0.00224 ( 14) SS BOND : angle 0.39584 ( 28) covalent geometry : bond 0.00307 (10780) covalent geometry : angle 0.60498 (14637) *********************** 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 400 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 380 time to evaluate : 2.062 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: A 26 MET cc_start: 0.8029 (mmm) cc_final: 0.7736 (mmp) REVERT: A 71 ASN cc_start: 0.8941 (t0) cc_final: 0.8650 (t0) REVERT: A 81 TRP cc_start: 0.7200 (t-100) cc_final: 0.6400 (t60) REVERT: A 167 GLU cc_start: 0.8905 (mp0) cc_final: 0.8557 (pm20) REVERT: A 169 ILE cc_start: 0.9228 (mt) cc_final: 0.8934 (tt) REVERT: B 26 MET cc_start: 0.7883 (mmm) cc_final: 0.7435 (mmp) REVERT: B 71 ASN cc_start: 0.8779 (t0) cc_final: 0.8382 (t0) REVERT: B 96 ARG cc_start: 0.7449 (mtp180) cc_final: 0.7125 (mtt180) REVERT: B 142 TYR cc_start: 0.8851 (m-80) cc_final: 0.8382 (m-10) REVERT: B 143 GLN cc_start: 0.8434 (mm110) cc_final: 0.8221 (mm110) REVERT: B 167 GLU cc_start: 0.8903 (mp0) cc_final: 0.8529 (pm20) REVERT: C 26 MET cc_start: 0.8056 (mmm) cc_final: 0.7742 (mmp) REVERT: C 40 THR cc_start: 0.9183 (t) cc_final: 0.8683 (p) REVERT: C 71 ASN cc_start: 0.9003 (t0) cc_final: 0.8783 (t0) REVERT: C 81 TRP cc_start: 0.6923 (t-100) cc_final: 0.5989 (t60) REVERT: C 96 ARG cc_start: 0.7435 (mtp180) cc_final: 0.7201 (mmt180) REVERT: C 142 TYR cc_start: 0.8963 (m-80) cc_final: 0.8466 (m-10) REVERT: C 167 GLU cc_start: 0.8943 (mp0) cc_final: 0.8546 (pm20) REVERT: C 179 ARG cc_start: 0.8750 (ttm110) cc_final: 0.8498 (ttp-110) REVERT: D 26 MET cc_start: 0.8066 (mmm) cc_final: 0.7781 (mmp) REVERT: D 68 TYR cc_start: 0.8680 (m-80) cc_final: 0.8305 (m-80) REVERT: D 71 ASN cc_start: 0.8917 (t0) cc_final: 0.8570 (t0) REVERT: D 81 TRP cc_start: 0.7365 (t-100) cc_final: 0.6445 (t60) REVERT: D 96 ARG cc_start: 0.7385 (mtp180) cc_final: 0.7150 (mmt180) REVERT: D 104 GLN cc_start: 0.8614 (mt0) cc_final: 0.8359 (mt0) REVERT: D 143 GLN cc_start: 0.8527 (mm110) cc_final: 0.8280 (mm110) REVERT: D 152 LYS cc_start: 0.9346 (mttt) cc_final: 0.9135 (mppt) REVERT: D 167 GLU cc_start: 0.9026 (mp0) cc_final: 0.8681 (pm20) REVERT: E 26 MET cc_start: 0.8053 (mmm) cc_final: 0.7761 (mmp) REVERT: E 68 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8311 (m-80) REVERT: E 71 ASN cc_start: 0.9056 (t0) cc_final: 0.8723 (t0) REVERT: E 81 TRP cc_start: 0.7333 (t-100) cc_final: 0.6570 (t60) REVERT: E 96 ARG cc_start: 0.7402 (mtp180) cc_final: 0.7127 (mmt180) REVERT: E 122 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8222 (mttp) REVERT: E 143 GLN cc_start: 0.8512 (mm110) cc_final: 0.8275 (mm110) REVERT: E 148 LYS cc_start: 0.9309 (mmpt) cc_final: 0.8955 (mmpt) REVERT: E 149 GLU cc_start: 0.9270 (pm20) cc_final: 0.9029 (pm20) REVERT: E 152 LYS cc_start: 0.9345 (mttt) cc_final: 0.8987 (mtmm) REVERT: E 167 GLU cc_start: 0.9003 (mp0) cc_final: 0.8692 (pm20) REVERT: F 71 ASN cc_start: 0.8912 (t0) cc_final: 0.8643 (t0) REVERT: F 81 TRP cc_start: 0.7065 (t-100) cc_final: 0.6241 (t60) REVERT: F 96 ARG cc_start: 0.7271 (mtp180) cc_final: 0.7057 (mmt180) REVERT: F 105 ARG cc_start: 0.9062 (mpt180) cc_final: 0.8849 (mmt-90) REVERT: F 136 GLU cc_start: 0.8852 (pm20) cc_final: 0.8630 (pm20) REVERT: F 142 TYR cc_start: 0.8846 (m-80) cc_final: 0.8106 (m-80) REVERT: F 152 LYS cc_start: 0.9363 (mttt) cc_final: 0.9135 (mtmm) REVERT: F 167 GLU cc_start: 0.8854 (mp0) cc_final: 0.8498 (pm20) REVERT: G 26 MET cc_start: 0.8139 (mmm) cc_final: 0.7833 (mmp) REVERT: G 68 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.8178 (t80) REVERT: G 71 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8234 (t0) REVERT: G 79 GLU cc_start: 0.9235 (tp30) cc_final: 0.8649 (tm-30) REVERT: G 96 ARG cc_start: 0.7469 (mtp180) cc_final: 0.7257 (mmt180) REVERT: G 105 ARG cc_start: 0.8956 (mmt90) cc_final: 0.8695 (mmt-90) REVERT: G 136 GLU cc_start: 0.8859 (pm20) cc_final: 0.8626 (pm20) REVERT: G 142 TYR cc_start: 0.8773 (m-10) cc_final: 0.8538 (m-10) REVERT: G 143 GLN cc_start: 0.8531 (mm110) cc_final: 0.8323 (mm110) REVERT: G 149 GLU cc_start: 0.9400 (mp0) cc_final: 0.9199 (pm20) REVERT: G 152 LYS cc_start: 0.9338 (mttt) cc_final: 0.9039 (mtmm) REVERT: G 167 GLU cc_start: 0.8991 (mp0) cc_final: 0.8683 (pm20) outliers start: 20 outliers final: 6 residues processed: 386 average time/residue: 1.6746 time to fit residues: 684.5637 Evaluate side-chains 377 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 367 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 D residue 161 ASP Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 71 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 25 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3576 r_free = 0.3576 target = 0.112994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.076319 restraints weight = 19297.616| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.32 r_work: 0.2768 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3688 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= 0.135 Angle : 0.626 5.500 14686 Z= 0.315 Chirality : 0.040 0.130 1708 Planarity : 0.004 0.041 1806 Dihedral : 3.951 18.055 1589 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.49 % Allowed : 21.94 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1309 helix: 1.95 (0.18), residues: 924 sheet: None (None), residues: 0 loop : -1.42 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 81 HIS 0.000 0.000 HIS F 166 PHE 0.005 0.001 PHE G 189 TYR 0.017 0.001 TYR D 49 ARG 0.012 0.001 ARG B 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00111 ( 7) link_NAG-ASN : angle 1.86137 ( 21) hydrogen bonds : bond 0.03933 ( 645) hydrogen bonds : angle 3.01055 ( 1935) SS BOND : bond 0.00247 ( 14) SS BOND : angle 0.44352 ( 28) covalent geometry : bond 0.00339 (10780) covalent geometry : angle 0.62300 (14637) *********************** 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 411 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 384 time to evaluate : 1.242 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: A 26 MET cc_start: 0.7981 (mmm) cc_final: 0.7695 (mmp) REVERT: A 32 GLN cc_start: 0.9094 (tp40) cc_final: 0.8535 (tm-30) REVERT: A 71 ASN cc_start: 0.8973 (t0) cc_final: 0.8629 (t0) REVERT: A 81 TRP cc_start: 0.7198 (t-100) cc_final: 0.6348 (t60) REVERT: A 142 TYR cc_start: 0.8887 (m-80) cc_final: 0.8580 (m-10) REVERT: A 152 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8946 (mtmm) REVERT: A 167 GLU cc_start: 0.8913 (mp0) cc_final: 0.8628 (pm20) REVERT: A 169 ILE cc_start: 0.9239 (mt) cc_final: 0.8941 (tt) REVERT: B 26 MET cc_start: 0.8037 (mmm) cc_final: 0.7633 (mmp) REVERT: B 96 ARG cc_start: 0.7444 (mtp180) cc_final: 0.7117 (mtt180) REVERT: B 142 TYR cc_start: 0.8970 (m-80) cc_final: 0.8510 (m-10) REVERT: B 143 GLN cc_start: 0.8638 (mm110) cc_final: 0.8343 (mm110) REVERT: B 148 LYS cc_start: 0.9263 (mmpt) cc_final: 0.9057 (mmpt) REVERT: B 152 LYS cc_start: 0.9313 (mttt) cc_final: 0.9080 (mtmm) REVERT: B 167 GLU cc_start: 0.8932 (mp0) cc_final: 0.8602 (pm20) REVERT: C 26 MET cc_start: 0.8095 (mmm) cc_final: 0.7739 (mmp) REVERT: C 40 THR cc_start: 0.9177 (t) cc_final: 0.8663 (p) REVERT: C 71 ASN cc_start: 0.8981 (t0) cc_final: 0.8740 (t0) REVERT: C 81 TRP cc_start: 0.6997 (t-100) cc_final: 0.6054 (t60) REVERT: C 82 LYS cc_start: 0.8894 (tmmt) cc_final: 0.8586 (ptmm) REVERT: C 96 ARG cc_start: 0.7438 (mtp180) cc_final: 0.7197 (mmt180) REVERT: C 122 LYS cc_start: 0.8804 (mttp) cc_final: 0.8468 (mttp) REVERT: C 142 TYR cc_start: 0.8890 (m-80) cc_final: 0.8463 (m-10) REVERT: C 152 LYS cc_start: 0.9308 (mttt) cc_final: 0.9094 (mppt) REVERT: C 167 GLU cc_start: 0.8916 (mp0) cc_final: 0.8598 (pm20) REVERT: D 26 MET cc_start: 0.8070 (mmm) cc_final: 0.7777 (mmp) REVERT: D 71 ASN cc_start: 0.8906 (t0) cc_final: 0.8506 (t0) REVERT: D 77 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8133 (mm) REVERT: D 81 TRP cc_start: 0.7401 (t-100) cc_final: 0.6594 (t60) REVERT: D 96 ARG cc_start: 0.7388 (mtp180) cc_final: 0.7150 (mmt180) REVERT: D 104 GLN cc_start: 0.8633 (mt0) cc_final: 0.8364 (mt0) REVERT: D 143 GLN cc_start: 0.8704 (mm110) cc_final: 0.8420 (mm110) REVERT: D 152 LYS cc_start: 0.9334 (mttt) cc_final: 0.9115 (mppt) REVERT: D 167 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8711 (pm20) REVERT: E 26 MET cc_start: 0.8099 (mmm) cc_final: 0.7849 (mmp) REVERT: E 71 ASN cc_start: 0.9073 (t0) cc_final: 0.8692 (t0) REVERT: E 81 TRP cc_start: 0.7317 (t-100) cc_final: 0.6555 (t60) REVERT: E 96 ARG cc_start: 0.7368 (mtp180) cc_final: 0.7094 (mmt180) REVERT: E 143 GLN cc_start: 0.8628 (mm110) cc_final: 0.8354 (mm110) REVERT: E 148 LYS cc_start: 0.9275 (mmpt) cc_final: 0.8978 (mmpt) REVERT: E 149 GLU cc_start: 0.9275 (pm20) cc_final: 0.9038 (pm20) REVERT: E 152 LYS cc_start: 0.9349 (mttt) cc_final: 0.9021 (mtmm) REVERT: E 167 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8743 (pm20) REVERT: F 40 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8383 (p) REVERT: F 71 ASN cc_start: 0.8902 (t0) cc_final: 0.8624 (t0) REVERT: F 73 ASN cc_start: 0.8876 (m-40) cc_final: 0.8501 (m-40) REVERT: F 81 TRP cc_start: 0.7064 (t-100) cc_final: 0.6269 (t60) REVERT: F 96 ARG cc_start: 0.7245 (mtp180) cc_final: 0.7036 (mmt180) REVERT: F 105 ARG cc_start: 0.9061 (mpt180) cc_final: 0.8846 (mmt-90) REVERT: F 122 LYS cc_start: 0.8817 (mttm) cc_final: 0.8603 (mttp) REVERT: F 136 GLU cc_start: 0.8936 (pm20) cc_final: 0.8703 (pm20) REVERT: F 142 TYR cc_start: 0.8864 (m-80) cc_final: 0.8106 (m-80) REVERT: F 152 LYS cc_start: 0.9344 (mttt) cc_final: 0.9110 (mtmm) REVERT: F 167 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8542 (pm20) REVERT: F 179 ARG cc_start: 0.8765 (ttm110) cc_final: 0.8390 (ttp-110) REVERT: G 26 MET cc_start: 0.8162 (mmm) cc_final: 0.7895 (mmp) REVERT: G 68 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.8182 (t80) REVERT: G 71 ASN cc_start: 0.8905 (t0) cc_final: 0.8309 (t0) REVERT: G 73 ASN cc_start: 0.8818 (m-40) cc_final: 0.8379 (m-40) REVERT: G 105 ARG cc_start: 0.8978 (mmt90) cc_final: 0.8709 (mmt-90) REVERT: G 122 LYS cc_start: 0.8748 (mttm) cc_final: 0.8350 (mttm) REVERT: G 136 GLU cc_start: 0.8934 (pm20) cc_final: 0.8714 (pm20) REVERT: G 143 GLN cc_start: 0.8694 (mm110) cc_final: 0.8480 (mm110) REVERT: G 148 LYS cc_start: 0.9330 (mmpt) cc_final: 0.9115 (mmpt) REVERT: G 149 GLU cc_start: 0.9352 (mp0) cc_final: 0.9145 (pm20) REVERT: G 152 LYS cc_start: 0.9337 (mttt) cc_final: 0.9046 (mtmm) REVERT: G 167 GLU cc_start: 0.8988 (mp0) cc_final: 0.8703 (pm20) outliers start: 27 outliers final: 10 residues processed: 398 average time/residue: 1.4841 time to fit residues: 624.9851 Evaluate side-chains 389 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 372 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 70 MET Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 LYS Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 167 GLU 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 124 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 127 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN E 104 GLN ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.111141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.074477 restraints weight = 19358.954| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.33 r_work: 0.2736 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10801 Z= 0.150 Angle : 0.655 5.684 14686 Z= 0.331 Chirality : 0.040 0.121 1708 Planarity : 0.005 0.043 1806 Dihedral : 3.871 16.733 1589 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.59 % Allowed : 22.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.24), residues: 1309 helix: 2.02 (0.18), residues: 924 sheet: None (None), residues: 0 loop : -1.40 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 81 HIS 0.001 0.000 HIS C 166 PHE 0.005 0.001 PHE G 189 TYR 0.020 0.001 TYR D 49 ARG 0.011 0.001 ARG G 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00100 ( 7) link_NAG-ASN : angle 2.24671 ( 21) hydrogen bonds : bond 0.04294 ( 645) hydrogen bonds : angle 3.05567 ( 1935) SS BOND : bond 0.00276 ( 14) SS BOND : angle 0.54554 ( 28) covalent geometry : bond 0.00382 (10780) covalent geometry : angle 0.65035 (14637) *********************** 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: 39 poor density : 374 time to evaluate : 1.103 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: 0.8057 (mmm) cc_final: 0.7767 (mmp) REVERT: A 32 GLN cc_start: 0.9107 (tp40) cc_final: 0.8538 (tm-30) REVERT: A 40 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8764 (p) REVERT: A 71 ASN cc_start: 0.8967 (t0) cc_final: 0.8570 (t0) REVERT: A 81 TRP cc_start: 0.7223 (t-100) cc_final: 0.6359 (t60) REVERT: A 167 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8678 (pm20) REVERT: B 26 MET cc_start: 0.8105 (mmm) cc_final: 0.7704 (mmp) REVERT: B 68 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.8122 (t80) REVERT: B 71 ASN cc_start: 0.8792 (t0) cc_final: 0.8483 (t0) REVERT: B 96 ARG cc_start: 0.7442 (mtp180) cc_final: 0.7116 (mmt180) REVERT: B 142 TYR cc_start: 0.9074 (m-80) cc_final: 0.8607 (m-10) REVERT: B 143 GLN cc_start: 0.8805 (mm110) cc_final: 0.8490 (mm110) REVERT: B 152 LYS cc_start: 0.9325 (mttt) cc_final: 0.9067 (mppt) REVERT: B 167 GLU cc_start: 0.8953 (mp0) cc_final: 0.8678 (pm20) REVERT: C 26 MET cc_start: 0.8180 (mmm) cc_final: 0.7853 (mmp) REVERT: C 40 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8526 (p) REVERT: C 71 ASN cc_start: 0.8972 (t0) cc_final: 0.8701 (t0) REVERT: C 81 TRP cc_start: 0.7019 (t-100) cc_final: 0.6117 (t60) REVERT: C 82 LYS cc_start: 0.8944 (tmmt) cc_final: 0.8572 (ptmm) REVERT: C 142 TYR cc_start: 0.8907 (m-80) cc_final: 0.8473 (m-10) REVERT: C 148 LYS cc_start: 0.9301 (mmpt) cc_final: 0.9091 (mmpt) REVERT: C 152 LYS cc_start: 0.9289 (mttt) cc_final: 0.9060 (mppt) REVERT: C 167 GLU cc_start: 0.8935 (mp0) cc_final: 0.8658 (pm20) REVERT: D 26 MET cc_start: 0.8152 (mmm) cc_final: 0.7863 (mmp) REVERT: D 40 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8547 (p) REVERT: D 71 ASN cc_start: 0.8889 (t0) cc_final: 0.8515 (t0) REVERT: D 77 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8095 (mm) REVERT: D 81 TRP cc_start: 0.7495 (t-100) cc_final: 0.6756 (t60) REVERT: D 96 ARG cc_start: 0.7397 (mtp180) cc_final: 0.7170 (mmt180) REVERT: D 143 GLN cc_start: 0.8884 (mm110) cc_final: 0.8567 (mm110) REVERT: D 152 LYS cc_start: 0.9323 (mttt) cc_final: 0.9114 (mppt) REVERT: D 167 GLU cc_start: 0.9042 (mp0) cc_final: 0.8721 (pm20) REVERT: E 26 MET cc_start: 0.8201 (mmm) cc_final: 0.7865 (mmp) REVERT: E 40 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8682 (p) REVERT: E 71 ASN cc_start: 0.9059 (t0) cc_final: 0.8672 (t0) REVERT: E 81 TRP cc_start: 0.7347 (t-100) cc_final: 0.6595 (t60) REVERT: E 96 ARG cc_start: 0.7334 (mtp180) cc_final: 0.7076 (mtt180) REVERT: E 122 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8328 (mtmp) REVERT: E 143 GLN cc_start: 0.8786 (mm110) cc_final: 0.8416 (mm110) REVERT: E 167 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8798 (pm20) REVERT: F 71 ASN cc_start: 0.8866 (t0) cc_final: 0.8663 (t0) REVERT: F 73 ASN cc_start: 0.8856 (m-40) cc_final: 0.8561 (m-40) REVERT: F 81 TRP cc_start: 0.7036 (t-100) cc_final: 0.6249 (t60) REVERT: F 105 ARG cc_start: 0.9073 (mpt180) cc_final: 0.8860 (mmt-90) REVERT: F 122 LYS cc_start: 0.8933 (mttm) cc_final: 0.8725 (mttp) REVERT: F 136 GLU cc_start: 0.8949 (pm20) cc_final: 0.8725 (pm20) REVERT: F 142 TYR cc_start: 0.8908 (m-80) cc_final: 0.8080 (m-80) REVERT: F 148 LYS cc_start: 0.9339 (mmpt) cc_final: 0.8879 (mmpt) REVERT: F 152 LYS cc_start: 0.9345 (mttt) cc_final: 0.9018 (mppt) REVERT: F 167 GLU cc_start: 0.8904 (mp0) cc_final: 0.8580 (pm20) REVERT: F 179 ARG cc_start: 0.8836 (ttm110) cc_final: 0.8563 (ttp-110) REVERT: G 26 MET cc_start: 0.8246 (mmm) cc_final: 0.8005 (mmp) REVERT: G 71 ASN cc_start: 0.8841 (t0) cc_final: 0.8215 (t0) REVERT: G 73 ASN cc_start: 0.8790 (m110) cc_final: 0.8016 (m-40) REVERT: G 105 ARG cc_start: 0.9002 (mmt90) cc_final: 0.8728 (mmt-90) REVERT: G 143 GLN cc_start: 0.8863 (mm110) cc_final: 0.8625 (mm110) REVERT: G 148 LYS cc_start: 0.9284 (mmpt) cc_final: 0.8913 (mmpt) REVERT: G 149 GLU cc_start: 0.9315 (mp0) cc_final: 0.9086 (pm20) REVERT: G 152 LYS cc_start: 0.9343 (mttt) cc_final: 0.8988 (mtmm) REVERT: G 165 GLU cc_start: 0.8830 (mp0) cc_final: 0.8568 (mp0) REVERT: G 167 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8745 (pm20) outliers start: 39 outliers final: 17 residues processed: 387 average time/residue: 1.4814 time to fit residues: 607.0064 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 : 1.115 ------------------------------------------------------------------------------- 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 68 TYR Chi-restraints excluded: chain A residue 70 MET 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 B residue 199 LEU Chi-restraints excluded: chain C residue 40 THR 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 D residue 199 LEU Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 122 LYS 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 124 PHE Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 167 GLU 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 124 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 38 optimal weight: 50.0000 chunk 46 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3556 r_free = 0.3556 target = 0.111733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.075048 restraints weight = 19363.461| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.36 r_work: 0.2752 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10801 Z= 0.144 Angle : 0.675 6.303 14686 Z= 0.341 Chirality : 0.040 0.120 1708 Planarity : 0.005 0.043 1806 Dihedral : 3.806 17.017 1589 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.04 % Allowed : 22.30 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.25), residues: 1309 helix: 2.16 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.48 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP G 81 HIS 0.000 0.000 HIS E 166 PHE 0.005 0.001 PHE G 189 TYR 0.015 0.001 TYR A 142 ARG 0.007 0.000 ARG E 179 Details of bonding type rmsd link_NAG-ASN : bond 0.00138 ( 7) link_NAG-ASN : angle 2.20980 ( 21) hydrogen bonds : bond 0.04048 ( 645) hydrogen bonds : angle 2.97107 ( 1935) SS BOND : bond 0.00275 ( 14) SS BOND : angle 0.45614 ( 28) covalent geometry : bond 0.00364 (10780) covalent geometry : angle 0.67070 (14637) *********************** 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 404 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 371 time to evaluate : 1.086 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: 0.8130 (mmm) cc_final: 0.7812 (mmp) REVERT: A 40 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8751 (p) REVERT: A 71 ASN cc_start: 0.8960 (t0) cc_final: 0.8570 (t0) REVERT: A 81 TRP cc_start: 0.7142 (t-100) cc_final: 0.6262 (t60) REVERT: A 96 ARG cc_start: 0.7639 (ptp-170) cc_final: 0.7364 (pmm-80) REVERT: A 167 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8669 (pm20) REVERT: A 169 ILE cc_start: 0.9235 (mt) cc_final: 0.8946 (tt) REVERT: B 26 MET cc_start: 0.8146 (mmm) cc_final: 0.7823 (mmp) REVERT: B 68 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.8123 (t80) REVERT: B 142 TYR cc_start: 0.9074 (m-80) cc_final: 0.8586 (m-10) REVERT: B 143 GLN cc_start: 0.8901 (mm110) cc_final: 0.8585 (mm110) REVERT: B 148 LYS cc_start: 0.9275 (mmpt) cc_final: 0.8881 (mmpt) REVERT: B 152 LYS cc_start: 0.9318 (mttt) cc_final: 0.8994 (mtmm) REVERT: B 167 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8613 (pm20) REVERT: C 26 MET cc_start: 0.8128 (mmm) cc_final: 0.7827 (mmp) REVERT: C 40 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8559 (p) REVERT: C 71 ASN cc_start: 0.8861 (t0) cc_final: 0.8579 (t0) REVERT: C 81 TRP cc_start: 0.7144 (t-100) cc_final: 0.6279 (t60) REVERT: C 82 LYS cc_start: 0.8949 (tmmt) cc_final: 0.8584 (ptmm) REVERT: C 96 ARG cc_start: 0.7386 (mtp180) cc_final: 0.7122 (mtm110) REVERT: C 152 LYS cc_start: 0.9275 (mttt) cc_final: 0.9051 (mppt) REVERT: C 167 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8667 (pm20) REVERT: C 199 LEU cc_start: 0.8971 (tp) cc_final: 0.8766 (tt) REVERT: D 26 MET cc_start: 0.8188 (mmm) cc_final: 0.7900 (mmp) REVERT: D 40 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8631 (p) REVERT: D 68 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.8124 (m-80) REVERT: D 71 ASN cc_start: 0.8878 (t0) cc_final: 0.8488 (t0) REVERT: D 77 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8090 (mm) REVERT: D 81 TRP cc_start: 0.7447 (t-100) cc_final: 0.6753 (t60) REVERT: D 82 LYS cc_start: 0.8848 (pptt) cc_final: 0.8636 (pptt) REVERT: D 96 ARG cc_start: 0.7343 (mtp180) cc_final: 0.7056 (mtm110) REVERT: D 143 GLN cc_start: 0.8988 (mm110) cc_final: 0.8580 (mm110) REVERT: D 167 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8735 (pm20) REVERT: E 26 MET cc_start: 0.8253 (mmm) cc_final: 0.7927 (mmp) REVERT: E 40 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8658 (p) REVERT: E 68 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.8382 (m-80) REVERT: E 71 ASN cc_start: 0.9047 (t0) cc_final: 0.8607 (t0) REVERT: E 81 TRP cc_start: 0.7264 (t-100) cc_final: 0.6594 (t60) REVERT: E 122 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8362 (mtmp) REVERT: E 143 GLN cc_start: 0.8849 (mm110) cc_final: 0.8493 (mm110) REVERT: E 148 LYS cc_start: 0.9252 (mmpt) cc_final: 0.8804 (mmpt) REVERT: E 149 GLU cc_start: 0.9266 (pm20) cc_final: 0.8992 (pm20) REVERT: E 152 LYS cc_start: 0.9365 (mttt) cc_final: 0.9038 (mtmm) REVERT: E 167 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8736 (pm20) REVERT: F 71 ASN cc_start: 0.8880 (t0) cc_final: 0.8644 (t0) REVERT: F 73 ASN cc_start: 0.8781 (m-40) cc_final: 0.8468 (m-40) REVERT: F 81 TRP cc_start: 0.7055 (t-100) cc_final: 0.6290 (t60) REVERT: F 82 LYS cc_start: 0.8828 (ptmm) cc_final: 0.8567 (ptmm) REVERT: F 105 ARG cc_start: 0.9083 (mpt180) cc_final: 0.8874 (mmt-90) REVERT: F 142 TYR cc_start: 0.8880 (m-80) cc_final: 0.8379 (m-80) REVERT: F 152 LYS cc_start: 0.9339 (mttt) cc_final: 0.9083 (mppt) REVERT: F 167 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8585 (pm20) REVERT: G 26 MET cc_start: 0.8240 (mmm) cc_final: 0.8029 (mmp) REVERT: G 71 ASN cc_start: 0.8838 (t0) cc_final: 0.8277 (t0) REVERT: G 73 ASN cc_start: 0.8676 (m110) cc_final: 0.8291 (m-40) REVERT: G 105 ARG cc_start: 0.9006 (mmt90) cc_final: 0.8731 (mmt-90) REVERT: G 122 LYS cc_start: 0.8850 (mttm) cc_final: 0.8468 (mttm) REVERT: G 143 GLN cc_start: 0.8937 (mm110) cc_final: 0.8630 (mm110) REVERT: G 167 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8778 (pm20) outliers start: 33 outliers final: 10 residues processed: 383 average time/residue: 1.4575 time to fit residues: 590.8162 Evaluate side-chains 390 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 364 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 167 GLU 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 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 E residue 167 GLU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 167 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 34 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 122 optimal weight: 0.4980 chunk 112 optimal weight: 0.6980 chunk 128 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3550 r_free = 0.3550 target = 0.111112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.074385 restraints weight = 19852.103| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.41 r_work: 0.2765 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10801 Z= 0.154 Angle : 0.723 6.822 14686 Z= 0.365 Chirality : 0.040 0.119 1708 Planarity : 0.005 0.044 1806 Dihedral : 3.741 17.479 1589 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.04 % Allowed : 24.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (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 TRP 0.029 0.001 TRP B 81 HIS 0.001 0.000 HIS B 166 PHE 0.005 0.001 PHE G 189 TYR 0.017 0.001 TYR C 142 ARG 0.010 0.001 ARG F 179 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 7) link_NAG-ASN : angle 2.23132 ( 21) hydrogen bonds : bond 0.04111 ( 645) hydrogen bonds : angle 2.96426 ( 1935) SS BOND : bond 0.00290 ( 14) SS BOND : angle 0.46674 ( 28) covalent geometry : bond 0.00394 (10780) covalent geometry : angle 0.71914 (14637) *********************** 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 398 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 365 time to evaluate : 1.082 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: 0.8194 (mmm) cc_final: 0.7855 (mmp) REVERT: A 40 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8764 (p) REVERT: A 71 ASN cc_start: 0.8957 (t0) cc_final: 0.8584 (t0) REVERT: A 81 TRP cc_start: 0.7218 (t-100) cc_final: 0.6330 (t60) REVERT: A 96 ARG cc_start: 0.7607 (ptp-170) cc_final: 0.7214 (pmm-80) REVERT: A 152 LYS cc_start: 0.9189 (mtmm) cc_final: 0.8587 (mtmm) REVERT: A 164 GLU cc_start: 0.8459 (pm20) cc_final: 0.8259 (pm20) REVERT: A 167 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8717 (pm20) REVERT: A 169 ILE cc_start: 0.9273 (mt) cc_final: 0.9002 (tt) REVERT: B 26 MET cc_start: 0.8167 (mmm) cc_final: 0.7855 (mmp) REVERT: B 68 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8190 (t80) REVERT: B 142 TYR cc_start: 0.9094 (m-80) cc_final: 0.8621 (m-10) REVERT: B 143 GLN cc_start: 0.8941 (mm110) cc_final: 0.8624 (mm110) REVERT: B 148 LYS cc_start: 0.9279 (mmpt) cc_final: 0.9058 (mmpt) REVERT: B 152 LYS cc_start: 0.9352 (mttt) cc_final: 0.9033 (mtmm) REVERT: B 164 GLU cc_start: 0.8578 (pm20) cc_final: 0.8363 (pm20) REVERT: B 167 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8605 (pm20) REVERT: C 26 MET cc_start: 0.8178 (mmm) cc_final: 0.7880 (mmp) REVERT: C 40 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8576 (p) REVERT: C 71 ASN cc_start: 0.8889 (t0) cc_final: 0.8601 (t0) REVERT: C 81 TRP cc_start: 0.7139 (t-100) cc_final: 0.6322 (t60) REVERT: C 82 LYS cc_start: 0.8975 (tmmt) cc_final: 0.8600 (ptmm) REVERT: C 122 LYS cc_start: 0.8996 (mttp) cc_final: 0.8591 (mttp) REVERT: C 152 LYS cc_start: 0.9288 (mttt) cc_final: 0.8995 (mtmm) REVERT: C 167 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8725 (pm20) REVERT: C 199 LEU cc_start: 0.9006 (tp) cc_final: 0.8795 (tt) REVERT: D 26 MET cc_start: 0.8241 (mmm) cc_final: 0.7943 (mmp) REVERT: D 38 GLU cc_start: 0.8722 (tp30) cc_final: 0.8511 (tp30) REVERT: D 40 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8693 (p) REVERT: D 68 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.8069 (m-80) REVERT: D 71 ASN cc_start: 0.8886 (t0) cc_final: 0.8497 (t0) REVERT: D 77 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8097 (mm) REVERT: D 81 TRP cc_start: 0.7393 (t-100) cc_final: 0.6682 (t60) REVERT: D 143 GLN cc_start: 0.9006 (mm110) cc_final: 0.8594 (mm110) REVERT: D 167 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8762 (pm20) REVERT: E 26 MET cc_start: 0.8297 (mmm) cc_final: 0.7947 (mmp) REVERT: E 40 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8701 (p) REVERT: E 68 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.8426 (m-80) REVERT: E 71 ASN cc_start: 0.9061 (t0) cc_final: 0.8626 (t0) REVERT: E 81 TRP cc_start: 0.7284 (t-100) cc_final: 0.6622 (t60) REVERT: E 82 LYS cc_start: 0.8828 (pptt) cc_final: 0.8565 (pptt) REVERT: E 122 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8384 (mtmp) REVERT: E 143 GLN cc_start: 0.8895 (mm110) cc_final: 0.8508 (mm110) REVERT: E 148 LYS cc_start: 0.9222 (mmpt) cc_final: 0.8794 (mmpt) REVERT: E 149 GLU cc_start: 0.9252 (pm20) cc_final: 0.8974 (pm20) REVERT: E 152 LYS cc_start: 0.9375 (mttt) cc_final: 0.9034 (mtmm) REVERT: E 167 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8729 (pm20) REVERT: E 199 LEU cc_start: 0.9132 (tp) cc_final: 0.8880 (tt) REVERT: F 71 ASN cc_start: 0.8880 (t0) cc_final: 0.8625 (t0) REVERT: F 73 ASN cc_start: 0.8769 (m-40) cc_final: 0.8461 (m-40) REVERT: F 81 TRP cc_start: 0.7024 (t-100) cc_final: 0.6293 (t60) REVERT: F 105 ARG cc_start: 0.9096 (mpt180) cc_final: 0.8890 (mmt-90) REVERT: F 142 TYR cc_start: 0.8974 (m-80) cc_final: 0.8465 (m-80) REVERT: F 152 LYS cc_start: 0.9343 (mttt) cc_final: 0.9119 (mtmm) REVERT: F 164 GLU cc_start: 0.8602 (pm20) cc_final: 0.8336 (pm20) REVERT: F 167 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8617 (pm20) REVERT: F 179 ARG cc_start: 0.8865 (ttm110) cc_final: 0.8574 (mtp-110) REVERT: G 26 MET cc_start: 0.8300 (mmm) cc_final: 0.7976 (mmp) REVERT: G 71 ASN cc_start: 0.8828 (t0) cc_final: 0.8250 (t0) REVERT: G 73 ASN cc_start: 0.8590 (m110) cc_final: 0.8246 (m-40) REVERT: G 105 ARG cc_start: 0.9012 (mmt90) cc_final: 0.8730 (mmt-90) REVERT: G 143 GLN cc_start: 0.8987 (mm110) cc_final: 0.8699 (mm110) REVERT: G 167 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8791 (pm20) outliers start: 33 outliers final: 13 residues processed: 376 average time/residue: 1.4544 time to fit residues: 578.7348 Evaluate side-chains 390 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 361 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 124 PHE 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 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 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 E residue 167 GLU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 124 PHE Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 193 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 101 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 57 optimal weight: 50.0000 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 98 optimal weight: 0.0270 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3567 r_free = 0.3567 target = 0.112227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.075860 restraints weight = 19613.296| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 3.40 r_work: 0.2792 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4280 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= 0.147 Angle : 0.750 7.205 14686 Z= 0.378 Chirality : 0.039 0.124 1708 Planarity : 0.005 0.044 1806 Dihedral : 3.656 16.607 1589 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.67 % Allowed : 25.71 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.25), residues: 1309 helix: 2.21 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.39 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP G 81 HIS 0.001 0.000 HIS D 166 PHE 0.006 0.001 PHE D 163 TYR 0.020 0.001 TYR C 142 ARG 0.015 0.001 ARG F 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 7) link_NAG-ASN : angle 2.09779 ( 21) hydrogen bonds : bond 0.03756 ( 645) hydrogen bonds : angle 2.91784 ( 1935) SS BOND : bond 0.00256 ( 14) SS BOND : angle 0.40031 ( 28) covalent geometry : bond 0.00369 (10780) covalent geometry : angle 0.74705 (14637) *********************** 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 398 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 369 time to evaluate : 1.052 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: 0.9124 (OUTLIER) cc_final: 0.8794 (p) REVERT: A 71 ASN cc_start: 0.8928 (t0) cc_final: 0.8556 (t0) REVERT: A 81 TRP cc_start: 0.7304 (t-100) cc_final: 0.6414 (t60) REVERT: A 152 LYS cc_start: 0.9179 (mtmm) cc_final: 0.8762 (mtmm) REVERT: A 167 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8730 (pm20) REVERT: A 169 ILE cc_start: 0.9257 (mt) cc_final: 0.8993 (tt) REVERT: A 199 LEU cc_start: 0.9115 (tp) cc_final: 0.8785 (tt) REVERT: B 26 MET cc_start: 0.8237 (mmm) cc_final: 0.7952 (mmp) REVERT: B 68 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.8092 (t80) REVERT: B 142 TYR cc_start: 0.9091 (m-80) cc_final: 0.8682 (m-10) REVERT: B 143 GLN cc_start: 0.8948 (mm110) cc_final: 0.8623 (mm110) REVERT: B 148 LYS cc_start: 0.9248 (mmpt) cc_final: 0.8906 (mmpt) REVERT: B 152 LYS cc_start: 0.9344 (mttt) cc_final: 0.9012 (mtmm) REVERT: B 167 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8626 (pm20) REVERT: C 26 MET cc_start: 0.8138 (mmm) cc_final: 0.7848 (mmp) REVERT: C 40 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8581 (p) REVERT: C 71 ASN cc_start: 0.8873 (t0) cc_final: 0.8555 (t0) REVERT: C 81 TRP cc_start: 0.7117 (t-100) cc_final: 0.6319 (t60) REVERT: C 82 LYS cc_start: 0.8967 (tmmt) cc_final: 0.8612 (ptmm) REVERT: C 122 LYS cc_start: 0.9004 (mttp) cc_final: 0.8552 (mttp) REVERT: C 152 LYS cc_start: 0.9294 (mttt) cc_final: 0.9000 (mtmm) REVERT: C 167 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8717 (pm20) REVERT: C 199 LEU cc_start: 0.9011 (tp) cc_final: 0.8803 (tt) REVERT: D 26 MET cc_start: 0.8358 (mmm) cc_final: 0.7875 (mmp) REVERT: D 38 GLU cc_start: 0.8738 (tp30) cc_final: 0.8532 (tp30) REVERT: D 40 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8724 (p) REVERT: D 68 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.8138 (m-80) REVERT: D 71 ASN cc_start: 0.8858 (t0) cc_final: 0.8443 (t0) REVERT: D 77 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8161 (mm) REVERT: D 81 TRP cc_start: 0.7365 (t-100) cc_final: 0.6626 (t60) REVERT: D 143 GLN cc_start: 0.9069 (mm110) cc_final: 0.8689 (mm110) REVERT: D 167 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8755 (pm20) REVERT: E 40 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8716 (p) REVERT: E 68 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8309 (m-80) REVERT: E 71 ASN cc_start: 0.9063 (t0) cc_final: 0.8623 (t0) REVERT: E 81 TRP cc_start: 0.7230 (t-100) cc_final: 0.6538 (t60) REVERT: E 122 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8424 (mtmp) REVERT: E 143 GLN cc_start: 0.8907 (mm110) cc_final: 0.8516 (mm110) REVERT: E 148 LYS cc_start: 0.9209 (mmpt) cc_final: 0.8826 (mmpt) REVERT: E 149 GLU cc_start: 0.9243 (pm20) cc_final: 0.8965 (pm20) REVERT: E 152 LYS cc_start: 0.9373 (mttt) cc_final: 0.9029 (mtmm) REVERT: E 199 LEU cc_start: 0.9145 (tp) cc_final: 0.8893 (tt) REVERT: F 71 ASN cc_start: 0.8871 (t0) cc_final: 0.8597 (t0) REVERT: F 73 ASN cc_start: 0.8690 (m-40) cc_final: 0.8102 (m-40) REVERT: F 81 TRP cc_start: 0.7150 (t-100) cc_final: 0.6376 (t60) REVERT: F 105 ARG cc_start: 0.9082 (mpt180) cc_final: 0.8875 (mmt-90) REVERT: F 142 TYR cc_start: 0.9018 (m-80) cc_final: 0.8539 (m-10) REVERT: F 152 LYS cc_start: 0.9343 (mttt) cc_final: 0.9115 (mtmm) REVERT: F 167 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8589 (pm20) REVERT: F 179 ARG cc_start: 0.8846 (ttm110) cc_final: 0.8551 (mtp-110) REVERT: G 26 MET cc_start: 0.8288 (mmm) cc_final: 0.7988 (mmp) REVERT: G 71 ASN cc_start: 0.8811 (t0) cc_final: 0.8309 (t0) REVERT: G 73 ASN cc_start: 0.8642 (m110) cc_final: 0.8330 (m-40) REVERT: G 102 MET cc_start: 0.9166 (ttm) cc_final: 0.8946 (ttp) REVERT: G 105 ARG cc_start: 0.9013 (mmt90) cc_final: 0.8730 (mmt-90) REVERT: G 143 GLN cc_start: 0.9012 (mm110) cc_final: 0.8753 (mm110) outliers start: 29 outliers final: 10 residues processed: 378 average time/residue: 1.4214 time to fit residues: 569.0924 Evaluate side-chains 387 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 363 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 167 GLU 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 193 ILE 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 167 GLU Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 68 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 105 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.111930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.075844 restraints weight = 19787.299| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.39 r_work: 0.2775 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10801 Z= 0.160 Angle : 0.795 7.651 14686 Z= 0.401 Chirality : 0.040 0.117 1708 Planarity : 0.005 0.044 1806 Dihedral : 3.614 17.267 1589 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.40 % Allowed : 26.64 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.24), residues: 1309 helix: 2.21 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.32 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP G 81 HIS 0.001 0.000 HIS G 166 PHE 0.006 0.001 PHE D 163 TYR 0.019 0.001 TYR C 142 ARG 0.009 0.001 ARG F 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 7) link_NAG-ASN : angle 2.08651 ( 21) hydrogen bonds : bond 0.03910 ( 645) hydrogen bonds : angle 2.93523 ( 1935) SS BOND : bond 0.00292 ( 14) SS BOND : angle 0.41415 ( 28) covalent geometry : bond 0.00408 (10780) covalent geometry : angle 0.79177 (14637) *********************** 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 381 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 355 time to evaluate : 1.381 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: 0.9149 (OUTLIER) cc_final: 0.8810 (p) REVERT: A 71 ASN cc_start: 0.8921 (t0) cc_final: 0.8590 (t0) REVERT: A 81 TRP cc_start: 0.7337 (t-100) cc_final: 0.6499 (t60) REVERT: A 96 ARG cc_start: 0.7612 (ptp-170) cc_final: 0.7238 (pmm-80) REVERT: A 149 GLU cc_start: 0.9271 (pm20) cc_final: 0.8949 (pm20) REVERT: A 152 LYS cc_start: 0.9190 (mtmm) cc_final: 0.8529 (mtmm) REVERT: A 167 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8706 (pm20) REVERT: A 169 ILE cc_start: 0.9259 (mt) cc_final: 0.9004 (tt) REVERT: A 199 LEU cc_start: 0.9128 (tp) cc_final: 0.8803 (tt) REVERT: B 26 MET cc_start: 0.8280 (mmm) cc_final: 0.8034 (mmp) REVERT: B 68 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.8062 (t80) REVERT: B 142 TYR cc_start: 0.9061 (m-80) cc_final: 0.8629 (m-10) REVERT: B 143 GLN cc_start: 0.8988 (mm110) cc_final: 0.8629 (mm110) REVERT: B 148 LYS cc_start: 0.9244 (mmpt) cc_final: 0.8919 (mmpt) REVERT: B 152 LYS cc_start: 0.9374 (mttt) cc_final: 0.9052 (mtmm) REVERT: B 167 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8629 (pm20) REVERT: C 26 MET cc_start: 0.8308 (mmm) cc_final: 0.7914 (mmp) REVERT: C 40 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8580 (p) REVERT: C 71 ASN cc_start: 0.8897 (t0) cc_final: 0.8578 (t0) REVERT: C 81 TRP cc_start: 0.7183 (t-100) cc_final: 0.6342 (t60) REVERT: C 82 LYS cc_start: 0.8978 (tmmt) cc_final: 0.8653 (ptmm) REVERT: C 122 LYS cc_start: 0.9020 (mttp) cc_final: 0.8565 (mttp) REVERT: C 152 LYS cc_start: 0.9299 (mttt) cc_final: 0.9057 (mtmm) REVERT: C 167 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8734 (pm20) REVERT: C 199 LEU cc_start: 0.9043 (tp) cc_final: 0.8836 (tt) REVERT: D 26 MET cc_start: 0.8396 (mmm) cc_final: 0.7931 (mmp) REVERT: D 38 GLU cc_start: 0.8771 (tp30) cc_final: 0.8530 (tp30) REVERT: D 40 THR cc_start: 0.9179 (OUTLIER) cc_final: 0.8734 (p) REVERT: D 68 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.8177 (m-80) REVERT: D 71 ASN cc_start: 0.8847 (t0) cc_final: 0.8448 (t0) REVERT: D 77 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8162 (mm) REVERT: D 81 TRP cc_start: 0.7378 (t-100) cc_final: 0.6559 (t60) REVERT: D 143 GLN cc_start: 0.9078 (mm110) cc_final: 0.8721 (mm110) REVERT: D 152 LYS cc_start: 0.9198 (mtmm) cc_final: 0.8870 (mtmm) REVERT: D 167 GLU cc_start: 0.9013 (mp0) cc_final: 0.8748 (pm20) REVERT: E 26 MET cc_start: 0.7934 (mmp) cc_final: 0.7733 (mmp) REVERT: E 40 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8723 (p) REVERT: E 68 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: E 71 ASN cc_start: 0.9056 (t0) cc_final: 0.8619 (t0) REVERT: E 81 TRP cc_start: 0.7230 (t-100) cc_final: 0.6580 (t60) REVERT: E 82 LYS cc_start: 0.8816 (pptt) cc_final: 0.8513 (pptt) REVERT: E 95 LEU cc_start: 0.8271 (mt) cc_final: 0.7925 (pp) REVERT: E 122 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8458 (mtmp) REVERT: E 143 GLN cc_start: 0.8963 (mm110) cc_final: 0.8582 (mm110) REVERT: E 148 LYS cc_start: 0.9228 (mmpt) cc_final: 0.8857 (mmpt) REVERT: E 149 GLU cc_start: 0.9225 (pm20) cc_final: 0.8944 (pm20) REVERT: E 152 LYS cc_start: 0.9385 (mttt) cc_final: 0.9035 (mtmm) REVERT: E 199 LEU cc_start: 0.9154 (tp) cc_final: 0.8912 (tt) REVERT: F 71 ASN cc_start: 0.8867 (t0) cc_final: 0.8582 (t0) REVERT: F 73 ASN cc_start: 0.8652 (m-40) cc_final: 0.8288 (m-40) REVERT: F 81 TRP cc_start: 0.7209 (t-100) cc_final: 0.6398 (t60) REVERT: F 105 ARG cc_start: 0.9092 (mpt180) cc_final: 0.8888 (mmt-90) REVERT: F 122 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8625 (mttp) REVERT: F 142 TYR cc_start: 0.9032 (m-80) cc_final: 0.8592 (m-10) REVERT: F 152 LYS cc_start: 0.9351 (mttt) cc_final: 0.9122 (mtmm) REVERT: F 167 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8609 (pm20) REVERT: F 179 ARG cc_start: 0.8864 (ttm110) cc_final: 0.8581 (mtp-110) REVERT: G 26 MET cc_start: 0.8346 (mmm) cc_final: 0.8074 (mmp) REVERT: G 71 ASN cc_start: 0.8831 (t0) cc_final: 0.8306 (t0) REVERT: G 73 ASN cc_start: 0.8660 (m110) cc_final: 0.8300 (m-40) REVERT: G 102 MET cc_start: 0.9170 (ttm) cc_final: 0.8941 (ttp) REVERT: G 143 GLN cc_start: 0.9029 (mm110) cc_final: 0.8775 (mm110) outliers start: 26 outliers final: 11 residues processed: 365 average time/residue: 1.5127 time to fit residues: 584.8239 Evaluate side-chains 380 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 355 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 167 GLU 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 C residue 193 ILE 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 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 122 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 80 optimal weight: 2.9990 chunk 114 optimal weight: 40.0000 chunk 6 optimal weight: 0.0030 chunk 109 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 26 optimal weight: 0.0870 chunk 124 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 overall best weight: 0.4968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.113206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.077565 restraints weight = 19787.024| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.38 r_work: 0.2809 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4543 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= 0.155 Angle : 0.813 8.114 14686 Z= 0.409 Chirality : 0.039 0.126 1708 Planarity : 0.005 0.044 1806 Dihedral : 3.636 18.867 1589 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.03 % Allowed : 27.10 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.24), residues: 1309 helix: 2.24 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.27 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP G 81 HIS 0.001 0.000 HIS D 166 PHE 0.009 0.001 PHE D 163 TYR 0.023 0.001 TYR A 142 ARG 0.008 0.001 ARG E 179 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 7) link_NAG-ASN : angle 1.99684 ( 21) hydrogen bonds : bond 0.03519 ( 645) hydrogen bonds : angle 2.88383 ( 1935) SS BOND : bond 0.00245 ( 14) SS BOND : angle 0.35571 ( 28) covalent geometry : bond 0.00390 (10780) covalent geometry : angle 0.81026 (14637) ********************** 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 378 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 356 time to evaluate : 1.758 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 40 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8796 (p) REVERT: A 71 ASN cc_start: 0.8897 (t0) cc_final: 0.8583 (t0) REVERT: A 81 TRP cc_start: 0.7313 (t-100) cc_final: 0.6479 (t60) REVERT: A 149 GLU cc_start: 0.9244 (pm20) cc_final: 0.8937 (pm20) REVERT: A 152 LYS cc_start: 0.9171 (mtmm) cc_final: 0.8508 (mtmm) REVERT: A 167 GLU cc_start: 0.8899 (mp0) cc_final: 0.8677 (pm20) REVERT: A 169 ILE cc_start: 0.9229 (mt) cc_final: 0.8971 (tt) REVERT: A 199 LEU cc_start: 0.9092 (tp) cc_final: 0.8780 (tt) REVERT: B 26 MET cc_start: 0.8193 (mmm) cc_final: 0.7915 (mmp) REVERT: B 40 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8621 (p) REVERT: B 68 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.8068 (t80) REVERT: B 142 TYR cc_start: 0.9052 (m-80) cc_final: 0.8693 (m-10) REVERT: B 143 GLN cc_start: 0.9040 (mm110) cc_final: 0.8725 (mm110) REVERT: B 148 LYS cc_start: 0.9257 (mmpt) cc_final: 0.8911 (mmpt) REVERT: B 152 LYS cc_start: 0.9362 (mttt) cc_final: 0.9030 (mtmm) REVERT: B 167 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8635 (pm20) REVERT: B 199 LEU cc_start: 0.9087 (tp) cc_final: 0.8798 (tt) REVERT: C 26 MET cc_start: 0.8322 (mmm) cc_final: 0.7921 (mmp) REVERT: C 40 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8559 (p) REVERT: C 71 ASN cc_start: 0.8862 (t0) cc_final: 0.8553 (t0) REVERT: C 81 TRP cc_start: 0.7162 (t-100) cc_final: 0.6330 (t60) REVERT: C 82 LYS cc_start: 0.8982 (tmmt) cc_final: 0.8655 (ptmm) REVERT: C 122 LYS cc_start: 0.8964 (mttp) cc_final: 0.8717 (mtmm) REVERT: C 152 LYS cc_start: 0.9290 (mttt) cc_final: 0.8975 (mtmm) REVERT: C 167 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8736 (pm20) REVERT: C 199 LEU cc_start: 0.9048 (tp) cc_final: 0.8825 (tt) REVERT: D 26 MET cc_start: 0.8416 (mmm) cc_final: 0.8089 (mmp) REVERT: D 38 GLU cc_start: 0.8770 (tp30) cc_final: 0.8526 (tp30) REVERT: D 40 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8736 (p) REVERT: D 68 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8194 (m-80) REVERT: D 71 ASN cc_start: 0.8815 (t0) cc_final: 0.8444 (t0) REVERT: D 77 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8173 (mm) REVERT: D 81 TRP cc_start: 0.7370 (t-100) cc_final: 0.6521 (t60) REVERT: D 143 GLN cc_start: 0.9117 (mm110) cc_final: 0.8788 (mm110) REVERT: D 167 GLU cc_start: 0.9008 (mp0) cc_final: 0.8747 (pm20) REVERT: D 169 ILE cc_start: 0.9154 (mt) cc_final: 0.8808 (tt) REVERT: E 40 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8696 (p) REVERT: E 68 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.8229 (m-80) REVERT: E 71 ASN cc_start: 0.9029 (t0) cc_final: 0.8591 (t0) REVERT: E 81 TRP cc_start: 0.7260 (t-100) cc_final: 0.6593 (t60) REVERT: E 95 LEU cc_start: 0.8230 (mt) cc_final: 0.7890 (pp) REVERT: E 122 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8449 (mtmp) REVERT: E 143 GLN cc_start: 0.8990 (mm110) cc_final: 0.8637 (mm110) REVERT: E 148 LYS cc_start: 0.9210 (mmpt) cc_final: 0.8846 (mmpt) REVERT: E 149 GLU cc_start: 0.9219 (pm20) cc_final: 0.8931 (pm20) REVERT: E 152 LYS cc_start: 0.9369 (mttt) cc_final: 0.9013 (mtmm) REVERT: E 199 LEU cc_start: 0.9124 (tp) cc_final: 0.8892 (tt) REVERT: F 71 ASN cc_start: 0.8871 (t0) cc_final: 0.8578 (t0) REVERT: F 73 ASN cc_start: 0.8560 (m-40) cc_final: 0.8261 (m-40) REVERT: F 81 TRP cc_start: 0.7226 (t-100) cc_final: 0.6421 (t60) REVERT: F 105 ARG cc_start: 0.9075 (mpt180) cc_final: 0.8869 (mmt-90) REVERT: F 122 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8599 (mttp) REVERT: F 142 TYR cc_start: 0.8982 (m-80) cc_final: 0.8496 (m-10) REVERT: F 152 LYS cc_start: 0.9338 (mttt) cc_final: 0.9105 (mtmm) REVERT: F 167 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8596 (pm20) REVERT: F 179 ARG cc_start: 0.8828 (ttm110) cc_final: 0.8550 (mtp-110) REVERT: G 71 ASN cc_start: 0.8814 (t0) cc_final: 0.8268 (t0) REVERT: G 102 MET cc_start: 0.9142 (ttm) cc_final: 0.8929 (ttp) REVERT: G 143 GLN cc_start: 0.9097 (mm110) cc_final: 0.8816 (mm110) outliers start: 22 outliers final: 9 residues processed: 364 average time/residue: 2.1742 time to fit residues: 853.0134 Evaluate side-chains 375 residues out of total 1169 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 352 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 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 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 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 122 LYS Chi-restraints excluded: chain F residue 161 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 110 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 22 optimal weight: 0.0170 chunk 61 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 31 optimal weight: 0.0170 chunk 109 optimal weight: 0.8980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.113642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.077775 restraints weight = 19654.469| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.38 r_work: 0.2817 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4602 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= 0.154 Angle : 0.819 8.477 14686 Z= 0.412 Chirality : 0.039 0.116 1708 Planarity : 0.005 0.044 1806 Dihedral : 3.604 18.255 1589 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.12 % Allowed : 27.10 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.24), residues: 1309 helix: 2.25 (0.18), residues: 917 sheet: None (None), residues: 0 loop : -1.22 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP G 81 HIS 0.001 0.000 HIS E 166 PHE 0.004 0.001 PHE D 163 TYR 0.021 0.001 TYR A 142 ARG 0.010 0.001 ARG C 201 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 7) link_NAG-ASN : angle 1.93073 ( 21) hydrogen bonds : bond 0.03424 ( 645) hydrogen bonds : angle 2.87682 ( 1935) SS BOND : bond 0.00229 ( 14) SS BOND : angle 0.42905 ( 28) covalent geometry : bond 0.00388 (10780) covalent geometry : angle 0.81682 (14637) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11207.12 seconds wall clock time: 198 minutes 3.86 seconds (11883.86 seconds total)