Starting phenix.real_space_refine on Fri Jul 3 03:09:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dsc_30830/07_2026/7dsc_30830.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dsc_30830/07_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_30830/07_2026/7dsc_30830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dsc_30830/07_2026/7dsc_30830.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7dsc_30830/07_2026/7dsc_30830.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dsc_30830/07_2026/7dsc_30830.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dsc_30830/07_2026/7dsc_30830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dsc_30830/07_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-6108/lib/python3.11/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 chiralities: 1 Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 1.65, per 1000 atoms: 0.14 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: 0.80 Conformation dependent library (CDL) restraints added in 503.9 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: 0.26 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: 1.46 Time building geometry restraints manager: 1.05 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: 6384 13.98 - 27.96: 544 27.96 - 41.94: 184 41.94 - 55.93: 64 55.93 - 69.91: 8 Dihedral angle restraints: 7184 sinusoidal: 2672 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 7181 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.400 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 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 : 12.787 69.908 4192 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/Z covalent geometry : bond 0.00384 / 0.17 (12120) covalent geometry : angle 0.56257 / 0.32 (16472) SS BOND : bond 0.00189 / 0.14 ( 16) SS BOND : angle 0.84744 / 0.67 ( 32) hydrogen bonds : bond 0.13841 / 9.12 ( 809) hydrogen bonds : angle 4.96381 / 3.56 ( 2427) link_NAG-ASN : bond 0.00430 / 0.28 ( 8) link_NAG-ASN : angle 3.34609 / 2.58 ( 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 : 0.538 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: 0.1017 time to fit residues: 99.9745 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 : 0.447 ------------------------------------------------------------------------------- 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... ** 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 = 0.4092 r_free = 0.4092 target = 0.157961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.123619 restraints weight = 23162.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.126914 restraints weight = 13503.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.129033 restraints weight = 9937.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.129973 restraints weight = 8352.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.129973 restraints weight = 7660.354| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3363 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= 0.154 Angle : 0.712 7.238 16528 Z= 0.362 Chirality : 0.042 0.168 1936 Planarity : 0.005 0.051 2024 Dihedral : 3.866 16.747 1624 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 4.80 % Allowed : 24.67 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.23), residues: 1480 helix: 1.74 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -2.42 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 171 TYR 0.022 0.002 TYR B 51 PHE 0.022 0.002 PHE A 99 TRP 0.017 0.002 TRP G 62 HIS 0.001 0.001 HIS G 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (12120) covalent geometry : angle 0.70773 / 0.36 (16472) SS BOND : bond 0.00250 / 0.18 ( 16) SS BOND : angle 1.46908 / 1.11 ( 32) hydrogen bonds : bond 0.04312 / 2.81 ( 809) hydrogen bonds : angle 3.88489 / 2.86 ( 2427) link_NAG-ASN : bond 0.00097 / 0.06 ( 8) link_NAG-ASN : angle 1.67156 / 1.30 ( 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 610 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 552 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: A 170 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8557 (t) REVERT: B 71 ASN cc_start: 0.8577 (m-40) cc_final: 0.7566 (t0) REVERT: B 170 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8613 (t) REVERT: B 185 CYS cc_start: 0.8909 (m) cc_final: 0.8337 (m) REVERT: C 170 SER cc_start: 0.8798 (OUTLIER) cc_final: 0.8567 (t) REVERT: D 71 ASN cc_start: 0.8577 (m-40) cc_final: 0.7720 (t0) REVERT: D 170 SER cc_start: 0.8849 (OUTLIER) cc_final: 0.8615 (t) REVERT: D 185 CYS cc_start: 0.8912 (m) cc_final: 0.8346 (m) REVERT: E 170 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8563 (t) REVERT: F 71 ASN cc_start: 0.8578 (m-40) cc_final: 0.7716 (t0) REVERT: F 170 SER cc_start: 0.8857 (OUTLIER) cc_final: 0.8619 (t) REVERT: F 185 CYS cc_start: 0.8928 (m) cc_final: 0.8360 (m) REVERT: G 170 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8572 (t) REVERT: H 71 ASN cc_start: 0.8571 (m-40) cc_final: 0.7551 (t0) REVERT: H 170 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8611 (t) REVERT: H 185 CYS cc_start: 0.8922 (m) cc_final: 0.8347 (m) outliers start: 58 outliers final: 37 residues processed: 576 average time/residue: 0.1049 time to fit residues: 86.6727 Evaluate side-chains 533 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 488 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 A residue 170 SER Chi-restraints excluded: chain B residue 40 THR 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 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 170 SER 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 161 ASP Chi-restraints excluded: chain D residue 169 ILE 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 146 SER Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 170 SER 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 161 ASP Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 170 SER 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 170 SER Chi-restraints excluded: chain G residue 194 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 169 ILE Chi-restraints excluded: chain H residue 170 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 13 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 97 optimal weight: 0.0070 chunk 134 optimal weight: 0.6980 chunk 142 optimal weight: 0.2980 chunk 140 optimal weight: 0.0570 chunk 11 optimal weight: 0.3980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.157655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.123689 restraints weight = 23148.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.126902 restraints weight = 13563.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.128996 restraints weight = 9965.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.129949 restraints weight = 8350.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.130946 restraints weight = 7649.494| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12144 Z= 0.139 Angle : 0.698 6.981 16528 Z= 0.344 Chirality : 0.042 0.190 1936 Planarity : 0.005 0.052 2024 Dihedral : 3.771 16.809 1624 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.56 % Allowed : 26.57 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.22), residues: 1480 helix: 1.96 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -2.00 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 171 TYR 0.020 0.002 TYR F 142 PHE 0.022 0.001 PHE F 99 TRP 0.013 0.001 TRP B 62 HIS 0.001 0.001 HIS G 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (12120) covalent geometry : angle 0.69568 / 0.34 (16472) SS BOND : bond 0.00114 / 0.08 ( 16) SS BOND : angle 0.62354 / 0.48 ( 32) hydrogen bonds : bond 0.03799 / 2.50 ( 809) hydrogen bonds : angle 3.62619 / 2.67 ( 2427) link_NAG-ASN : bond 0.00245 / 0.16 ( 8) link_NAG-ASN : angle 1.67956 / 1.29 ( 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 625 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 582 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 MET cc_start: 0.7106 (mmm) cc_final: 0.6789 (mmm) REVERT: A 170 SER cc_start: 0.8834 (t) cc_final: 0.8607 (t) REVERT: B 71 ASN cc_start: 0.8070 (m-40) cc_final: 0.7640 (t0) REVERT: C 26 MET cc_start: 0.7097 (mmm) cc_final: 0.6779 (mmm) REVERT: C 170 SER cc_start: 0.8840 (t) cc_final: 0.8609 (t) REVERT: D 71 ASN cc_start: 0.8108 (m-40) cc_final: 0.7754 (t0) REVERT: E 26 MET cc_start: 0.7107 (mmm) cc_final: 0.6790 (mmm) REVERT: E 170 SER cc_start: 0.8825 (t) cc_final: 0.8597 (t) REVERT: F 71 ASN cc_start: 0.8097 (m-40) cc_final: 0.7750 (t0) REVERT: F 170 SER cc_start: 0.8820 (t) cc_final: 0.8619 (t) REVERT: G 26 MET cc_start: 0.7104 (mmm) cc_final: 0.6791 (mmm) REVERT: G 170 SER cc_start: 0.8822 (t) cc_final: 0.8596 (t) REVERT: H 71 ASN cc_start: 0.8064 (m-40) cc_final: 0.7630 (t0) REVERT: H 170 SER cc_start: 0.8804 (t) cc_final: 0.8604 (t) outliers start: 43 outliers final: 32 residues processed: 598 average time/residue: 0.0892 time to fit residues: 80.8705 Evaluate side-chains 528 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 496 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 77 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 77 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 77 LEU Chi-restraints excluded: chain C residue 185 CYS Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 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 77 LEU Chi-restraints excluded: chain E residue 185 CYS Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 77 LEU 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 77 LEU Chi-restraints excluded: chain G residue 185 CYS Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 161 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 77 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 12 optimal weight: 0.0030 chunk 119 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.156220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.122371 restraints weight = 23461.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.125655 restraints weight = 13505.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.127806 restraints weight = 9812.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.128911 restraints weight = 8176.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.129470 restraints weight = 7431.726| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12144 Z= 0.136 Angle : 0.738 10.233 16528 Z= 0.354 Chirality : 0.042 0.145 1936 Planarity : 0.005 0.053 2024 Dihedral : 3.861 16.668 1624 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 5.30 % Allowed : 25.83 % Favored : 68.87 % 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: 1.67 (0.22), residues: 1480 helix: 2.07 (0.16), residues: 1112 sheet: None (None), residues: 0 loop : -2.04 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 96 TYR 0.019 0.001 TYR A 142 PHE 0.024 0.001 PHE D 99 TRP 0.015 0.001 TRP F 62 HIS 0.001 0.000 HIS G 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (12120) covalent geometry : angle 0.73675 / 0.35 (16472) SS BOND : bond 0.00082 / 0.06 ( 16) SS BOND : angle 0.64654 / 0.52 ( 32) hydrogen bonds : bond 0.03702 / 2.43 ( 809) hydrogen bonds : angle 3.72878 / 2.74 ( 2427) link_NAG-ASN : bond 0.00258 / 0.17 ( 8) link_NAG-ASN : angle 1.56819 / 1.20 ( 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 573 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 509 time to evaluate : 0.477 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: 0.6994 (mmm) cc_final: 0.6640 (mmm) REVERT: A 68 TYR cc_start: 0.6989 (OUTLIER) cc_final: 0.6634 (m-80) REVERT: A 160 LYS cc_start: 0.7318 (tppt) cc_final: 0.6938 (tppt) REVERT: A 170 SER cc_start: 0.8876 (t) cc_final: 0.8642 (t) REVERT: B 165 GLU cc_start: 0.7232 (mp0) cc_final: 0.6994 (mp0) REVERT: B 185 CYS cc_start: 0.8848 (m) cc_final: 0.8358 (m) REVERT: C 26 MET cc_start: 0.6992 (mmm) cc_final: 0.6637 (mmm) REVERT: C 68 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.6639 (m-80) REVERT: C 160 LYS cc_start: 0.7322 (tppt) cc_final: 0.6939 (tppt) REVERT: C 170 SER cc_start: 0.8900 (t) cc_final: 0.8678 (t) REVERT: D 185 CYS cc_start: 0.8860 (m) cc_final: 0.8377 (m) REVERT: E 26 MET cc_start: 0.6998 (mmm) cc_final: 0.6641 (mmm) REVERT: E 68 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.6645 (m-80) REVERT: E 160 LYS cc_start: 0.7322 (tppt) cc_final: 0.6942 (tppt) REVERT: E 170 SER cc_start: 0.8905 (t) cc_final: 0.8681 (t) REVERT: F 165 GLU cc_start: 0.7244 (mp0) cc_final: 0.6997 (mp0) REVERT: F 170 SER cc_start: 0.8882 (t) cc_final: 0.8680 (t) REVERT: F 185 CYS cc_start: 0.8859 (m) cc_final: 0.8378 (m) REVERT: G 26 MET cc_start: 0.7001 (mmm) cc_final: 0.6646 (mmm) REVERT: G 68 TYR cc_start: 0.6993 (OUTLIER) cc_final: 0.6637 (m-80) REVERT: G 160 LYS cc_start: 0.7315 (tppt) cc_final: 0.6933 (tppt) REVERT: G 170 SER cc_start: 0.8902 (t) cc_final: 0.8680 (t) REVERT: H 170 SER cc_start: 0.8879 (t) cc_final: 0.8678 (t) REVERT: H 185 CYS cc_start: 0.8849 (m) cc_final: 0.8372 (m) outliers start: 64 outliers final: 49 residues processed: 551 average time/residue: 0.0948 time to fit residues: 77.4649 Evaluate side-chains 531 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 478 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 A residue 153 ILE 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 66 LEU 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 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 77 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 153 ILE 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 125 LEU 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 68 TYR Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 66 LEU 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 77 LEU Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 153 ILE 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 125 LEU Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 161 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 78 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 64 optimal weight: 0.2980 chunk 131 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 20 optimal weight: 0.0370 chunk 36 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 71 ASN D 71 ASN F 71 ASN H 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.156839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.123320 restraints weight = 23610.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.126393 restraints weight = 13658.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.128643 restraints weight = 10009.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.129619 restraints weight = 8330.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.129619 restraints weight = 7586.423| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12144 Z= 0.135 Angle : 0.761 13.997 16528 Z= 0.361 Chirality : 0.043 0.153 1936 Planarity : 0.005 0.054 2024 Dihedral : 4.042 17.786 1624 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 4.39 % Allowed : 27.40 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.84 (0.22), residues: 1480 helix: 2.05 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -1.52 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 96 TYR 0.012 0.001 TYR E 142 PHE 0.016 0.001 PHE D 99 TRP 0.016 0.001 TRP C 62 HIS 0.001 0.000 HIS H 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (12120) covalent geometry : angle 0.75801 / 0.36 (16472) SS BOND : bond 0.00509 / 0.38 ( 16) SS BOND : angle 1.09850 / 0.93 ( 32) hydrogen bonds : bond 0.03510 / 2.30 ( 809) hydrogen bonds : angle 3.66803 / 2.69 ( 2427) link_NAG-ASN : bond 0.00539 / 0.36 ( 8) link_NAG-ASN : angle 1.74486 / 1.35 ( 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 563 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 510 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.6620 (m-80) REVERT: A 145 LEU cc_start: 0.5076 (mp) cc_final: 0.4805 (pt) REVERT: A 170 SER cc_start: 0.8894 (t) cc_final: 0.8681 (t) REVERT: B 32 GLN cc_start: 0.8559 (tp40) cc_final: 0.7641 (tm-30) REVERT: B 33 MET cc_start: 0.7001 (mmt) cc_final: 0.6720 (mmt) REVERT: B 68 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.6256 (m-80) REVERT: B 71 ASN cc_start: 0.7874 (OUTLIER) cc_final: 0.7215 (t0) REVERT: C 68 TYR cc_start: 0.7090 (OUTLIER) cc_final: 0.6616 (m-80) REVERT: C 170 SER cc_start: 0.8882 (t) cc_final: 0.8674 (t) REVERT: D 68 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6210 (m-80) REVERT: D 71 ASN cc_start: 0.7853 (OUTLIER) cc_final: 0.7284 (t0) REVERT: E 68 TYR cc_start: 0.7067 (OUTLIER) cc_final: 0.6603 (m-80) REVERT: E 170 SER cc_start: 0.8886 (t) cc_final: 0.8679 (t) REVERT: F 68 TYR cc_start: 0.7097 (OUTLIER) cc_final: 0.6196 (m-80) REVERT: F 71 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7301 (t0) REVERT: F 170 SER cc_start: 0.8954 (t) cc_final: 0.8704 (t) REVERT: G 68 TYR cc_start: 0.7064 (OUTLIER) cc_final: 0.6598 (m-80) REVERT: G 170 SER cc_start: 0.8894 (t) cc_final: 0.8684 (t) REVERT: H 71 ASN cc_start: 0.7853 (OUTLIER) cc_final: 0.7198 (t0) REVERT: H 170 SER cc_start: 0.8945 (t) cc_final: 0.8700 (t) outliers start: 53 outliers final: 32 residues processed: 540 average time/residue: 0.0879 time to fit residues: 70.5510 Evaluate side-chains 534 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 491 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 65 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 66 LEU Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 71 ASN 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 40 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 71 ASN 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 40 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 65 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 71 ASN 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 65 LEU Chi-restraints excluded: chain G residue 68 TYR Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 71 ASN Chi-restraints excluded: chain H residue 125 LEU 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: 6.9990 chunk 91 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 83 optimal weight: 0.0040 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4006 r_free = 0.4006 target = 0.152450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.118662 restraints weight = 23852.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.121805 restraints weight = 13953.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.123753 restraints weight = 10306.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.124636 restraints weight = 8708.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.125276 restraints weight = 7999.072| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12144 Z= 0.170 Angle : 0.800 13.603 16528 Z= 0.382 Chirality : 0.044 0.161 1936 Planarity : 0.005 0.056 2024 Dihedral : 4.216 18.433 1624 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 6.71 % Allowed : 25.75 % Favored : 67.55 % 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: 1.83 (0.22), residues: 1480 helix: 2.05 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -1.57 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 171 TYR 0.014 0.002 TYR E 142 PHE 0.019 0.002 PHE E 99 TRP 0.024 0.002 TRP A 62 HIS 0.000 0.000 HIS F 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (12120) covalent geometry : angle 0.79747 / 0.38 (16472) SS BOND : bond 0.00045 / 0.03 ( 16) SS BOND : angle 1.14657 / 0.95 ( 32) hydrogen bonds : bond 0.03628 / 2.37 ( 809) hydrogen bonds : angle 3.83684 / 2.80 ( 2427) link_NAG-ASN : bond 0.00170 / 0.11 ( 8) link_NAG-ASN : angle 1.66407 / 1.32 ( 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 605 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 524 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.7146 (OUTLIER) cc_final: 0.6706 (m-80) REVERT: A 104 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.6378 (mp-120) REVERT: A 170 SER cc_start: 0.8889 (t) cc_final: 0.8526 (m) REVERT: B 68 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: C 68 TYR cc_start: 0.7137 (OUTLIER) cc_final: 0.6688 (m-80) REVERT: C 104 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6385 (mp-120) REVERT: C 160 LYS cc_start: 0.7384 (tppt) cc_final: 0.6969 (tppt) REVERT: C 170 SER cc_start: 0.8883 (t) cc_final: 0.8512 (m) REVERT: D 68 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.6455 (m-80) REVERT: D 104 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7936 (mp10) REVERT: E 68 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6711 (m-80) REVERT: E 104 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.6374 (mp-120) REVERT: E 160 LYS cc_start: 0.7387 (tppt) cc_final: 0.6974 (tppt) REVERT: E 170 SER cc_start: 0.8879 (t) cc_final: 0.8513 (m) REVERT: F 68 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.6411 (m-80) REVERT: F 170 SER cc_start: 0.8935 (t) cc_final: 0.8421 (m) REVERT: G 68 TYR cc_start: 0.7148 (OUTLIER) cc_final: 0.6705 (m-80) REVERT: G 104 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.6383 (mp-120) REVERT: G 160 LYS cc_start: 0.7387 (tppt) cc_final: 0.6975 (tppt) REVERT: G 170 SER cc_start: 0.8879 (t) cc_final: 0.8512 (m) REVERT: H 68 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.6424 (m-80) REVERT: H 170 SER cc_start: 0.8933 (t) cc_final: 0.8416 (m) outliers start: 81 outliers final: 58 residues processed: 558 average time/residue: 0.0815 time to fit residues: 66.9116 Evaluate side-chains 574 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 504 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 103 THR 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 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 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 77 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 56 LEU 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 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 77 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 146 SER 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 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 F residue 180 CYS 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 77 LEU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 180 CYS 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 125 LEU Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 161 ASP Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 146 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 57 optimal weight: 50.0000 chunk 142 optimal weight: 0.2980 chunk 132 optimal weight: 0.9980 chunk 106 optimal weight: 0.0030 chunk 8 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN C 104 GLN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 GLN G 104 GLN ** H 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.152070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.117943 restraints weight = 23523.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.121035 restraints weight = 13753.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.123214 restraints weight = 10158.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.123843 restraints weight = 8511.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.124493 restraints weight = 7897.329| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12144 Z= 0.152 Angle : 0.813 14.204 16528 Z= 0.384 Chirality : 0.043 0.157 1936 Planarity : 0.005 0.056 2024 Dihedral : 4.230 18.492 1624 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 5.30 % Allowed : 29.88 % Favored : 64.82 % 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: 1.82 (0.22), residues: 1480 helix: 2.11 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -1.81 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 96 TYR 0.021 0.001 TYR G 142 PHE 0.028 0.001 PHE B 99 TRP 0.025 0.002 TRP E 62 HIS 0.001 0.000 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (12120) covalent geometry : angle 0.81081 / 0.38 (16472) SS BOND : bond 0.00060 / 0.05 ( 16) SS BOND : angle 0.89711 / 0.74 ( 32) hydrogen bonds : bond 0.03493 / 2.28 ( 809) hydrogen bonds : angle 3.87569 / 2.84 ( 2427) link_NAG-ASN : bond 0.00200 / 0.13 ( 8) link_NAG-ASN : angle 1.73423 / 1.37 ( 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 587 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 523 time to evaluate : 0.400 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: A 68 TYR cc_start: 0.7089 (OUTLIER) cc_final: 0.6661 (m-80) REVERT: A 104 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.7044 (mp10) REVERT: A 142 TYR cc_start: 0.6144 (m-80) cc_final: 0.5941 (m-80) REVERT: A 145 LEU cc_start: 0.5200 (mp) cc_final: 0.4904 (pt) REVERT: B 32 GLN cc_start: 0.8585 (tp40) cc_final: 0.7812 (tm-30) REVERT: B 68 TYR cc_start: 0.7339 (OUTLIER) cc_final: 0.6455 (m-80) REVERT: B 104 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7280 (mp-120) REVERT: C 68 TYR cc_start: 0.7067 (OUTLIER) cc_final: 0.6636 (m-80) REVERT: C 104 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.7045 (mp10) REVERT: C 160 LYS cc_start: 0.7469 (tppt) cc_final: 0.7072 (tppt) REVERT: D 68 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6465 (m-80) REVERT: E 68 TYR cc_start: 0.7090 (OUTLIER) cc_final: 0.6665 (m-80) REVERT: E 104 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.7088 (mp10) REVERT: E 160 LYS cc_start: 0.7468 (tppt) cc_final: 0.7076 (tppt) REVERT: F 68 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.6413 (m-80) REVERT: F 104 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7230 (mp-120) REVERT: F 170 SER cc_start: 0.8968 (t) cc_final: 0.8423 (m) REVERT: G 68 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: G 104 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.7047 (mp10) REVERT: G 160 LYS cc_start: 0.7465 (tppt) cc_final: 0.7075 (tppt) REVERT: G 170 SER cc_start: 0.8963 (t) cc_final: 0.8761 (t) REVERT: H 32 GLN cc_start: 0.8586 (tp40) cc_final: 0.7821 (tm-30) REVERT: H 68 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6416 (m-80) REVERT: H 104 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7242 (mp-120) REVERT: H 170 SER cc_start: 0.8954 (t) cc_final: 0.8414 (m) outliers start: 64 outliers final: 46 residues processed: 552 average time/residue: 0.0805 time to fit residues: 65.6263 Evaluate side-chains 569 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 508 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 104 GLN Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 40 THR 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 104 GLN 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 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 77 LEU Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain C residue 146 SER 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 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 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 77 LEU Chi-restraints excluded: chain E residue 104 GLN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 180 CYS 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 104 GLN 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 77 LEU Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain H residue 40 THR 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 104 GLN Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 146 SER 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: 0.7980 chunk 76 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 0.0070 chunk 21 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 90 optimal weight: 0.0980 chunk 150 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 104 GLN D 104 GLN F 104 GLN H 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.153595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.119941 restraints weight = 23240.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.123193 restraints weight = 13642.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125229 restraints weight = 10046.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.125895 restraints weight = 8439.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.127146 restraints weight = 7815.703| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.5477 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= 0.140 Angle : 0.824 14.850 16528 Z= 0.386 Chirality : 0.043 0.154 1936 Planarity : 0.005 0.055 2024 Dihedral : 4.147 17.878 1624 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.73 % Allowed : 29.72 % Favored : 66.56 % 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: 1.82 (0.22), residues: 1480 helix: 2.13 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -1.90 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 96 TYR 0.021 0.001 TYR E 142 PHE 0.023 0.001 PHE B 99 TRP 0.027 0.001 TRP G 62 HIS 0.000 0.000 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (12120) covalent geometry : angle 0.82225 / 0.39 (16472) SS BOND : bond 0.00080 / 0.06 ( 16) SS BOND : angle 0.62645 / 0.52 ( 32) hydrogen bonds : bond 0.03513 / 2.30 ( 809) hydrogen bonds : angle 3.79427 / 2.79 ( 2427) link_NAG-ASN : bond 0.00210 / 0.14 ( 8) link_NAG-ASN : angle 1.76327 / 1.40 ( 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 561 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 516 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.7023 (OUTLIER) cc_final: 0.6611 (m-80) REVERT: A 142 TYR cc_start: 0.6098 (m-80) cc_final: 0.5806 (m-80) REVERT: B 32 GLN cc_start: 0.8499 (tp40) cc_final: 0.7609 (tm-30) REVERT: B 68 TYR cc_start: 0.7199 (OUTLIER) cc_final: 0.6332 (m-80) REVERT: B 103 THR cc_start: 0.8559 (m) cc_final: 0.8355 (p) REVERT: B 185 CYS cc_start: 0.8801 (m) cc_final: 0.8469 (t) REVERT: C 68 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.6595 (m-80) REVERT: C 160 LYS cc_start: 0.7494 (tppt) cc_final: 0.7105 (tppt) REVERT: D 68 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6340 (m-80) REVERT: E 68 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.6622 (m-80) REVERT: E 160 LYS cc_start: 0.7497 (tppt) cc_final: 0.7103 (tppt) REVERT: F 68 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.6294 (m-80) REVERT: F 156 LYS cc_start: 0.8007 (mtpt) cc_final: 0.7750 (mtpt) REVERT: F 170 SER cc_start: 0.8968 (t) cc_final: 0.8730 (t) REVERT: F 185 CYS cc_start: 0.8823 (m) cc_final: 0.8481 (t) REVERT: G 68 TYR cc_start: 0.7005 (OUTLIER) cc_final: 0.6595 (m-80) REVERT: G 160 LYS cc_start: 0.7499 (tppt) cc_final: 0.7108 (tppt) REVERT: H 32 GLN cc_start: 0.8519 (tp40) cc_final: 0.7630 (tm-30) REVERT: H 68 TYR cc_start: 0.7175 (OUTLIER) cc_final: 0.6306 (m-80) REVERT: H 103 THR cc_start: 0.8613 (m) cc_final: 0.8406 (p) REVERT: H 170 SER cc_start: 0.8971 (t) cc_final: 0.8747 (t) REVERT: H 185 CYS cc_start: 0.8796 (m) cc_final: 0.8469 (t) outliers start: 45 outliers final: 35 residues processed: 544 average time/residue: 0.0849 time to fit residues: 68.0854 Evaluate side-chains 546 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 503 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 77 LEU Chi-restraints excluded: chain A residue 181 LEU 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 77 LEU Chi-restraints excluded: chain C residue 146 SER 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 77 LEU Chi-restraints excluded: chain E residue 146 SER 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 125 LEU 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 77 LEU Chi-restraints excluded: chain G residue 146 SER 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 125 LEU Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 161 ASP 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: 3.9990 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 140 optimal weight: 0.1980 chunk 121 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 71 ASN ** 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 = 0.3973 r_free = 0.3973 target = 0.149719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115518 restraints weight = 23379.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118431 restraints weight = 13916.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.120550 restraints weight = 10418.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.121479 restraints weight = 8788.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121867 restraints weight = 8059.934| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12144 Z= 0.181 Angle : 0.911 15.171 16528 Z= 0.424 Chirality : 0.046 0.173 1936 Planarity : 0.005 0.056 2024 Dihedral : 4.283 22.586 1624 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 5.05 % Allowed : 29.22 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.22), residues: 1480 helix: 1.98 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -2.05 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 171 TYR 0.016 0.002 TYR E 142 PHE 0.024 0.002 PHE F 99 TRP 0.029 0.002 TRP G 62 HIS 0.002 0.001 HIS C 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.18 (12120) covalent geometry : angle 0.90301 / 0.42 (16472) SS BOND : bond 0.00231 / 0.17 ( 16) SS BOND : angle 2.51795 / 2.28 ( 32) hydrogen bonds : bond 0.03594 / 2.35 ( 809) hydrogen bonds : angle 4.03586 / 2.96 ( 2427) link_NAG-ASN : bond 0.00162 / 0.11 ( 8) link_NAG-ASN : angle 1.87188 / 1.50 ( 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 576 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 515 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.6706 (m-80) REVERT: A 104 GLN cc_start: 0.7505 (mp10) cc_final: 0.7191 (mp10) REVERT: A 108 ILE cc_start: 0.9518 (mt) cc_final: 0.9265 (mt) REVERT: B 32 GLN cc_start: 0.8580 (tp40) cc_final: 0.7823 (tm-30) REVERT: B 68 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6490 (m-80) REVERT: B 104 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7076 (mp-120) REVERT: C 68 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.6654 (m-80) REVERT: C 104 GLN cc_start: 0.7517 (mp10) cc_final: 0.7207 (mp10) REVERT: C 108 ILE cc_start: 0.9521 (mt) cc_final: 0.9274 (mt) REVERT: C 160 LYS cc_start: 0.7545 (tppt) cc_final: 0.7210 (tppt) REVERT: C 191 MET cc_start: 0.8098 (tpp) cc_final: 0.7873 (mmt) REVERT: D 68 TYR cc_start: 0.7340 (OUTLIER) cc_final: 0.6492 (m-80) REVERT: D 104 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7058 (mp-120) REVERT: E 68 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6689 (m-80) REVERT: E 104 GLN cc_start: 0.7518 (mp10) cc_final: 0.7207 (mp10) REVERT: E 108 ILE cc_start: 0.9520 (mt) cc_final: 0.9273 (mt) REVERT: E 160 LYS cc_start: 0.7548 (tppt) cc_final: 0.7203 (tppt) REVERT: F 68 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6421 (m-80) REVERT: F 104 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.6972 (mp-120) REVERT: F 170 SER cc_start: 0.9073 (t) cc_final: 0.8565 (m) REVERT: F 185 CYS cc_start: 0.8694 (m) cc_final: 0.8235 (m) REVERT: G 68 TYR cc_start: 0.7162 (OUTLIER) cc_final: 0.6707 (m-80) REVERT: G 104 GLN cc_start: 0.7511 (mp10) cc_final: 0.7192 (mp10) REVERT: G 108 ILE cc_start: 0.9520 (mt) cc_final: 0.9268 (mt) REVERT: G 160 LYS cc_start: 0.7536 (tppt) cc_final: 0.7192 (tppt) REVERT: H 32 GLN cc_start: 0.8587 (tp40) cc_final: 0.7820 (tm-30) REVERT: H 68 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.6506 (m-80) REVERT: H 104 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7100 (mp-120) REVERT: H 170 SER cc_start: 0.9049 (t) cc_final: 0.8569 (m) REVERT: H 185 CYS cc_start: 0.8728 (m) cc_final: 0.8268 (m) outliers start: 61 outliers final: 48 residues processed: 543 average time/residue: 0.0838 time to fit residues: 66.4810 Evaluate side-chains 569 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 509 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 77 LEU Chi-restraints excluded: chain A residue 181 LEU 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 104 GLN 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 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 77 LEU Chi-restraints excluded: chain C residue 146 SER Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain D residue 46 ASP Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 68 TYR Chi-restraints excluded: chain D residue 104 GLN 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 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 77 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain F residue 40 THR 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 104 GLN 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 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 77 LEU Chi-restraints excluded: chain G residue 146 SER Chi-restraints excluded: chain G residue 180 CYS 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 104 GLN 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 180 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 57 optimal weight: 50.0000 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 117 optimal weight: 0.0870 chunk 55 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN B 143 GLN C 104 GLN ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN E 104 GLN F 143 GLN G 104 GLN ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.151057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.116667 restraints weight = 23520.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.119660 restraints weight = 14071.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.121744 restraints weight = 10529.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.122944 restraints weight = 8886.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.123321 restraints weight = 8079.721| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12144 Z= 0.150 Angle : 0.914 15.220 16528 Z= 0.420 Chirality : 0.046 0.183 1936 Planarity : 0.005 0.055 2024 Dihedral : 4.300 28.743 1624 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.22 % Allowed : 31.29 % Favored : 64.49 % 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: 1.65 (0.22), residues: 1480 helix: 2.03 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -2.04 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 171 TYR 0.021 0.001 TYR D 51 PHE 0.031 0.001 PHE D 99 TRP 0.030 0.002 TRP G 62 HIS 0.001 0.000 HIS G 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (12120) covalent geometry : angle 0.90642 / 0.42 (16472) SS BOND : bond 0.00229 / 0.16 ( 16) SS BOND : angle 2.49532 / 2.07 ( 32) hydrogen bonds : bond 0.03596 / 2.34 ( 809) hydrogen bonds : angle 3.97449 / 2.91 ( 2427) link_NAG-ASN : bond 0.00197 / 0.13 ( 8) link_NAG-ASN : angle 1.91407 / 1.55 ( 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 575 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 524 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.7190 (OUTLIER) cc_final: 0.6770 (m-80) REVERT: B 32 GLN cc_start: 0.8546 (tp40) cc_final: 0.7650 (tm-30) REVERT: B 68 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.6450 (m-80) REVERT: B 103 THR cc_start: 0.8496 (m) cc_final: 0.8190 (p) REVERT: B 104 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.6859 (mp-120) REVERT: C 68 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6772 (m-80) REVERT: C 160 LYS cc_start: 0.7537 (tppt) cc_final: 0.7274 (tppt) REVERT: D 68 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6459 (m-80) REVERT: D 104 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.6966 (mp-120) REVERT: D 160 LYS cc_start: 0.7551 (tppt) cc_final: 0.7284 (tppt) REVERT: E 68 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: E 160 LYS cc_start: 0.7528 (tppt) cc_final: 0.7254 (tppt) REVERT: F 68 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.6439 (m-80) REVERT: F 104 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.6872 (mp-120) REVERT: F 156 LYS cc_start: 0.8080 (mtpt) cc_final: 0.7867 (mtpt) REVERT: F 170 SER cc_start: 0.9081 (t) cc_final: 0.8853 (t) REVERT: G 68 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: G 160 LYS cc_start: 0.7531 (tppt) cc_final: 0.7277 (tppt) REVERT: H 32 GLN cc_start: 0.8559 (tp40) cc_final: 0.7681 (tm-30) REVERT: H 68 TYR cc_start: 0.7410 (OUTLIER) cc_final: 0.6422 (m-80) REVERT: H 103 THR cc_start: 0.8624 (m) cc_final: 0.8255 (p) REVERT: H 104 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.6886 (mp-120) REVERT: H 170 SER cc_start: 0.9091 (t) cc_final: 0.8866 (t) outliers start: 51 outliers final: 34 residues processed: 547 average time/residue: 0.0842 time to fit residues: 67.2163 Evaluate side-chains 556 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 510 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 77 LEU Chi-restraints excluded: chain A residue 181 LEU 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 104 GLN Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 161 ASP 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 77 LEU Chi-restraints excluded: chain C residue 180 CYS 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 104 GLN Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 161 ASP 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 77 LEU Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 104 GLN Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 146 SER 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 77 LEU 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 104 GLN Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 146 SER 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: 0.0270 chunk 143 optimal weight: 0.0370 chunk 55 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 chunk 19 optimal weight: 50.0000 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.152948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.119910 restraints weight = 23167.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.123052 restraints weight = 13882.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.125142 restraints weight = 10255.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.125951 restraints weight = 8573.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.126372 restraints weight = 7871.847| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.6124 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= 0.152 Angle : 0.910 14.676 16528 Z= 0.423 Chirality : 0.045 0.181 1936 Planarity : 0.005 0.054 2024 Dihedral : 4.249 30.295 1624 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.64 % Allowed : 31.79 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.76 (0.22), residues: 1480 helix: 2.10 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -1.99 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 171 TYR 0.020 0.002 TYR G 49 PHE 0.032 0.001 PHE D 99 TRP 0.026 0.001 TRP G 62 HIS 0.001 0.000 HIS E 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (12120) covalent geometry : angle 0.90394 / 0.42 (16472) SS BOND : bond 0.00322 / 0.20 ( 16) SS BOND : angle 2.06739 / 1.77 ( 32) hydrogen bonds : bond 0.03490 / 2.27 ( 809) hydrogen bonds : angle 3.86191 / 2.82 ( 2427) link_NAG-ASN : bond 0.00271 / 0.18 ( 8) link_NAG-ASN : angle 1.81702 / 1.47 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2294.79 seconds wall clock time: 40 minutes 13.41 seconds (2413.41 seconds total)