Starting phenix.real_space_refine on Wed Mar 4 07:21:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dsc_30830/03_2026/7dsc_30830.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsc_30830/03_2026/7dsc_30830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dsc_30830/03_2026/7dsc_30830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsc_30830/03_2026/7dsc_30830.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dsc_30830/03_2026/7dsc_30830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsc_30830/03_2026/7dsc_30830.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 104 5.16 5 C 7736 2.51 5 N 1888 2.21 5 O 2120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11848 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1467 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 41 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: B, C, D, E, F, G, H Time building chain proxies: 1.52, per 1000 atoms: 0.13 Number of scatterers: 11848 At special positions: 0 Unit cell: (124.722, 124.722, 88.218, 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 104 16.00 O 2120 8.00 N 1888 7.00 C 7736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 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 " " NAG H1001 " - " ASN H 139 " Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 354.9 milliseconds 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 75.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 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: 3.629A pdb=" N LEU A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 107 Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.689A pdb=" N ALA A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'A' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 204 Processing helix chain 'B' and resid 6 through 18 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: 3.628A pdb=" N LEU B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 107 Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.689A pdb=" N ALA B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'B' and resid 146 through 156 removed outlier: 4.036A pdb=" N LYS B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 204 Processing helix chain 'C' and resid 6 through 18 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: 3.629A pdb=" N LEU C 77 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 107 Processing helix chain 'C' and resid 107 through 120 removed outlier: 3.689A pdb=" N ALA C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 129 Processing helix chain 'C' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 204 Processing helix chain 'D' and resid 6 through 18 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: 3.629A pdb=" N LEU D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 107 Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.688A pdb=" N ALA D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 129 Processing helix chain 'D' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 153 " --> pdb=" O GLU D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 204 Processing helix chain 'E' and resid 6 through 18 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: 3.629A pdb=" N LEU E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 107 Processing helix chain 'E' and resid 107 through 120 removed outlier: 3.689A pdb=" N ALA E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 129 Processing helix chain 'E' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE E 153 " --> pdb=" O GLU E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 204 Processing helix chain 'F' and resid 6 through 18 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: 3.628A pdb=" N LEU F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 107 Processing helix chain 'F' and resid 107 through 120 removed outlier: 3.689A pdb=" N ALA F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 129 Processing helix chain 'F' and resid 146 through 156 removed outlier: 4.036A pdb=" N LYS F 152 " --> pdb=" O LYS F 148 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE F 153 " --> pdb=" O GLU F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 204 Processing helix chain 'G' and resid 6 through 18 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: 3.629A pdb=" N LEU G 77 " --> pdb=" O ASN G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 107 Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.689A pdb=" N ALA G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 129 Processing helix chain 'G' and resid 146 through 156 removed outlier: 4.037A pdb=" N LYS G 152 " --> pdb=" O LYS G 148 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE G 153 " --> pdb=" O GLU G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 204 Processing helix chain 'H' and resid 6 through 18 Processing helix chain 'H' and resid 25 through 36 Processing helix chain 'H' and resid 47 through 70 Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 73 through 83 removed outlier: 3.628A pdb=" N LEU H 77 " --> pdb=" O ASN H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 107 Processing helix chain 'H' and resid 107 through 120 removed outlier: 3.689A pdb=" N ALA H 111 " --> pdb=" O LEU H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 129 Processing helix chain 'H' and resid 146 through 156 removed outlier: 4.036A pdb=" N LYS H 152 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE H 153 " --> pdb=" O GLU H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 204 809 hydrogen bonds defined for protein. 2427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.81 Time building geometry restraints manager: 1.01 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: 3624 1.34 - 1.46: 2598 1.46 - 1.58: 5738 1.58 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 12120 Sorted by residual: 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 1.97e+00 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 1.97e+00 bond pdb=" C1 NAG H1001 " pdb=" O5 NAG H1001 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+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 1.94e+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 1.94e+00 ... (remaining 12115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 15639 1.07 - 2.15: 674 2.15 - 3.22: 95 3.22 - 4.29: 24 4.29 - 5.36: 40 Bond angle restraints: 16472 Sorted by residual: angle pdb=" N VAL H 58 " pdb=" CA VAL H 58 " pdb=" C VAL H 58 " ideal model delta sigma weight residual 108.88 113.31 -4.43 2.16e+00 2.14e-01 4.21e+00 angle pdb=" N VAL E 58 " pdb=" CA VAL E 58 " pdb=" C VAL E 58 " ideal model delta sigma weight residual 108.88 113.27 -4.39 2.16e+00 2.14e-01 4.13e+00 angle pdb=" N VAL A 58 " pdb=" CA VAL A 58 " pdb=" C VAL A 58 " ideal model delta sigma weight residual 108.88 113.27 -4.39 2.16e+00 2.14e-01 4.13e+00 angle pdb=" N VAL C 58 " pdb=" CA VAL C 58 " pdb=" C VAL C 58 " ideal model delta sigma weight residual 108.88 113.27 -4.39 2.16e+00 2.14e-01 4.13e+00 angle pdb=" N VAL G 58 " pdb=" CA VAL G 58 " pdb=" C VAL G 58 " ideal model delta sigma weight residual 108.88 113.27 -4.39 2.16e+00 2.14e-01 4.13e+00 ... (remaining 16467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.98: 6520 13.98 - 27.96: 560 27.96 - 41.94: 200 41.94 - 55.93: 64 55.93 - 69.91: 8 Dihedral angle restraints: 7352 sinusoidal: 2840 harmonic: 4512 Sorted by residual: dihedral pdb=" CB CYS H 43 " pdb=" SG CYS H 43 " pdb=" SG CYS H 159 " pdb=" CB CYS H 159 " ideal model delta sinusoidal sigma weight residual 93.00 119.88 -26.88 1 1.00e+01 1.00e-02 1.04e+01 dihedral pdb=" CB CYS F 43 " pdb=" SG CYS F 43 " pdb=" SG CYS F 159 " pdb=" CB CYS F 159 " ideal model delta sinusoidal sigma weight residual 93.00 119.87 -26.87 1 1.00e+01 1.00e-02 1.04e+01 dihedral pdb=" CB CYS B 43 " pdb=" SG CYS B 43 " pdb=" SG CYS B 159 " pdb=" CB CYS B 159 " ideal model delta sinusoidal sigma weight residual 93.00 119.87 -26.87 1 1.00e+01 1.00e-02 1.04e+01 ... (remaining 7349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1284 0.036 - 0.071: 501 0.071 - 0.107: 116 0.107 - 0.142: 27 0.142 - 0.178: 8 Chirality restraints: 1936 Sorted by residual: chirality pdb=" CB VAL D 58 " pdb=" CA VAL D 58 " pdb=" CG1 VAL D 58 " pdb=" CG2 VAL D 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CB VAL B 58 " pdb=" CA VAL B 58 " pdb=" CG1 VAL B 58 " pdb=" CG2 VAL B 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CB VAL E 58 " pdb=" CA VAL E 58 " pdb=" CG1 VAL E 58 " pdb=" CG2 VAL E 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.81e-01 ... (remaining 1933 not shown) Planarity restraints: 2032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO F 59 " -0.031 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO F 60 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 60 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 60 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 59 " 0.031 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO B 60 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 60 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 60 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 59 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO C 60 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.026 5.00e-02 4.00e+02 ... (remaining 2029 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3552 2.82 - 3.34: 11795 3.34 - 3.86: 19114 3.86 - 4.38: 20138 4.38 - 4.90: 36138 Nonbonded interactions: 90737 Sorted by model distance: nonbonded pdb=" OH TYR G 68 " pdb=" OG1 THR G 103 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR H 68 " pdb=" OG1 THR H 103 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR A 68 " pdb=" OG1 THR A 103 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR E 68 " pdb=" OG1 THR E 103 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR C 68 " pdb=" OG1 THR C 103 " model vdw 2.300 3.040 ... (remaining 90732 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.110 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 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 0.039 12144 Z= 0.168 Angle : 0.577 5.363 16528 Z= 0.324 Chirality : 0.040 0.178 1936 Planarity : 0.004 0.046 2024 Dihedral : 12.770 69.908 4360 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.00 % Allowed : 17.22 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.21), residues: 1480 helix: 0.64 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -2.98 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 201 TYR 0.008 0.001 TYR H 177 PHE 0.007 0.001 PHE D 64 TRP 0.008 0.001 TRP D 62 HIS 0.001 0.000 HIS F 166 Details of bonding type rmsd covalent geometry : bond 0.00384 (12120) covalent geometry : angle 0.56257 (16472) SS BOND : bond 0.00189 ( 16) SS BOND : angle 0.84744 ( 32) hydrogen bonds : bond 0.13841 ( 809) hydrogen bonds : angle 4.96381 ( 2427) link_NAG-ASN : bond 0.00430 ( 8) link_NAG-ASN : angle 3.34609 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 684 time to evaluate : 0.462 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: A 95 LEU cc_start: 0.8749 (mt) cc_final: 0.8504 (tp) REVERT: A 134 LEU cc_start: 0.7989 (mt) cc_final: 0.7573 (mt) REVERT: A 159 CYS cc_start: 0.4649 (m) cc_final: 0.4133 (m) REVERT: B 26 MET cc_start: 0.7042 (mmm) cc_final: 0.6798 (mmm) REVERT: B 95 LEU cc_start: 0.8719 (mt) cc_final: 0.8514 (tp) REVERT: B 134 LEU cc_start: 0.7898 (mt) cc_final: 0.7489 (mt) REVERT: B 185 CYS cc_start: 0.9068 (m) cc_final: 0.8527 (m) REVERT: C 95 LEU cc_start: 0.8748 (mt) cc_final: 0.8503 (tp) REVERT: C 134 LEU cc_start: 0.7986 (mt) cc_final: 0.7572 (mt) REVERT: C 159 CYS cc_start: 0.4643 (m) cc_final: 0.4128 (m) REVERT: D 26 MET cc_start: 0.7038 (mmm) cc_final: 0.6790 (mmm) REVERT: D 95 LEU cc_start: 0.8718 (mt) cc_final: 0.8515 (tp) REVERT: D 134 LEU cc_start: 0.7891 (mt) cc_final: 0.7482 (mt) REVERT: D 185 CYS cc_start: 0.9068 (m) cc_final: 0.8525 (m) REVERT: E 95 LEU cc_start: 0.8742 (mt) cc_final: 0.8497 (tp) REVERT: E 134 LEU cc_start: 0.7989 (mt) cc_final: 0.7576 (mt) REVERT: E 159 CYS cc_start: 0.4646 (m) cc_final: 0.4129 (m) REVERT: F 26 MET cc_start: 0.7039 (mmm) cc_final: 0.6794 (mmm) REVERT: F 95 LEU cc_start: 0.8721 (mt) cc_final: 0.8516 (tp) REVERT: F 134 LEU cc_start: 0.7892 (mt) cc_final: 0.7485 (mt) REVERT: F 185 CYS cc_start: 0.9068 (m) cc_final: 0.8532 (m) REVERT: G 95 LEU cc_start: 0.8743 (mt) cc_final: 0.8497 (tp) REVERT: G 134 LEU cc_start: 0.7993 (mt) cc_final: 0.7581 (mt) REVERT: G 159 CYS cc_start: 0.4648 (m) cc_final: 0.4129 (m) REVERT: H 26 MET cc_start: 0.7041 (mmm) cc_final: 0.6798 (mmm) REVERT: H 95 LEU cc_start: 0.8722 (mt) cc_final: 0.8517 (tp) REVERT: H 134 LEU cc_start: 0.7899 (mt) cc_final: 0.7489 (mt) REVERT: H 185 CYS cc_start: 0.9065 (m) cc_final: 0.8529 (m) outliers start: 0 outliers final: 0 residues processed: 684 average time/residue: 0.1016 time to fit residues: 99.3226 Evaluate side-chains 510 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 510 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.157715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.123537 restraints weight = 23062.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.126800 restraints weight = 13536.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.128913 restraints weight = 9967.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.129816 restraints weight = 8357.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.129836 restraints weight = 7666.668| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12144 Z= 0.152 Angle : 0.716 7.421 16528 Z= 0.365 Chirality : 0.042 0.160 1936 Planarity : 0.005 0.051 2024 Dihedral : 4.621 22.644 1792 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 4.14 % Allowed : 26.57 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.23), residues: 1480 helix: 1.75 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -2.47 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 171 TYR 0.022 0.002 TYR B 51 PHE 0.022 0.002 PHE C 99 TRP 0.017 0.002 TRP E 62 HIS 0.001 0.000 HIS G 166 Details of bonding type rmsd covalent geometry : bond 0.00350 (12120) covalent geometry : angle 0.71202 (16472) SS BOND : bond 0.00352 ( 16) SS BOND : angle 1.36916 ( 32) hydrogen bonds : bond 0.04173 ( 809) hydrogen bonds : angle 3.90353 ( 2427) link_NAG-ASN : bond 0.00092 ( 8) link_NAG-ASN : angle 1.67337 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 550 time to evaluate : 0.433 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: A 95 LEU cc_start: 0.8727 (mt) cc_final: 0.8522 (tp) REVERT: A 140 GLU cc_start: 0.6602 (pm20) cc_final: 0.6080 (pm20) REVERT: A 170 SER cc_start: 0.8802 (t) cc_final: 0.8583 (t) REVERT: B 71 ASN cc_start: 0.8571 (m-40) cc_final: 0.7706 (t0) REVERT: B 170 SER cc_start: 0.8859 (t) cc_final: 0.8648 (t) REVERT: B 185 CYS cc_start: 0.8899 (m) cc_final: 0.8327 (m) REVERT: C 95 LEU cc_start: 0.8720 (mt) cc_final: 0.8517 (tp) REVERT: C 140 GLU cc_start: 0.6604 (pm20) cc_final: 0.6088 (pm20) REVERT: C 170 SER cc_start: 0.8807 (t) cc_final: 0.8589 (t) REVERT: D 71 ASN cc_start: 0.8573 (m-40) cc_final: 0.7700 (t0) REVERT: D 170 SER cc_start: 0.8868 (t) cc_final: 0.8652 (t) REVERT: D 185 CYS cc_start: 0.8900 (m) cc_final: 0.8339 (m) REVERT: E 95 LEU cc_start: 0.8727 (mt) cc_final: 0.8522 (tp) REVERT: E 140 GLU cc_start: 0.6620 (pm20) cc_final: 0.6098 (pm20) REVERT: E 170 SER cc_start: 0.8803 (t) cc_final: 0.8587 (t) REVERT: F 71 ASN cc_start: 0.8576 (m-40) cc_final: 0.7545 (t0) REVERT: F 170 SER cc_start: 0.8867 (t) cc_final: 0.8652 (t) REVERT: F 185 CYS cc_start: 0.8912 (m) cc_final: 0.8350 (m) REVERT: G 95 LEU cc_start: 0.8729 (mt) cc_final: 0.8527 (tp) REVERT: G 140 GLU cc_start: 0.6612 (pm20) cc_final: 0.6088 (pm20) REVERT: G 170 SER cc_start: 0.8814 (t) cc_final: 0.8593 (t) REVERT: H 71 ASN cc_start: 0.8568 (m-40) cc_final: 0.7686 (t0) REVERT: H 170 SER cc_start: 0.8854 (t) cc_final: 0.8639 (t) REVERT: H 185 CYS cc_start: 0.8910 (m) cc_final: 0.8343 (m) outliers start: 50 outliers final: 37 residues processed: 574 average time/residue: 0.1001 time to fit residues: 82.3964 Evaluate side-chains 531 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 494 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 161 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 13 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.150973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116073 restraints weight = 23174.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.119112 restraints weight = 13667.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.121084 restraints weight = 10165.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121691 restraints weight = 8604.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.122432 restraints weight = 8021.426| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12144 Z= 0.193 Angle : 0.715 7.258 16528 Z= 0.364 Chirality : 0.043 0.173 1936 Planarity : 0.005 0.055 2024 Dihedral : 4.258 19.910 1792 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 6.21 % Allowed : 23.34 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.22), residues: 1480 helix: 1.83 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -2.27 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 171 TYR 0.016 0.002 TYR D 142 PHE 0.025 0.002 PHE B 99 TRP 0.020 0.002 TRP E 62 HIS 0.002 0.001 HIS E 166 Details of bonding type rmsd covalent geometry : bond 0.00475 (12120) covalent geometry : angle 0.71101 (16472) SS BOND : bond 0.00094 ( 16) SS BOND : angle 0.93923 ( 32) hydrogen bonds : bond 0.03935 ( 809) hydrogen bonds : angle 3.88868 ( 2427) link_NAG-ASN : bond 0.00163 ( 8) link_NAG-ASN : angle 2.03344 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 490 time to evaluate : 0.442 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: 0.7045 (mmm) cc_final: 0.6732 (mmm) REVERT: A 68 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6665 (m-80) REVERT: A 156 LYS cc_start: 0.8093 (mttt) cc_final: 0.7840 (mtpt) REVERT: A 165 GLU cc_start: 0.7604 (mp0) cc_final: 0.7050 (mp0) REVERT: A 170 SER cc_start: 0.8893 (OUTLIER) cc_final: 0.8525 (m) REVERT: B 71 ASN cc_start: 0.8276 (m-40) cc_final: 0.7816 (t0) REVERT: B 170 SER cc_start: 0.9028 (OUTLIER) cc_final: 0.8544 (m) REVERT: B 185 CYS cc_start: 0.8801 (m) cc_final: 0.8340 (m) REVERT: C 26 MET cc_start: 0.7039 (mmm) cc_final: 0.6724 (mmm) REVERT: C 68 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.6677 (m-80) REVERT: C 156 LYS cc_start: 0.8097 (mttt) cc_final: 0.7844 (mtpt) REVERT: C 165 GLU cc_start: 0.7603 (mp0) cc_final: 0.7051 (mp0) REVERT: C 170 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8522 (m) REVERT: D 71 ASN cc_start: 0.8275 (m-40) cc_final: 0.7814 (t0) REVERT: D 170 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8544 (m) REVERT: D 185 CYS cc_start: 0.8806 (m) cc_final: 0.8349 (m) REVERT: E 26 MET cc_start: 0.7037 (mmm) cc_final: 0.6719 (mmm) REVERT: E 68 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.6686 (m-80) REVERT: E 156 LYS cc_start: 0.8089 (mttt) cc_final: 0.7840 (mtpt) REVERT: E 165 GLU cc_start: 0.7607 (mp0) cc_final: 0.7048 (mp0) REVERT: E 170 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8528 (m) REVERT: F 71 ASN cc_start: 0.8277 (m-40) cc_final: 0.7980 (t0) REVERT: F 170 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8545 (m) REVERT: F 185 CYS cc_start: 0.8806 (m) cc_final: 0.8335 (m) REVERT: G 26 MET cc_start: 0.7042 (mmm) cc_final: 0.6729 (mmm) REVERT: G 68 TYR cc_start: 0.7168 (OUTLIER) cc_final: 0.6666 (m-80) REVERT: G 156 LYS cc_start: 0.8091 (mttt) cc_final: 0.7843 (mtpt) REVERT: G 165 GLU cc_start: 0.7598 (mp0) cc_final: 0.7095 (mp0) REVERT: G 170 SER cc_start: 0.8891 (OUTLIER) cc_final: 0.8530 (m) REVERT: H 71 ASN cc_start: 0.8266 (m-40) cc_final: 0.7799 (t0) REVERT: H 170 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8538 (m) REVERT: H 185 CYS cc_start: 0.8797 (m) cc_final: 0.8336 (m) outliers start: 75 outliers final: 59 residues processed: 523 average time/residue: 0.0952 time to fit residues: 72.8203 Evaluate side-chains 540 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 469 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 180 CYS Chi-restraints excluded: chain H residue 194 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 77 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 chunk 119 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 147 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 HIS D 166 HIS F 166 HIS H 166 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.151736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.117475 restraints weight = 23443.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.120571 restraints weight = 13549.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.122603 restraints weight = 9961.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.123811 restraints weight = 8384.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.124168 restraints weight = 7619.954| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12144 Z= 0.130 Angle : 0.678 9.259 16528 Z= 0.333 Chirality : 0.042 0.178 1936 Planarity : 0.005 0.053 2024 Dihedral : 4.046 17.353 1792 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.89 % Allowed : 27.07 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.22), residues: 1480 helix: 2.05 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -2.12 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 171 TYR 0.017 0.001 TYR A 142 PHE 0.024 0.001 PHE D 99 TRP 0.018 0.001 TRP D 62 HIS 0.001 0.000 HIS G 166 Details of bonding type rmsd covalent geometry : bond 0.00291 (12120) covalent geometry : angle 0.67607 (16472) SS BOND : bond 0.00117 ( 16) SS BOND : angle 0.55164 ( 32) hydrogen bonds : bond 0.03500 ( 809) hydrogen bonds : angle 3.61772 ( 2427) link_NAG-ASN : bond 0.00321 ( 8) link_NAG-ASN : angle 1.47764 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 514 time to evaluate : 0.433 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: A 26 MET cc_start: 0.6962 (mmm) cc_final: 0.6325 (mmm) REVERT: A 68 TYR cc_start: 0.7138 (OUTLIER) cc_final: 0.6701 (m-80) REVERT: A 160 LYS cc_start: 0.7473 (tppt) cc_final: 0.7031 (tppt) REVERT: A 170 SER cc_start: 0.8930 (t) cc_final: 0.8696 (t) REVERT: B 68 TYR cc_start: 0.7237 (OUTLIER) cc_final: 0.6372 (m-80) REVERT: B 71 ASN cc_start: 0.8224 (t0) cc_final: 0.7687 (t0) REVERT: B 102 MET cc_start: 0.8532 (tpp) cc_final: 0.8328 (tpp) REVERT: B 170 SER cc_start: 0.9067 (OUTLIER) cc_final: 0.8840 (t) REVERT: B 185 CYS cc_start: 0.8716 (m) cc_final: 0.8325 (m) REVERT: C 26 MET cc_start: 0.6950 (mmm) cc_final: 0.6319 (mmm) REVERT: C 68 TYR cc_start: 0.7146 (OUTLIER) cc_final: 0.6670 (m-80) REVERT: C 160 LYS cc_start: 0.7474 (tppt) cc_final: 0.7031 (tppt) REVERT: C 170 SER cc_start: 0.8946 (t) cc_final: 0.8708 (t) REVERT: D 68 TYR cc_start: 0.7247 (OUTLIER) cc_final: 0.6375 (m-80) REVERT: D 71 ASN cc_start: 0.8235 (t0) cc_final: 0.7692 (t0) REVERT: D 102 MET cc_start: 0.8543 (tpp) cc_final: 0.8338 (tpp) REVERT: D 170 SER cc_start: 0.9076 (OUTLIER) cc_final: 0.8846 (t) REVERT: D 185 CYS cc_start: 0.8716 (m) cc_final: 0.8329 (m) REVERT: E 26 MET cc_start: 0.6944 (mmm) cc_final: 0.6309 (mmm) REVERT: E 68 TYR cc_start: 0.7144 (OUTLIER) cc_final: 0.6668 (m-80) REVERT: E 160 LYS cc_start: 0.7473 (tppt) cc_final: 0.7032 (tppt) REVERT: E 170 SER cc_start: 0.8932 (t) cc_final: 0.8701 (t) REVERT: F 68 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6367 (m-80) REVERT: F 71 ASN cc_start: 0.8199 (m-40) cc_final: 0.7705 (t0) REVERT: F 170 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8847 (t) REVERT: F 185 CYS cc_start: 0.8715 (m) cc_final: 0.8332 (m) REVERT: G 26 MET cc_start: 0.6950 (mmm) cc_final: 0.6319 (mmm) REVERT: G 68 TYR cc_start: 0.7146 (OUTLIER) cc_final: 0.6669 (m-80) REVERT: G 160 LYS cc_start: 0.7439 (tppt) cc_final: 0.6990 (tppt) REVERT: G 170 SER cc_start: 0.8928 (t) cc_final: 0.8699 (t) REVERT: H 71 ASN cc_start: 0.8216 (m-40) cc_final: 0.7689 (t0) REVERT: H 102 MET cc_start: 0.8560 (tpp) cc_final: 0.8314 (tpp) REVERT: H 170 SER cc_start: 0.9061 (OUTLIER) cc_final: 0.8835 (t) REVERT: H 185 CYS cc_start: 0.8712 (m) cc_final: 0.8328 (m) outliers start: 47 outliers final: 22 residues processed: 542 average time/residue: 0.0949 time to fit residues: 75.0910 Evaluate side-chains 526 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 493 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 170 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 78 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 131 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 20 optimal weight: 0.0370 chunk 36 optimal weight: 0.6980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN C 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 = 0.4010 r_free = 0.4010 target = 0.153122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119031 restraints weight = 23488.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.122155 restraints weight = 13831.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.124125 restraints weight = 10296.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.124966 restraints weight = 8718.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.125320 restraints weight = 8042.606| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12144 Z= 0.131 Angle : 0.718 13.759 16528 Z= 0.347 Chirality : 0.042 0.148 1936 Planarity : 0.005 0.055 2024 Dihedral : 3.936 17.318 1792 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.22 % Allowed : 27.15 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.22), residues: 1480 helix: 2.19 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -1.87 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 171 TYR 0.012 0.001 TYR B 34 PHE 0.020 0.001 PHE A 99 TRP 0.017 0.001 TRP B 62 HIS 0.002 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00299 (12120) covalent geometry : angle 0.71591 (16472) SS BOND : bond 0.00094 ( 16) SS BOND : angle 0.47213 ( 32) hydrogen bonds : bond 0.03417 ( 809) hydrogen bonds : angle 3.59102 ( 2427) link_NAG-ASN : bond 0.00228 ( 8) link_NAG-ASN : angle 1.68873 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 517 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 68 TYR cc_start: 0.7022 (OUTLIER) cc_final: 0.6507 (m-80) REVERT: A 103 THR cc_start: 0.8772 (m) cc_final: 0.8474 (p) REVERT: A 104 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.6338 (mp-120) REVERT: A 160 LYS cc_start: 0.7480 (tppt) cc_final: 0.7096 (tppt) REVERT: B 32 GLN cc_start: 0.8446 (tp40) cc_final: 0.7747 (tm-30) REVERT: B 33 MET cc_start: 0.6943 (mmt) cc_final: 0.6654 (mmt) REVERT: B 68 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.6369 (m-80) REVERT: B 71 ASN cc_start: 0.8138 (t0) cc_final: 0.7468 (t0) REVERT: B 170 SER cc_start: 0.8956 (t) cc_final: 0.8410 (m) REVERT: B 185 CYS cc_start: 0.8657 (m) cc_final: 0.8343 (m) REVERT: C 68 TYR cc_start: 0.7001 (OUTLIER) cc_final: 0.6529 (m-80) REVERT: C 103 THR cc_start: 0.8773 (m) cc_final: 0.8468 (p) REVERT: C 104 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.6354 (mp-120) REVERT: C 160 LYS cc_start: 0.7491 (tppt) cc_final: 0.7104 (tppt) REVERT: D 68 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6354 (m-80) REVERT: D 71 ASN cc_start: 0.8137 (t0) cc_final: 0.7469 (t0) REVERT: D 170 SER cc_start: 0.8983 (t) cc_final: 0.8428 (m) REVERT: D 185 CYS cc_start: 0.8674 (m) cc_final: 0.8366 (m) REVERT: E 68 TYR cc_start: 0.7023 (OUTLIER) cc_final: 0.6543 (m-80) REVERT: E 103 THR cc_start: 0.8775 (m) cc_final: 0.8471 (p) REVERT: E 104 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6350 (mp-120) REVERT: E 160 LYS cc_start: 0.7491 (tppt) cc_final: 0.7105 (tppt) REVERT: F 68 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.6330 (m-80) REVERT: F 71 ASN cc_start: 0.8016 (m-40) cc_final: 0.7664 (t0) REVERT: F 185 CYS cc_start: 0.8672 (m) cc_final: 0.8372 (m) REVERT: G 68 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.6544 (m-80) REVERT: G 103 THR cc_start: 0.8777 (m) cc_final: 0.8464 (p) REVERT: G 104 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6341 (mp-120) REVERT: G 160 LYS cc_start: 0.7484 (tppt) cc_final: 0.7102 (tppt) REVERT: H 32 GLN cc_start: 0.8473 (tp40) cc_final: 0.7752 (tm-30) REVERT: H 33 MET cc_start: 0.6958 (mmt) cc_final: 0.6677 (mmt) REVERT: H 68 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6293 (m-80) REVERT: H 71 ASN cc_start: 0.8149 (t0) cc_final: 0.7474 (t0) REVERT: H 102 MET cc_start: 0.8469 (tpp) cc_final: 0.8263 (tpp) REVERT: H 170 SER cc_start: 0.8959 (t) cc_final: 0.8417 (m) REVERT: H 185 CYS cc_start: 0.8650 (m) cc_final: 0.8339 (m) outliers start: 51 outliers final: 34 residues processed: 549 average time/residue: 0.0942 time to fit residues: 75.6486 Evaluate side-chains 541 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 495 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 161 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 64 optimal weight: 0.0040 chunk 79 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.148418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113886 restraints weight = 23712.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116834 restraints weight = 13953.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118939 restraints weight = 10369.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119844 restraints weight = 8717.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.120231 restraints weight = 7989.724| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12144 Z= 0.213 Angle : 0.800 13.152 16528 Z= 0.393 Chirality : 0.046 0.171 1936 Planarity : 0.005 0.057 2024 Dihedral : 4.331 22.079 1792 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.72 % Allowed : 28.56 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.22), residues: 1480 helix: 1.98 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -1.95 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 171 TYR 0.013 0.002 TYR B 34 PHE 0.011 0.002 PHE D 99 TRP 0.023 0.002 TRP C 62 HIS 0.001 0.000 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00515 (12120) covalent geometry : angle 0.79462 (16472) SS BOND : bond 0.00096 ( 16) SS BOND : angle 0.75081 ( 32) hydrogen bonds : bond 0.03623 ( 809) hydrogen bonds : angle 3.88730 ( 2427) link_NAG-ASN : bond 0.00673 ( 8) link_NAG-ASN : angle 2.55400 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 498 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.6907 (mmm) cc_final: 0.6235 (mmm) REVERT: A 68 TYR cc_start: 0.7180 (OUTLIER) cc_final: 0.6733 (m-80) REVERT: A 119 MET cc_start: 0.7780 (mmp) cc_final: 0.7532 (mmt) REVERT: A 156 LYS cc_start: 0.8274 (mttt) cc_final: 0.8003 (mtpt) REVERT: B 68 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.6548 (m-80) REVERT: B 71 ASN cc_start: 0.8175 (t0) cc_final: 0.7813 (t0) REVERT: B 102 MET cc_start: 0.8595 (tpp) cc_final: 0.8369 (tpp) REVERT: B 170 SER cc_start: 0.9133 (t) cc_final: 0.8626 (m) REVERT: B 185 CYS cc_start: 0.8744 (m) cc_final: 0.8369 (m) REVERT: C 26 MET cc_start: 0.6915 (mmm) cc_final: 0.6235 (mmm) REVERT: C 68 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.6711 (m-80) REVERT: C 156 LYS cc_start: 0.8277 (mttt) cc_final: 0.8007 (mtpt) REVERT: D 68 TYR cc_start: 0.7454 (OUTLIER) cc_final: 0.6544 (m-80) REVERT: D 71 ASN cc_start: 0.8185 (t0) cc_final: 0.7824 (t0) REVERT: D 102 MET cc_start: 0.8605 (tpp) cc_final: 0.8371 (tpp) REVERT: D 170 SER cc_start: 0.9146 (t) cc_final: 0.8635 (m) REVERT: D 185 CYS cc_start: 0.8760 (m) cc_final: 0.8384 (m) REVERT: E 26 MET cc_start: 0.6922 (mmm) cc_final: 0.6237 (mmm) REVERT: E 68 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.6703 (m-80) REVERT: E 156 LYS cc_start: 0.8270 (mttt) cc_final: 0.8002 (mtpt) REVERT: F 68 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.6604 (m-80) REVERT: F 102 MET cc_start: 0.8532 (tpp) cc_final: 0.8208 (tpp) REVERT: F 119 MET cc_start: 0.8097 (mmm) cc_final: 0.7891 (mmp) REVERT: F 185 CYS cc_start: 0.8763 (m) cc_final: 0.8402 (m) REVERT: G 26 MET cc_start: 0.6905 (mmm) cc_final: 0.6220 (mmm) REVERT: G 68 TYR cc_start: 0.7214 (OUTLIER) cc_final: 0.6718 (m-80) REVERT: G 156 LYS cc_start: 0.8270 (mttt) cc_final: 0.8004 (mtpt) REVERT: H 68 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.6560 (m-80) REVERT: H 71 ASN cc_start: 0.8202 (t0) cc_final: 0.7894 (t0) REVERT: H 119 MET cc_start: 0.8071 (mmm) cc_final: 0.7867 (mmp) REVERT: H 170 SER cc_start: 0.9130 (OUTLIER) cc_final: 0.8625 (m) REVERT: H 185 CYS cc_start: 0.8740 (m) cc_final: 0.8371 (m) outliers start: 57 outliers final: 41 residues processed: 530 average time/residue: 0.1000 time to fit residues: 76.5244 Evaluate side-chains 536 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 486 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 146 SER Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 170 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 146 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN C 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 = 0.3963 r_free = 0.3963 target = 0.150030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115590 restraints weight = 23180.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118749 restraints weight = 13767.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120778 restraints weight = 10190.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.121660 restraints weight = 8577.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122311 restraints weight = 7865.907| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12144 Z= 0.146 Angle : 0.801 14.221 16528 Z= 0.378 Chirality : 0.044 0.186 1936 Planarity : 0.005 0.056 2024 Dihedral : 4.032 17.342 1792 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 4.80 % Allowed : 29.88 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.22), residues: 1480 helix: 2.19 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -2.16 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 171 TYR 0.013 0.001 TYR D 51 PHE 0.030 0.001 PHE H 99 TRP 0.025 0.002 TRP A 62 HIS 0.000 0.000 HIS F 166 Details of bonding type rmsd covalent geometry : bond 0.00349 (12120) covalent geometry : angle 0.79745 (16472) SS BOND : bond 0.00078 ( 16) SS BOND : angle 0.60491 ( 32) hydrogen bonds : bond 0.03446 ( 809) hydrogen bonds : angle 3.84027 ( 2427) link_NAG-ASN : bond 0.00271 ( 8) link_NAG-ASN : angle 2.33557 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 531 time to evaluate : 0.462 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: 0.6736 (mmm) cc_final: 0.6073 (mmm) REVERT: A 68 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.6702 (m-80) REVERT: A 103 THR cc_start: 0.8735 (m) cc_final: 0.8471 (p) REVERT: A 104 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.6338 (mp-120) REVERT: A 156 LYS cc_start: 0.8233 (mttt) cc_final: 0.7977 (mtpt) REVERT: B 32 GLN cc_start: 0.8571 (tp40) cc_final: 0.7820 (tm-30) REVERT: B 68 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.6477 (m-80) REVERT: B 71 ASN cc_start: 0.8181 (t0) cc_final: 0.7686 (t0) REVERT: B 102 MET cc_start: 0.8580 (tpp) cc_final: 0.8165 (tpp) REVERT: B 103 THR cc_start: 0.8818 (m) cc_final: 0.8569 (p) REVERT: B 170 SER cc_start: 0.9145 (OUTLIER) cc_final: 0.8931 (t) REVERT: C 26 MET cc_start: 0.6729 (mmm) cc_final: 0.6065 (mmm) REVERT: C 68 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.6704 (m-80) REVERT: C 103 THR cc_start: 0.8748 (m) cc_final: 0.8472 (p) REVERT: C 104 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.6297 (mp-120) REVERT: C 156 LYS cc_start: 0.8240 (mttt) cc_final: 0.7985 (mtpt) REVERT: D 68 TYR cc_start: 0.7460 (OUTLIER) cc_final: 0.6545 (m-80) REVERT: D 71 ASN cc_start: 0.8179 (t0) cc_final: 0.7699 (t0) REVERT: D 102 MET cc_start: 0.8597 (tpp) cc_final: 0.8154 (tpp) REVERT: D 170 SER cc_start: 0.9143 (OUTLIER) cc_final: 0.8911 (t) REVERT: D 185 CYS cc_start: 0.8777 (m) cc_final: 0.8420 (m) REVERT: E 26 MET cc_start: 0.6738 (mmm) cc_final: 0.6078 (mmm) REVERT: E 68 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.6715 (m-80) REVERT: E 103 THR cc_start: 0.8746 (m) cc_final: 0.8473 (p) REVERT: E 104 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.6294 (mp-120) REVERT: E 156 LYS cc_start: 0.8236 (mttt) cc_final: 0.7988 (mtpt) REVERT: F 68 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.6541 (m-80) REVERT: F 102 MET cc_start: 0.8606 (tpp) cc_final: 0.8369 (tpp) REVERT: F 185 CYS cc_start: 0.8756 (m) cc_final: 0.8408 (m) REVERT: G 26 MET cc_start: 0.6739 (mmm) cc_final: 0.6078 (mmm) REVERT: G 68 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6710 (m-80) REVERT: G 103 THR cc_start: 0.8749 (m) cc_final: 0.8470 (p) REVERT: G 104 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6288 (mp-120) REVERT: G 156 LYS cc_start: 0.8230 (mttt) cc_final: 0.7979 (mtpt) REVERT: H 32 GLN cc_start: 0.8584 (tp40) cc_final: 0.7824 (tm-30) REVERT: H 68 TYR cc_start: 0.7460 (OUTLIER) cc_final: 0.6486 (m-80) REVERT: H 71 ASN cc_start: 0.8165 (t0) cc_final: 0.7184 (t0) REVERT: H 102 MET cc_start: 0.8557 (tpp) cc_final: 0.8239 (tpp) REVERT: H 170 SER cc_start: 0.9146 (t) cc_final: 0.8931 (t) REVERT: H 185 CYS cc_start: 0.8758 (m) cc_final: 0.8399 (m) outliers start: 58 outliers final: 40 residues processed: 559 average time/residue: 0.1005 time to fit residues: 80.5889 Evaluate side-chains 560 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 506 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 161 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 83 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 chunk 21 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 chunk 87 optimal weight: 0.0980 chunk 3 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN C 104 GLN E 104 GLN ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 GLN G 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.151509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116833 restraints weight = 22948.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.120012 restraints weight = 13631.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.122029 restraints weight = 10101.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.123036 restraints weight = 8513.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.123049 restraints weight = 7788.859| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12144 Z= 0.142 Angle : 0.870 15.263 16528 Z= 0.394 Chirality : 0.044 0.167 1936 Planarity : 0.005 0.056 2024 Dihedral : 4.031 17.352 1792 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.73 % Allowed : 32.95 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.22), residues: 1480 helix: 2.24 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -2.16 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 105 TYR 0.011 0.001 TYR F 51 PHE 0.030 0.001 PHE D 99 TRP 0.020 0.001 TRP D 62 HIS 0.001 0.001 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00331 (12120) covalent geometry : angle 0.86725 (16472) SS BOND : bond 0.00091 ( 16) SS BOND : angle 0.51212 ( 32) hydrogen bonds : bond 0.03424 ( 809) hydrogen bonds : angle 3.84961 ( 2427) link_NAG-ASN : bond 0.00248 ( 8) link_NAG-ASN : angle 2.21630 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 515 time to evaluate : 0.358 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: 0.6801 (mmm) cc_final: 0.6316 (mmm) REVERT: A 68 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6572 (m-80) REVERT: A 104 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.7083 (mp10) REVERT: A 156 LYS cc_start: 0.8201 (mttt) cc_final: 0.7973 (mtpt) REVERT: B 32 GLN cc_start: 0.8530 (tp40) cc_final: 0.7648 (tm-30) REVERT: B 68 TYR cc_start: 0.7420 (OUTLIER) cc_final: 0.6481 (m-80) REVERT: B 71 ASN cc_start: 0.8166 (t0) cc_final: 0.7585 (t0) REVERT: B 102 MET cc_start: 0.8556 (tpp) cc_final: 0.8235 (tpp) REVERT: B 170 SER cc_start: 0.9117 (OUTLIER) cc_final: 0.8906 (t) REVERT: C 26 MET cc_start: 0.6790 (mmm) cc_final: 0.6259 (mmm) REVERT: C 68 TYR cc_start: 0.7119 (OUTLIER) cc_final: 0.6594 (m-80) REVERT: C 104 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.7086 (mp10) REVERT: C 156 LYS cc_start: 0.8210 (mttt) cc_final: 0.7979 (mtpt) REVERT: D 68 TYR cc_start: 0.7442 (OUTLIER) cc_final: 0.6479 (m-80) REVERT: D 71 ASN cc_start: 0.8172 (t0) cc_final: 0.7598 (t0) REVERT: D 102 MET cc_start: 0.8607 (tpp) cc_final: 0.8257 (tpp) REVERT: D 170 SER cc_start: 0.9121 (t) cc_final: 0.8908 (t) REVERT: D 185 CYS cc_start: 0.8714 (m) cc_final: 0.8410 (m) REVERT: E 26 MET cc_start: 0.6807 (mmm) cc_final: 0.6268 (mmm) REVERT: E 68 TYR cc_start: 0.7130 (OUTLIER) cc_final: 0.6613 (m-80) REVERT: E 104 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7080 (mp10) REVERT: E 156 LYS cc_start: 0.8205 (mttt) cc_final: 0.7957 (mtpt) REVERT: F 68 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.6426 (m-80) REVERT: F 102 MET cc_start: 0.8551 (tpp) cc_final: 0.8321 (tpp) REVERT: G 26 MET cc_start: 0.6810 (mmm) cc_final: 0.6316 (mmm) REVERT: G 68 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.6592 (m-80) REVERT: G 104 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.7080 (mp10) REVERT: G 156 LYS cc_start: 0.8203 (mttt) cc_final: 0.7978 (mtpt) REVERT: H 32 GLN cc_start: 0.8526 (tp40) cc_final: 0.7642 (tm-30) REVERT: H 68 TYR cc_start: 0.7370 (OUTLIER) cc_final: 0.6489 (m-80) REVERT: H 71 ASN cc_start: 0.8162 (t0) cc_final: 0.7167 (t0) REVERT: H 102 MET cc_start: 0.8534 (tpp) cc_final: 0.8265 (tpp) REVERT: H 170 SER cc_start: 0.9099 (t) cc_final: 0.8895 (t) REVERT: H 185 CYS cc_start: 0.8694 (m) cc_final: 0.8392 (m) outliers start: 45 outliers final: 29 residues processed: 535 average time/residue: 0.0957 time to fit residues: 74.7681 Evaluate side-chains 542 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 500 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 161 ASP 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 125 LEU Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 125 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 38 optimal weight: 40.0000 chunk 139 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 121 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.151195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.116950 restraints weight = 23051.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.120068 restraints weight = 13683.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122125 restraints weight = 10191.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122999 restraints weight = 8602.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.123974 restraints weight = 7912.459| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12144 Z= 0.147 Angle : 0.893 15.543 16528 Z= 0.402 Chirality : 0.045 0.184 1936 Planarity : 0.005 0.056 2024 Dihedral : 3.870 17.125 1792 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.14 % Allowed : 32.62 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.22), residues: 1480 helix: 2.24 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -2.08 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 105 TYR 0.018 0.001 TYR G 142 PHE 0.033 0.001 PHE B 99 TRP 0.021 0.001 TRP D 62 HIS 0.001 0.001 HIS F 166 Details of bonding type rmsd covalent geometry : bond 0.00348 (12120) covalent geometry : angle 0.89064 (16472) SS BOND : bond 0.00090 ( 16) SS BOND : angle 0.44994 ( 32) hydrogen bonds : bond 0.03406 ( 809) hydrogen bonds : angle 3.87348 ( 2427) link_NAG-ASN : bond 0.00291 ( 8) link_NAG-ASN : angle 2.21087 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 500 time to evaluate : 0.432 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: 0.6846 (mmm) cc_final: 0.6351 (mmm) REVERT: A 68 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.6652 (m-80) REVERT: A 156 LYS cc_start: 0.8177 (mttt) cc_final: 0.7937 (mtpt) REVERT: A 165 GLU cc_start: 0.7343 (mp0) cc_final: 0.6760 (pm20) REVERT: B 32 GLN cc_start: 0.8486 (tp40) cc_final: 0.7624 (tm-30) REVERT: B 68 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.6495 (m-80) REVERT: B 71 ASN cc_start: 0.8151 (t0) cc_final: 0.7862 (t0) REVERT: B 102 MET cc_start: 0.8490 (tpp) cc_final: 0.7991 (tpp) REVERT: B 104 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7063 (mp-120) REVERT: B 170 SER cc_start: 0.9116 (OUTLIER) cc_final: 0.8911 (t) REVERT: C 26 MET cc_start: 0.6834 (mmm) cc_final: 0.6337 (mmm) REVERT: C 68 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.6647 (m-80) REVERT: C 156 LYS cc_start: 0.8189 (mttt) cc_final: 0.7953 (mtpt) REVERT: C 165 GLU cc_start: 0.7354 (mp0) cc_final: 0.6766 (pm20) REVERT: D 68 TYR cc_start: 0.7467 (OUTLIER) cc_final: 0.6502 (m-80) REVERT: D 71 ASN cc_start: 0.8185 (t0) cc_final: 0.7917 (t0) REVERT: D 102 MET cc_start: 0.8557 (tpp) cc_final: 0.8078 (tpp) REVERT: D 170 SER cc_start: 0.9128 (t) cc_final: 0.8920 (t) REVERT: D 185 CYS cc_start: 0.8712 (m) cc_final: 0.8408 (m) REVERT: E 26 MET cc_start: 0.6836 (mmm) cc_final: 0.6337 (mmm) REVERT: E 68 TYR cc_start: 0.7112 (OUTLIER) cc_final: 0.6671 (m-80) REVERT: E 156 LYS cc_start: 0.8184 (mttt) cc_final: 0.7940 (mtpt) REVERT: E 165 GLU cc_start: 0.7319 (mp0) cc_final: 0.6734 (pm20) REVERT: F 68 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.6394 (m-80) REVERT: F 103 THR cc_start: 0.8716 (m) cc_final: 0.8373 (p) REVERT: F 104 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.6950 (mp-120) REVERT: G 26 MET cc_start: 0.6848 (mmm) cc_final: 0.6363 (mmm) REVERT: G 68 TYR cc_start: 0.7097 (OUTLIER) cc_final: 0.6664 (m-80) REVERT: G 156 LYS cc_start: 0.8185 (mttt) cc_final: 0.7948 (mtpt) REVERT: G 165 GLU cc_start: 0.7317 (mp0) cc_final: 0.6702 (pm20) REVERT: H 32 GLN cc_start: 0.8496 (tp40) cc_final: 0.7622 (tm-30) REVERT: H 68 TYR cc_start: 0.7449 (OUTLIER) cc_final: 0.6473 (m-80) REVERT: H 71 ASN cc_start: 0.8145 (t0) cc_final: 0.7109 (t0) REVERT: H 102 MET cc_start: 0.8511 (tpp) cc_final: 0.8269 (tpp) REVERT: H 185 CYS cc_start: 0.8686 (m) cc_final: 0.8372 (m) outliers start: 50 outliers final: 36 residues processed: 518 average time/residue: 0.1000 time to fit residues: 75.3234 Evaluate side-chains 540 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 493 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 161 ASP 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 125 LEU Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 104 GLN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 117 optimal weight: 0.0070 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 104 GLN H 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.147369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112614 restraints weight = 23284.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115673 restraints weight = 13841.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.117628 restraints weight = 10349.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.118563 restraints weight = 8781.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.118563 restraints weight = 8081.405| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.6168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12144 Z= 0.175 Angle : 0.916 15.993 16528 Z= 0.417 Chirality : 0.046 0.165 1936 Planarity : 0.005 0.057 2024 Dihedral : 3.936 16.814 1792 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.22 % Allowed : 32.45 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.22), residues: 1480 helix: 2.14 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -2.03 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 171 TYR 0.015 0.002 TYR A 142 PHE 0.035 0.002 PHE F 99 TRP 0.028 0.002 TRP F 62 HIS 0.001 0.000 HIS B 166 Details of bonding type rmsd covalent geometry : bond 0.00432 (12120) covalent geometry : angle 0.91225 (16472) SS BOND : bond 0.00050 ( 16) SS BOND : angle 0.69655 ( 32) hydrogen bonds : bond 0.03521 ( 809) hydrogen bonds : angle 4.08273 ( 2427) link_NAG-ASN : bond 0.00153 ( 8) link_NAG-ASN : angle 2.34433 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 493 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.6958 (mmm) cc_final: 0.6297 (mmm) REVERT: A 68 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.6799 (m-80) REVERT: A 156 LYS cc_start: 0.8285 (mttt) cc_final: 0.8069 (mtpt) REVERT: B 32 GLN cc_start: 0.8561 (tp40) cc_final: 0.7830 (tm-30) REVERT: B 68 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.6637 (m-80) REVERT: B 71 ASN cc_start: 0.8357 (t0) cc_final: 0.7717 (t0) REVERT: B 102 MET cc_start: 0.8654 (tpp) cc_final: 0.8258 (tpp) REVERT: B 170 SER cc_start: 0.9122 (OUTLIER) cc_final: 0.8625 (m) REVERT: C 26 MET cc_start: 0.6915 (mmm) cc_final: 0.6238 (mmm) REVERT: C 68 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.6832 (m-80) REVERT: C 156 LYS cc_start: 0.8294 (mttt) cc_final: 0.8071 (mtpt) REVERT: D 68 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.6633 (m-80) REVERT: D 71 ASN cc_start: 0.8369 (t0) cc_final: 0.7740 (t0) REVERT: D 102 MET cc_start: 0.8673 (tpp) cc_final: 0.8268 (tpp) REVERT: D 170 SER cc_start: 0.9134 (t) cc_final: 0.8637 (m) REVERT: D 185 CYS cc_start: 0.8778 (m) cc_final: 0.8396 (m) REVERT: E 26 MET cc_start: 0.6916 (mmm) cc_final: 0.6266 (mmm) REVERT: E 68 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: E 119 MET cc_start: 0.7783 (mmp) cc_final: 0.7513 (mmt) REVERT: E 156 LYS cc_start: 0.8303 (mttt) cc_final: 0.8052 (mtpt) REVERT: E 165 GLU cc_start: 0.7439 (mp0) cc_final: 0.7134 (pm20) REVERT: F 68 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.6584 (m-80) REVERT: F 104 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7429 (mp10) REVERT: G 26 MET cc_start: 0.6930 (mmm) cc_final: 0.6248 (mmm) REVERT: G 68 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.6839 (m-80) REVERT: G 156 LYS cc_start: 0.8287 (mttt) cc_final: 0.8066 (mtpt) REVERT: H 32 GLN cc_start: 0.8569 (tp40) cc_final: 0.7829 (tm-30) REVERT: H 68 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.6625 (m-80) REVERT: H 71 ASN cc_start: 0.8202 (t0) cc_final: 0.7488 (t0) REVERT: H 73 ASN cc_start: 0.8462 (p0) cc_final: 0.7500 (p0) REVERT: H 102 MET cc_start: 0.8586 (tpp) cc_final: 0.7756 (tpp) REVERT: H 185 CYS cc_start: 0.8753 (m) cc_final: 0.8344 (m) outliers start: 51 outliers final: 37 residues processed: 514 average time/residue: 0.0997 time to fit residues: 74.1829 Evaluate side-chains 529 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 482 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 161 ASP Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 161 ASP 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 125 LEU Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain E residue 40 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 68 TYR Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 104 GLN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 68 TYR Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 70 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 19 optimal weight: 50.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.147966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114107 restraints weight = 23203.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117089 restraints weight = 13898.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119093 restraints weight = 10419.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119926 restraints weight = 8800.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120706 restraints weight = 8135.674| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.6328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12144 Z= 0.177 Angle : 0.934 15.769 16528 Z= 0.425 Chirality : 0.047 0.191 1936 Planarity : 0.005 0.058 2024 Dihedral : 4.012 16.930 1792 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.89 % Allowed : 32.53 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.22), residues: 1480 helix: 2.07 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -2.02 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 171 TYR 0.020 0.002 TYR A 142 PHE 0.033 0.002 PHE B 99 TRP 0.034 0.002 TRP A 62 HIS 0.002 0.000 HIS G 166 Details of bonding type rmsd covalent geometry : bond 0.00436 (12120) covalent geometry : angle 0.93152 (16472) SS BOND : bond 0.00087 ( 16) SS BOND : angle 0.70169 ( 32) hydrogen bonds : bond 0.03425 ( 809) hydrogen bonds : angle 4.16100 ( 2427) link_NAG-ASN : bond 0.00253 ( 8) link_NAG-ASN : angle 2.26054 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2376.04 seconds wall clock time: 41 minutes 33.32 seconds (2493.32 seconds total)