Starting phenix.real_space_refine on Thu Feb 5 14:44:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umr_42382/02_2026/8umr_42382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umr_42382/02_2026/8umr_42382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8umr_42382/02_2026/8umr_42382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umr_42382/02_2026/8umr_42382.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8umr_42382/02_2026/8umr_42382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umr_42382/02_2026/8umr_42382.map" } resolution = 4.42 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= 0.003 sd= 0.025 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 21 5.16 5 C 11952 2.51 5 N 3120 2.21 5 O 3522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18615 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "B" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Restraints were copied for chains: C, G, I, K, M, Q, U, W, D, F, H, J, L, N, P, R, T, V, X Time building chain proxies: 1.51, per 1000 atoms: 0.08 Number of scatterers: 18615 At special positions: 0 Unit cell: (141.9, 134.2, 105.6, 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 21 16.00 O 3522 8.00 N 3120 7.00 C 11952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 904.4 milliseconds 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4554 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 4 sheets defined 63.1% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 removed outlier: 3.607A pdb=" N LYS A 17 " --> pdb=" O ILE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 34 Processing helix chain 'A' and resid 37 through 52 Processing helix chain 'A' and resid 53 through 68 removed outlier: 3.866A pdb=" N ALA A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 86 Processing helix chain 'A' and resid 88 through 102 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 81 through 95 removed outlier: 4.220A pdb=" N ASP B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 122 Processing helix chain 'C' and resid 3 through 17 removed outlier: 3.608A pdb=" N LYS C 17 " --> pdb=" O ILE C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 34 Processing helix chain 'C' and resid 37 through 52 Processing helix chain 'C' and resid 53 through 68 removed outlier: 3.865A pdb=" N ALA C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 88 through 102 Processing helix chain 'C' and resid 105 through 121 Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 81 through 95 removed outlier: 4.222A pdb=" N ASP D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 81 through 95 removed outlier: 4.221A pdb=" N ASP F 85 " --> pdb=" O ARG F 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA F 86 " --> pdb=" O GLU F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 122 Processing helix chain 'G' and resid 3 through 17 removed outlier: 3.608A pdb=" N LYS G 17 " --> pdb=" O ILE G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 34 Processing helix chain 'G' and resid 37 through 52 Processing helix chain 'G' and resid 53 through 68 removed outlier: 3.866A pdb=" N ALA G 57 " --> pdb=" O ASN G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 86 Processing helix chain 'G' and resid 88 through 102 Processing helix chain 'G' and resid 105 through 121 Processing helix chain 'H' and resid 32 through 46 Processing helix chain 'H' and resid 81 through 95 removed outlier: 4.221A pdb=" N ASP H 85 " --> pdb=" O ARG H 81 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ALA H 86 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 122 Processing helix chain 'I' and resid 3 through 17 removed outlier: 3.608A pdb=" N LYS I 17 " --> pdb=" O ILE I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 34 Processing helix chain 'I' and resid 37 through 52 Processing helix chain 'I' and resid 53 through 68 removed outlier: 3.866A pdb=" N ALA I 57 " --> pdb=" O ASN I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 86 Processing helix chain 'I' and resid 88 through 102 Processing helix chain 'I' and resid 105 through 121 Processing helix chain 'J' and resid 32 through 46 Processing helix chain 'J' and resid 81 through 95 removed outlier: 4.222A pdb=" N ASP J 85 " --> pdb=" O ARG J 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA J 86 " --> pdb=" O GLU J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 122 Processing helix chain 'K' and resid 3 through 17 removed outlier: 3.607A pdb=" N LYS K 17 " --> pdb=" O ILE K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 34 Processing helix chain 'K' and resid 37 through 52 Processing helix chain 'K' and resid 53 through 68 removed outlier: 3.866A pdb=" N ALA K 57 " --> pdb=" O ASN K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 86 Processing helix chain 'K' and resid 88 through 102 Processing helix chain 'K' and resid 105 through 121 Processing helix chain 'L' and resid 32 through 46 Processing helix chain 'L' and resid 81 through 95 removed outlier: 4.222A pdb=" N ASP L 85 " --> pdb=" O ARG L 81 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA L 86 " --> pdb=" O GLU L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 122 Processing helix chain 'M' and resid 3 through 17 removed outlier: 3.608A pdb=" N LYS M 17 " --> pdb=" O ILE M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 34 Processing helix chain 'M' and resid 37 through 52 Processing helix chain 'M' and resid 53 through 68 removed outlier: 3.867A pdb=" N ALA M 57 " --> pdb=" O ASN M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 86 Processing helix chain 'M' and resid 88 through 102 Processing helix chain 'M' and resid 105 through 121 Processing helix chain 'N' and resid 32 through 46 Processing helix chain 'N' and resid 81 through 95 removed outlier: 4.221A pdb=" N ASP N 85 " --> pdb=" O ARG N 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA N 86 " --> pdb=" O GLU N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 122 Processing helix chain 'P' and resid 32 through 46 Processing helix chain 'P' and resid 81 through 95 removed outlier: 4.222A pdb=" N ASP P 85 " --> pdb=" O ARG P 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA P 86 " --> pdb=" O GLU P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 122 Processing helix chain 'Q' and resid 3 through 17 removed outlier: 3.608A pdb=" N LYS Q 17 " --> pdb=" O ILE Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 34 Processing helix chain 'Q' and resid 37 through 52 Processing helix chain 'Q' and resid 53 through 68 removed outlier: 3.865A pdb=" N ALA Q 57 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 86 Processing helix chain 'Q' and resid 88 through 102 Processing helix chain 'Q' and resid 105 through 121 Processing helix chain 'R' and resid 32 through 46 Processing helix chain 'R' and resid 81 through 95 removed outlier: 4.221A pdb=" N ASP R 85 " --> pdb=" O ARG R 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA R 86 " --> pdb=" O GLU R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 122 Processing helix chain 'T' and resid 32 through 46 Processing helix chain 'T' and resid 81 through 95 removed outlier: 4.221A pdb=" N ASP T 85 " --> pdb=" O ARG T 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA T 86 " --> pdb=" O GLU T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 112 through 122 Processing helix chain 'U' and resid 3 through 17 removed outlier: 3.608A pdb=" N LYS U 17 " --> pdb=" O ILE U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 34 Processing helix chain 'U' and resid 37 through 52 Processing helix chain 'U' and resid 53 through 68 removed outlier: 3.866A pdb=" N ALA U 57 " --> pdb=" O ASN U 53 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 86 Processing helix chain 'U' and resid 88 through 102 Processing helix chain 'U' and resid 105 through 121 Processing helix chain 'V' and resid 32 through 46 Processing helix chain 'V' and resid 81 through 95 removed outlier: 4.221A pdb=" N ASP V 85 " --> pdb=" O ARG V 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA V 86 " --> pdb=" O GLU V 82 " (cutoff:3.500A) Processing helix chain 'V' and resid 112 through 122 Processing helix chain 'W' and resid 3 through 17 removed outlier: 3.607A pdb=" N LYS W 17 " --> pdb=" O ILE W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 34 Processing helix chain 'W' and resid 37 through 52 Processing helix chain 'W' and resid 53 through 68 removed outlier: 3.866A pdb=" N ALA W 57 " --> pdb=" O ASN W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 86 Processing helix chain 'W' and resid 88 through 102 Processing helix chain 'W' and resid 105 through 121 Processing helix chain 'X' and resid 32 through 46 Processing helix chain 'X' and resid 81 through 95 removed outlier: 4.221A pdb=" N ASP X 85 " --> pdb=" O ARG X 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA X 86 " --> pdb=" O GLU X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 122 Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 19 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 17 through 19 current: chain 'B' and resid 66 through 80 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 66 through 80 current: chain 'N' and resid 66 through 80 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 66 through 80 current: chain 'T' and resid 66 through 80 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 17 through 19 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 17 through 19 current: chain 'D' and resid 66 through 80 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 66 through 80 current: chain 'J' and resid 66 through 80 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 66 through 80 current: chain 'V' and resid 66 through 80 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 17 through 19 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 17 through 19 current: chain 'F' and resid 66 through 80 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 66 through 80 current: chain 'L' and resid 66 through 80 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 66 through 80 current: chain 'R' and resid 66 through 80 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 17 through 19 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 17 through 19 current: chain 'H' and resid 66 through 80 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 66 through 80 current: chain 'P' and resid 66 through 80 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 66 through 80 current: chain 'X' and resid 66 through 80 No H-bonds generated for sheet with id=AA4 1054 hydrogen bonds defined for protein. 3162 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5769 1.34 - 1.45: 2229 1.45 - 1.57: 10905 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 18933 Sorted by residual: bond pdb=" N ASN P 64 " pdb=" CA ASN P 64 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.83e+00 bond pdb=" N ASN H 64 " pdb=" CA ASN H 64 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.76e+00 bond pdb=" N ASN D 64 " pdb=" CA ASN D 64 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.76e+00 bond pdb=" N ASN T 64 " pdb=" CA ASN T 64 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.73e+00 bond pdb=" N ASN B 64 " pdb=" CA ASN B 64 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.68e+00 ... (remaining 18928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 24420 1.62 - 3.23: 1032 3.23 - 4.85: 252 4.85 - 6.47: 27 6.47 - 8.08: 30 Bond angle restraints: 25761 Sorted by residual: angle pdb=" N GLN M 62 " pdb=" CA GLN M 62 " pdb=" CB GLN M 62 " ideal model delta sigma weight residual 110.28 115.63 -5.35 1.55e+00 4.16e-01 1.19e+01 angle pdb=" N GLN C 62 " pdb=" CA GLN C 62 " pdb=" CB GLN C 62 " ideal model delta sigma weight residual 110.28 115.61 -5.33 1.55e+00 4.16e-01 1.18e+01 angle pdb=" N GLN A 62 " pdb=" CA GLN A 62 " pdb=" CB GLN A 62 " ideal model delta sigma weight residual 110.28 115.60 -5.32 1.55e+00 4.16e-01 1.18e+01 angle pdb=" N GLN W 62 " pdb=" CA GLN W 62 " pdb=" CB GLN W 62 " ideal model delta sigma weight residual 110.28 115.60 -5.32 1.55e+00 4.16e-01 1.18e+01 angle pdb=" N GLN G 62 " pdb=" CA GLN G 62 " pdb=" CB GLN G 62 " ideal model delta sigma weight residual 110.28 115.59 -5.31 1.55e+00 4.16e-01 1.17e+01 ... (remaining 25756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.42: 9504 10.42 - 20.83: 1098 20.83 - 31.25: 754 31.25 - 41.66: 137 41.66 - 52.08: 36 Dihedral angle restraints: 11529 sinusoidal: 4506 harmonic: 7023 Sorted by residual: dihedral pdb=" CA ASN G 53 " pdb=" C ASN G 53 " pdb=" N TYR G 54 " pdb=" CA TYR G 54 " ideal model delta harmonic sigma weight residual -180.00 -159.88 -20.12 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ASN U 53 " pdb=" C ASN U 53 " pdb=" N TYR U 54 " pdb=" CA TYR U 54 " ideal model delta harmonic sigma weight residual -180.00 -159.89 -20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ASN A 53 " pdb=" C ASN A 53 " pdb=" N TYR A 54 " pdb=" CA TYR A 54 " ideal model delta harmonic sigma weight residual -180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 11526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2056 0.037 - 0.075: 693 0.075 - 0.112: 222 0.112 - 0.149: 68 0.149 - 0.186: 12 Chirality restraints: 3051 Sorted by residual: chirality pdb=" CG LEU T 53 " pdb=" CB LEU T 53 " pdb=" CD1 LEU T 53 " pdb=" CD2 LEU T 53 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CG LEU H 53 " pdb=" CB LEU H 53 " pdb=" CD1 LEU H 53 " pdb=" CD2 LEU H 53 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CG LEU B 53 " pdb=" CB LEU B 53 " pdb=" CD1 LEU B 53 " pdb=" CD2 LEU B 53 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.18 2.00e-01 2.50e+01 8.56e-01 ... (remaining 3048 not shown) Planarity restraints: 3249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 38 " 0.007 2.00e-02 2.50e+03 1.46e-02 4.25e+00 pdb=" CG TYR J 38 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR J 38 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR J 38 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR J 38 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR J 38 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR J 38 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR J 38 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 38 " 0.007 2.00e-02 2.50e+03 1.45e-02 4.22e+00 pdb=" CG TYR R 38 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR R 38 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR R 38 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR R 38 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR R 38 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR R 38 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 38 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 38 " 0.007 2.00e-02 2.50e+03 1.45e-02 4.18e+00 pdb=" CG TYR F 38 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR F 38 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR F 38 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR F 38 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 38 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 38 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 38 " -0.001 2.00e-02 2.50e+03 ... (remaining 3246 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 484 2.62 - 3.19: 19027 3.19 - 3.76: 33025 3.76 - 4.33: 41605 4.33 - 4.90: 64594 Nonbonded interactions: 158735 Sorted by model distance: nonbonded pdb=" O ALA K 110 " pdb=" OH TYR L 38 " model vdw 2.052 3.040 nonbonded pdb=" O VAL N 52 " pdb=" NH2 ARG T 61 " model vdw 2.167 3.120 nonbonded pdb=" O ALA C 110 " pdb=" OH TYR D 38 " model vdw 2.172 3.040 nonbonded pdb=" NH2 ARG H 61 " pdb=" O VAL X 52 " model vdw 2.202 3.120 nonbonded pdb=" OH TYR A 54 " pdb=" NH1 ARG B 93 " model vdw 2.217 3.120 ... (remaining 158730 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'Q' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.830 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 0.032 18933 Z= 0.202 Angle : 0.822 8.084 25761 Z= 0.449 Chirality : 0.045 0.186 3051 Planarity : 0.007 0.048 3249 Dihedral : 12.523 52.077 6975 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 27.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % 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: -0.03 (0.16), residues: 2322 helix: 0.38 (0.13), residues: 1437 sheet: -0.07 (0.27), residues: 300 loop : -0.68 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 61 TYR 0.034 0.004 TYR R 38 PHE 0.017 0.003 PHE D 77 TRP 0.007 0.001 TRP F 117 HIS 0.001 0.000 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00417 (18933) covalent geometry : angle 0.82212 (25761) hydrogen bonds : bond 0.14702 ( 1054) hydrogen bonds : angle 5.82419 ( 3162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 775 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 113 LYS cc_start: 0.9703 (tttt) cc_final: 0.9422 (mttt) REVERT: B 24 ARG cc_start: 0.9099 (mpt180) cc_final: 0.8193 (mmt-90) REVERT: B 52 VAL cc_start: 0.8383 (m) cc_final: 0.7413 (m) REVERT: B 103 LEU cc_start: 0.9333 (mt) cc_final: 0.8685 (mp) REVERT: C 14 GLU cc_start: 0.9508 (tp30) cc_final: 0.9005 (tp30) REVERT: C 80 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8244 (pt0) REVERT: D 26 LEU cc_start: 0.9624 (tp) cc_final: 0.9404 (tp) REVERT: D 28 THR cc_start: 0.8695 (m) cc_final: 0.8350 (m) REVERT: D 52 VAL cc_start: 0.9408 (m) cc_final: 0.9194 (m) REVERT: D 63 GLU cc_start: 0.8911 (tp30) cc_final: 0.8144 (pm20) REVERT: D 66 LYS cc_start: 0.8895 (mptt) cc_final: 0.8552 (mmmm) REVERT: D 68 VAL cc_start: 0.9536 (p) cc_final: 0.9192 (m) REVERT: D 80 THR cc_start: 0.9677 (p) cc_final: 0.9440 (p) REVERT: D 83 ARG cc_start: 0.8787 (tpp80) cc_final: 0.8414 (ttt180) REVERT: D 95 HIS cc_start: 0.7394 (t-90) cc_final: 0.6904 (t-170) REVERT: F 85 ASP cc_start: 0.9290 (m-30) cc_final: 0.8846 (t70) REVERT: F 116 ASP cc_start: 0.8510 (m-30) cc_final: 0.8226 (p0) REVERT: F 119 ARG cc_start: 0.5043 (tpm170) cc_final: 0.4475 (ptm-80) REVERT: G 20 TYR cc_start: 0.8927 (m-10) cc_final: 0.8665 (m-10) REVERT: G 68 ASP cc_start: 0.8380 (t0) cc_final: 0.8099 (p0) REVERT: G 78 LEU cc_start: 0.9543 (tp) cc_final: 0.9243 (tp) REVERT: G 99 LEU cc_start: 0.9411 (pp) cc_final: 0.9202 (pp) REVERT: H 101 GLU cc_start: 0.8763 (tp30) cc_final: 0.8271 (tp30) REVERT: H 103 LEU cc_start: 0.9035 (mt) cc_final: 0.8582 (mp) REVERT: K 14 GLU cc_start: 0.9100 (tp30) cc_final: 0.8440 (tp30) REVERT: K 19 ASN cc_start: 0.8803 (m110) cc_final: 0.8165 (m110) REVERT: K 22 THR cc_start: 0.9438 (p) cc_final: 0.8988 (p) REVERT: L 26 LEU cc_start: 0.9592 (tp) cc_final: 0.9314 (tp) REVERT: L 39 LEU cc_start: 0.9530 (mm) cc_final: 0.9121 (pp) REVERT: L 73 TYR cc_start: 0.8900 (m-80) cc_final: 0.8490 (m-80) REVERT: L 75 LEU cc_start: 0.9606 (mt) cc_final: 0.9300 (mt) REVERT: L 77 PHE cc_start: 0.9171 (m-10) cc_final: 0.8507 (m-80) REVERT: L 90 TRP cc_start: 0.9342 (t60) cc_final: 0.9131 (t60) REVERT: N 75 LEU cc_start: 0.9408 (mt) cc_final: 0.8854 (tp) REVERT: P 24 ARG cc_start: 0.8405 (mpt180) cc_final: 0.8076 (mmt-90) REVERT: P 55 THR cc_start: 0.9046 (p) cc_final: 0.8819 (t) REVERT: P 94 ARG cc_start: 0.8511 (tpm170) cc_final: 0.7830 (tpm170) REVERT: R 25 LEU cc_start: 0.9542 (mm) cc_final: 0.9293 (mm) REVERT: R 71 ASP cc_start: 0.8662 (m-30) cc_final: 0.8049 (t0) REVERT: T 26 LEU cc_start: 0.9532 (tp) cc_final: 0.9130 (tp) REVERT: T 101 GLU cc_start: 0.8516 (tp30) cc_final: 0.8166 (mp0) REVERT: U 14 GLU cc_start: 0.9189 (tp30) cc_final: 0.8670 (tp30) REVERT: U 93 GLU cc_start: 0.9323 (mp0) cc_final: 0.9018 (mp0) REVERT: V 24 ARG cc_start: 0.8508 (mpt180) cc_final: 0.7835 (mmt-90) REVERT: V 52 VAL cc_start: 0.7939 (m) cc_final: 0.7430 (m) REVERT: V 87 LEU cc_start: 0.9576 (tt) cc_final: 0.9307 (pp) REVERT: W 39 GLU cc_start: 0.9375 (mp0) cc_final: 0.9075 (mp0) REVERT: X 24 ARG cc_start: 0.8700 (mpt180) cc_final: 0.8439 (mmt-90) REVERT: X 26 LEU cc_start: 0.9527 (tp) cc_final: 0.9222 (tp) REVERT: X 75 LEU cc_start: 0.9562 (mt) cc_final: 0.9286 (pp) REVERT: X 103 LEU cc_start: 0.9262 (mt) cc_final: 0.8843 (mt) outliers start: 0 outliers final: 0 residues processed: 775 average time/residue: 0.1535 time to fit residues: 168.6660 Evaluate side-chains 446 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.0040 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.0870 overall best weight: 1.2374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 43 ASN C 19 ASN C 43 ASN G 19 ASN G 43 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 ASN I 43 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 ASN K 43 ASN K 77 ASN M 19 ASN M 43 ASN Q 19 ASN Q 43 ASN U 19 ASN U 43 ASN U 77 ASN W 19 ASN ** W 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.060572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.045384 restraints weight = 105467.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.046843 restraints weight = 75958.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.047974 restraints weight = 58633.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.048701 restraints weight = 47742.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.049489 restraints weight = 40835.654| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18933 Z= 0.149 Angle : 0.726 10.189 25761 Z= 0.368 Chirality : 0.043 0.150 3051 Planarity : 0.006 0.081 3249 Dihedral : 4.419 22.395 2601 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.47 % Allowed : 6.83 % Favored : 92.70 % 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: 0.55 (0.17), residues: 2322 helix: 0.95 (0.13), residues: 1494 sheet: 0.30 (0.28), residues: 300 loop : -1.09 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 93 TYR 0.032 0.003 TYR G 82 PHE 0.020 0.003 PHE W 95 TRP 0.017 0.001 TRP J 90 HIS 0.006 0.001 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00324 (18933) covalent geometry : angle 0.72570 (25761) hydrogen bonds : bond 0.04946 ( 1054) hydrogen bonds : angle 4.43168 ( 3162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 594 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 53 ASN cc_start: 0.8641 (t0) cc_final: 0.8414 (t0) REVERT: A 59 GLU cc_start: 0.9333 (pt0) cc_final: 0.8945 (pp20) REVERT: A 95 PHE cc_start: 0.8949 (m-80) cc_final: 0.8740 (m-10) REVERT: B 28 THR cc_start: 0.8314 (m) cc_final: 0.7654 (m) REVERT: B 38 TYR cc_start: 0.7435 (m-80) cc_final: 0.7030 (m-80) REVERT: B 52 VAL cc_start: 0.8278 (m) cc_final: 0.7537 (m) REVERT: B 57 VAL cc_start: 0.9049 (t) cc_final: 0.8665 (m) REVERT: B 79 THR cc_start: 0.9292 (p) cc_final: 0.8862 (p) REVERT: B 101 GLU cc_start: 0.9117 (tp30) cc_final: 0.8726 (tp30) REVERT: B 108 ILE cc_start: 0.8868 (tp) cc_final: 0.8666 (tp) REVERT: C 14 GLU cc_start: 0.9514 (tp30) cc_final: 0.9156 (tp30) REVERT: C 80 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7777 (pt0) REVERT: D 26 LEU cc_start: 0.9532 (tp) cc_final: 0.9331 (tp) REVERT: D 28 THR cc_start: 0.8747 (m) cc_final: 0.7851 (m) REVERT: D 80 THR cc_start: 0.9600 (p) cc_final: 0.9383 (p) REVERT: D 94 ARG cc_start: 0.9311 (tpm170) cc_final: 0.8982 (tpm170) REVERT: D 101 GLU cc_start: 0.8801 (tp30) cc_final: 0.7917 (tp30) REVERT: D 118 LEU cc_start: 0.9627 (mp) cc_final: 0.9367 (pp) REVERT: F 38 TYR cc_start: 0.8963 (m-80) cc_final: 0.8646 (m-10) REVERT: F 71 ASP cc_start: 0.9067 (m-30) cc_final: 0.8297 (t0) REVERT: F 119 ARG cc_start: 0.5353 (tpm170) cc_final: 0.4830 (ptm-80) REVERT: G 7 MET cc_start: 0.8282 (ptt) cc_final: 0.7862 (ttp) REVERT: H 101 GLU cc_start: 0.9145 (tp30) cc_final: 0.8543 (tp30) REVERT: H 103 LEU cc_start: 0.9037 (mt) cc_final: 0.8835 (mt) REVERT: J 46 LYS cc_start: 0.8935 (ptpp) cc_final: 0.8435 (pttt) REVERT: K 14 GLU cc_start: 0.9177 (tp30) cc_final: 0.8265 (tp30) REVERT: K 19 ASN cc_start: 0.8687 (m-40) cc_final: 0.8022 (m-40) REVERT: K 22 THR cc_start: 0.9435 (p) cc_final: 0.9146 (p) REVERT: L 39 LEU cc_start: 0.9566 (mm) cc_final: 0.9157 (pp) REVERT: L 48 LEU cc_start: 0.9008 (mt) cc_final: 0.8254 (tp) REVERT: L 73 TYR cc_start: 0.8872 (m-80) cc_final: 0.8452 (m-10) REVERT: M 112 LEU cc_start: 0.9366 (mt) cc_final: 0.9131 (mt) REVERT: N 75 LEU cc_start: 0.9537 (mt) cc_final: 0.9079 (tp) REVERT: N 85 ASP cc_start: 0.9125 (p0) cc_final: 0.8916 (p0) REVERT: N 92 GLN cc_start: 0.9099 (mt0) cc_final: 0.8870 (pp30) REVERT: P 79 THR cc_start: 0.7557 (m) cc_final: 0.6956 (m) REVERT: P 101 GLU cc_start: 0.8056 (tp30) cc_final: 0.7067 (mp0) REVERT: Q 95 PHE cc_start: 0.8868 (m-80) cc_final: 0.8405 (m-80) REVERT: Q 97 LYS cc_start: 0.9527 (mtpt) cc_final: 0.9324 (ptpt) REVERT: R 45 GLU cc_start: 0.9175 (pp20) cc_final: 0.8639 (pp20) REVERT: R 46 LYS cc_start: 0.8900 (pttp) cc_final: 0.8637 (pttp) REVERT: R 63 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8048 (mm-30) REVERT: R 70 GLU cc_start: 0.9263 (mp0) cc_final: 0.9052 (pm20) REVERT: R 71 ASP cc_start: 0.8845 (m-30) cc_final: 0.8173 (t0) REVERT: T 101 GLU cc_start: 0.9040 (tp30) cc_final: 0.8802 (mp0) REVERT: U 95 PHE cc_start: 0.9397 (m-80) cc_final: 0.9177 (m-10) REVERT: V 22 ASP cc_start: 0.7900 (t0) cc_final: 0.7460 (t0) REVERT: V 24 ARG cc_start: 0.8554 (mpt180) cc_final: 0.7883 (mmt-90) REVERT: V 52 VAL cc_start: 0.8004 (m) cc_final: 0.7775 (m) REVERT: W 39 GLU cc_start: 0.9286 (mp0) cc_final: 0.9055 (mp0) REVERT: X 17 LEU cc_start: 0.8201 (tt) cc_final: 0.7993 (mm) REVERT: X 26 LEU cc_start: 0.9637 (tp) cc_final: 0.9406 (tp) REVERT: X 103 LEU cc_start: 0.9355 (mt) cc_final: 0.9132 (mm) outliers start: 9 outliers final: 7 residues processed: 599 average time/residue: 0.1333 time to fit residues: 118.2419 Evaluate side-chains 418 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 411 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 158 optimal weight: 0.9990 chunk 150 optimal weight: 30.0000 chunk 131 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 104 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 ASN I 77 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN K 90 ASN M 43 ASN Q 43 ASN U 43 ASN W 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.059567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.044744 restraints weight = 109913.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.046161 restraints weight = 78272.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.047253 restraints weight = 60461.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.048107 restraints weight = 49186.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.048748 restraints weight = 41722.268| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18933 Z= 0.148 Angle : 0.697 9.323 25761 Z= 0.353 Chirality : 0.041 0.142 3051 Planarity : 0.005 0.039 3249 Dihedral : 4.351 22.615 2601 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.10 % Allowed : 6.10 % Favored : 93.79 % 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: 0.67 (0.17), residues: 2322 helix: 1.00 (0.13), residues: 1458 sheet: 0.40 (0.29), residues: 300 loop : -0.79 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 24 TYR 0.028 0.003 TYR W 61 PHE 0.016 0.002 PHE W 95 TRP 0.009 0.001 TRP W 41 HIS 0.004 0.001 HIS T 95 Details of bonding type rmsd covalent geometry : bond 0.00319 (18933) covalent geometry : angle 0.69737 (25761) hydrogen bonds : bond 0.04512 ( 1054) hydrogen bonds : angle 4.38825 ( 3162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 516 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 PHE cc_start: 0.8927 (m-80) cc_final: 0.8707 (m-10) REVERT: B 24 ARG cc_start: 0.8777 (mpt180) cc_final: 0.7895 (mpt90) REVERT: B 38 TYR cc_start: 0.7407 (m-80) cc_final: 0.7104 (m-80) REVERT: B 57 VAL cc_start: 0.9143 (t) cc_final: 0.8821 (m) REVERT: B 79 THR cc_start: 0.9245 (p) cc_final: 0.8698 (p) REVERT: B 81 ARG cc_start: 0.8481 (ptt-90) cc_final: 0.8055 (ptt-90) REVERT: B 95 HIS cc_start: 0.6459 (t-170) cc_final: 0.5485 (t-170) REVERT: C 14 GLU cc_start: 0.9525 (tp30) cc_final: 0.9145 (tp30) REVERT: C 28 THR cc_start: 0.9680 (p) cc_final: 0.9470 (p) REVERT: C 61 TYR cc_start: 0.8353 (m-10) cc_final: 0.7977 (m-80) REVERT: D 22 ASP cc_start: 0.8149 (t0) cc_final: 0.7624 (t0) REVERT: D 28 THR cc_start: 0.8735 (m) cc_final: 0.8413 (m) REVERT: D 80 THR cc_start: 0.9527 (p) cc_final: 0.9321 (p) REVERT: D 118 LEU cc_start: 0.9619 (mp) cc_final: 0.9383 (pp) REVERT: F 38 TYR cc_start: 0.9029 (m-80) cc_final: 0.8737 (m-10) REVERT: F 71 ASP cc_start: 0.9122 (m-30) cc_final: 0.8410 (t0) REVERT: F 116 ASP cc_start: 0.9022 (p0) cc_final: 0.8690 (m-30) REVERT: F 119 ARG cc_start: 0.5570 (tpm170) cc_final: 0.4823 (ptm-80) REVERT: G 7 MET cc_start: 0.8240 (ptt) cc_final: 0.7874 (ttp) REVERT: G 20 TYR cc_start: 0.8602 (m-80) cc_final: 0.8400 (m-10) REVERT: G 82 TYR cc_start: 0.8797 (m-80) cc_final: 0.8593 (m-80) REVERT: H 22 ASP cc_start: 0.8907 (t0) cc_final: 0.8651 (t0) REVERT: H 26 LEU cc_start: 0.9089 (tp) cc_final: 0.8882 (tp) REVERT: H 101 GLU cc_start: 0.9211 (tp30) cc_final: 0.8773 (mp0) REVERT: J 22 ASP cc_start: 0.8655 (p0) cc_final: 0.8105 (t0) REVERT: J 63 GLU cc_start: 0.8655 (pm20) cc_final: 0.8426 (pm20) REVERT: K 14 GLU cc_start: 0.9189 (tp30) cc_final: 0.8370 (tp30) REVERT: K 19 ASN cc_start: 0.8761 (m-40) cc_final: 0.7994 (m110) REVERT: K 22 THR cc_start: 0.9471 (p) cc_final: 0.9230 (p) REVERT: K 39 GLU cc_start: 0.9438 (mp0) cc_final: 0.9172 (mp0) REVERT: K 78 LEU cc_start: 0.9499 (tp) cc_final: 0.9298 (tp) REVERT: L 39 LEU cc_start: 0.9607 (mm) cc_final: 0.9217 (pp) REVERT: L 73 TYR cc_start: 0.9023 (m-80) cc_final: 0.8628 (m-10) REVERT: M 93 GLU cc_start: 0.9424 (pt0) cc_final: 0.9111 (pt0) REVERT: M 112 LEU cc_start: 0.9412 (mt) cc_final: 0.9096 (mt) REVERT: N 29 THR cc_start: 0.9354 (t) cc_final: 0.9123 (m) REVERT: N 45 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8661 (mm-30) REVERT: N 92 GLN cc_start: 0.9154 (mt0) cc_final: 0.8713 (tp40) REVERT: P 24 ARG cc_start: 0.8604 (mpt180) cc_final: 0.8386 (mmt-90) REVERT: P 38 TYR cc_start: 0.5938 (m-80) cc_final: 0.5734 (m-80) REVERT: P 63 GLU cc_start: 0.8551 (mp0) cc_final: 0.8310 (mp0) REVERT: P 101 GLU cc_start: 0.8111 (tp30) cc_final: 0.7315 (mp0) REVERT: Q 95 PHE cc_start: 0.8873 (m-80) cc_final: 0.8335 (m-80) REVERT: R 45 GLU cc_start: 0.9199 (pp20) cc_final: 0.8687 (pp20) REVERT: R 70 GLU cc_start: 0.9271 (mp0) cc_final: 0.8870 (mp0) REVERT: R 71 ASP cc_start: 0.9042 (m-30) cc_final: 0.8150 (t0) REVERT: R 91 LEU cc_start: 0.9358 (tp) cc_final: 0.9128 (tp) REVERT: T 101 GLU cc_start: 0.9141 (tp30) cc_final: 0.8821 (mp0) REVERT: U 61 TYR cc_start: 0.8858 (m-80) cc_final: 0.8169 (m-80) REVERT: U 95 PHE cc_start: 0.9391 (m-80) cc_final: 0.9018 (m-10) REVERT: V 22 ASP cc_start: 0.7975 (t0) cc_final: 0.7549 (t0) REVERT: V 24 ARG cc_start: 0.8623 (mpt180) cc_final: 0.7910 (mmt-90) REVERT: V 28 THR cc_start: 0.8553 (m) cc_final: 0.8095 (m) REVERT: V 87 LEU cc_start: 0.9578 (tt) cc_final: 0.9274 (pp) REVERT: V 91 LEU cc_start: 0.9435 (tp) cc_final: 0.9229 (tp) REVERT: W 61 TYR cc_start: 0.8807 (m-80) cc_final: 0.8537 (m-80) REVERT: W 97 LYS cc_start: 0.9721 (mtpt) cc_final: 0.9307 (mmmt) REVERT: X 17 LEU cc_start: 0.8320 (tt) cc_final: 0.7979 (mm) REVERT: X 26 LEU cc_start: 0.9636 (tp) cc_final: 0.9356 (tp) REVERT: X 103 LEU cc_start: 0.9368 (mt) cc_final: 0.9160 (mm) outliers start: 2 outliers final: 1 residues processed: 517 average time/residue: 0.1228 time to fit residues: 96.1423 Evaluate side-chains 384 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 383 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 146 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 161 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 90 ASN ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN F 92 GLN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 ASN I 90 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN M 43 ASN Q 43 ASN Q 90 ASN U 43 ASN W 77 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.057054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.042378 restraints weight = 114048.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.043778 restraints weight = 80559.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.044875 restraints weight = 61450.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.045706 restraints weight = 49741.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.046324 restraints weight = 41941.036| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18933 Z= 0.155 Angle : 0.679 10.279 25761 Z= 0.348 Chirality : 0.041 0.174 3051 Planarity : 0.005 0.069 3249 Dihedral : 4.407 23.070 2601 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.05 % Allowed : 6.78 % Favored : 93.17 % 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: 0.59 (0.17), residues: 2322 helix: 1.08 (0.13), residues: 1458 sheet: -0.30 (0.28), residues: 276 loop : -0.83 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 93 TYR 0.042 0.003 TYR K 48 PHE 0.013 0.002 PHE C 95 TRP 0.013 0.001 TRP D 117 HIS 0.003 0.001 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00329 (18933) covalent geometry : angle 0.67863 (25761) hydrogen bonds : bond 0.04309 ( 1054) hydrogen bonds : angle 4.31238 ( 3162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 491 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.8639 (t0) cc_final: 0.8376 (t0) REVERT: A 95 PHE cc_start: 0.8906 (m-80) cc_final: 0.8659 (m-80) REVERT: B 45 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8467 (mm-30) REVERT: B 57 VAL cc_start: 0.9217 (t) cc_final: 0.8917 (m) REVERT: C 14 GLU cc_start: 0.9511 (tp30) cc_final: 0.9210 (tp30) REVERT: D 22 ASP cc_start: 0.8260 (t0) cc_final: 0.7651 (t0) REVERT: D 80 THR cc_start: 0.9517 (p) cc_final: 0.9274 (p) REVERT: D 118 LEU cc_start: 0.9603 (mp) cc_final: 0.9363 (pp) REVERT: F 38 TYR cc_start: 0.8859 (m-80) cc_final: 0.8640 (m-80) REVERT: F 71 ASP cc_start: 0.9112 (m-30) cc_final: 0.8451 (t0) REVERT: F 116 ASP cc_start: 0.8998 (p0) cc_final: 0.8625 (m-30) REVERT: F 119 ARG cc_start: 0.5056 (tpm170) cc_final: 0.4240 (ptm-80) REVERT: G 7 MET cc_start: 0.8282 (ptt) cc_final: 0.7828 (ttp) REVERT: G 61 TYR cc_start: 0.8006 (m-80) cc_final: 0.7711 (m-80) REVERT: G 82 TYR cc_start: 0.8754 (m-80) cc_final: 0.8371 (m-80) REVERT: H 22 ASP cc_start: 0.8831 (t0) cc_final: 0.8588 (t0) REVERT: H 101 GLU cc_start: 0.9154 (tp30) cc_final: 0.8737 (mp0) REVERT: H 119 ARG cc_start: 0.8872 (tpm170) cc_final: 0.8652 (tpm170) REVERT: J 20 THR cc_start: 0.7644 (t) cc_final: 0.6280 (t) REVERT: J 22 ASP cc_start: 0.8874 (p0) cc_final: 0.8171 (t0) REVERT: K 39 GLU cc_start: 0.9468 (mp0) cc_final: 0.9200 (mp0) REVERT: K 68 ASP cc_start: 0.8309 (t0) cc_final: 0.8056 (t0) REVERT: L 22 ASP cc_start: 0.7541 (t0) cc_final: 0.7211 (t0) REVERT: L 23 LEU cc_start: 0.9280 (mm) cc_final: 0.8997 (mm) REVERT: L 24 ARG cc_start: 0.8373 (mpt180) cc_final: 0.8096 (mpt90) REVERT: L 39 LEU cc_start: 0.9631 (mm) cc_final: 0.9334 (pp) REVERT: L 73 TYR cc_start: 0.9058 (m-80) cc_final: 0.8551 (m-10) REVERT: L 106 THR cc_start: 0.8296 (m) cc_final: 0.7912 (m) REVERT: N 48 LEU cc_start: 0.9337 (mm) cc_final: 0.8544 (tt) REVERT: N 92 GLN cc_start: 0.9211 (mt0) cc_final: 0.8780 (tp40) REVERT: P 63 GLU cc_start: 0.8588 (mp0) cc_final: 0.8356 (mp0) REVERT: Q 68 ASP cc_start: 0.9067 (t0) cc_final: 0.8841 (t0) REVERT: Q 95 PHE cc_start: 0.9024 (m-80) cc_final: 0.8492 (m-80) REVERT: R 45 GLU cc_start: 0.9207 (pp20) cc_final: 0.8685 (pp20) REVERT: T 101 GLU cc_start: 0.9174 (tp30) cc_final: 0.8872 (mp0) REVERT: U 61 TYR cc_start: 0.8881 (m-80) cc_final: 0.8276 (m-80) REVERT: U 95 PHE cc_start: 0.9417 (m-80) cc_final: 0.8961 (m-10) REVERT: V 22 ASP cc_start: 0.8255 (t0) cc_final: 0.7834 (t0) REVERT: V 24 ARG cc_start: 0.8679 (mpt180) cc_final: 0.7813 (mmt-90) REVERT: V 87 LEU cc_start: 0.9581 (tt) cc_final: 0.9328 (pp) REVERT: V 104 VAL cc_start: 0.9656 (m) cc_final: 0.9439 (p) REVERT: W 97 LYS cc_start: 0.9605 (mtpt) cc_final: 0.9270 (mttt) REVERT: X 26 LEU cc_start: 0.9632 (tp) cc_final: 0.9280 (tp) REVERT: X 75 LEU cc_start: 0.9547 (pp) cc_final: 0.9102 (pp) REVERT: X 77 PHE cc_start: 0.9620 (m-80) cc_final: 0.9295 (m-80) REVERT: X 103 LEU cc_start: 0.9434 (mt) cc_final: 0.9227 (mt) outliers start: 1 outliers final: 0 residues processed: 491 average time/residue: 0.1219 time to fit residues: 91.8107 Evaluate side-chains 374 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 36 optimal weight: 8.9990 chunk 156 optimal weight: 8.9990 chunk 184 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 199 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN H 92 GLN I 43 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN M 43 ASN Q 43 ASN U 43 ASN U 90 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.056409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.042022 restraints weight = 111773.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.043374 restraints weight = 79803.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.044425 restraints weight = 60574.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.045143 restraints weight = 49552.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.045749 restraints weight = 42292.777| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18933 Z= 0.162 Angle : 0.706 9.916 25761 Z= 0.360 Chirality : 0.042 0.226 3051 Planarity : 0.005 0.065 3249 Dihedral : 4.501 22.979 2601 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.26 % Allowed : 4.85 % Favored : 94.89 % 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: 0.66 (0.17), residues: 2322 helix: 1.12 (0.13), residues: 1434 sheet: -0.48 (0.28), residues: 276 loop : -0.53 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 61 TYR 0.029 0.002 TYR B 38 PHE 0.022 0.002 PHE K 95 TRP 0.015 0.001 TRP D 117 HIS 0.005 0.001 HIS X 95 Details of bonding type rmsd covalent geometry : bond 0.00343 (18933) covalent geometry : angle 0.70619 (25761) hydrogen bonds : bond 0.04256 ( 1054) hydrogen bonds : angle 4.46562 ( 3162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 464 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8874 (m-80) cc_final: 0.8624 (m-80) REVERT: B 24 ARG cc_start: 0.8778 (mpt180) cc_final: 0.7914 (mpt90) REVERT: B 45 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8574 (mm-30) REVERT: B 78 LYS cc_start: 0.9155 (pttp) cc_final: 0.8890 (pttp) REVERT: B 79 THR cc_start: 0.9250 (p) cc_final: 0.8944 (p) REVERT: B 95 HIS cc_start: 0.6559 (t-170) cc_final: 0.6347 (t-170) REVERT: C 14 GLU cc_start: 0.9571 (tp30) cc_final: 0.9207 (tp30) REVERT: D 22 ASP cc_start: 0.8313 (t0) cc_final: 0.7962 (t0) REVERT: D 28 THR cc_start: 0.8907 (m) cc_final: 0.8306 (p) REVERT: D 80 THR cc_start: 0.9508 (p) cc_final: 0.9303 (t) REVERT: D 118 LEU cc_start: 0.9647 (mp) cc_final: 0.9371 (pp) REVERT: F 38 TYR cc_start: 0.8818 (m-80) cc_final: 0.8614 (m-80) REVERT: F 71 ASP cc_start: 0.9150 (m-30) cc_final: 0.8471 (t0) REVERT: F 116 ASP cc_start: 0.8962 (p0) cc_final: 0.8643 (m-30) REVERT: F 119 ARG cc_start: 0.6370 (tpm170) cc_final: 0.5776 (ptm-80) REVERT: G 7 MET cc_start: 0.8264 (ptt) cc_final: 0.7837 (ttp) REVERT: G 61 TYR cc_start: 0.8082 (m-80) cc_final: 0.7787 (m-80) REVERT: G 82 TYR cc_start: 0.8596 (m-80) cc_final: 0.8127 (m-80) REVERT: G 114 LEU cc_start: 0.9251 (mt) cc_final: 0.9035 (mt) REVERT: H 101 GLU cc_start: 0.9089 (tp30) cc_final: 0.8800 (mp0) REVERT: J 20 THR cc_start: 0.7674 (t) cc_final: 0.6336 (t) REVERT: J 22 ASP cc_start: 0.8935 (p0) cc_final: 0.8268 (t0) REVERT: K 39 GLU cc_start: 0.9489 (mp0) cc_final: 0.9213 (mp0) REVERT: K 68 ASP cc_start: 0.8349 (t0) cc_final: 0.8063 (t0) REVERT: K 95 PHE cc_start: 0.8971 (m-80) cc_final: 0.8641 (m-10) REVERT: L 22 ASP cc_start: 0.7497 (t0) cc_final: 0.7195 (t0) REVERT: L 23 LEU cc_start: 0.9380 (mm) cc_final: 0.9040 (mm) REVERT: L 24 ARG cc_start: 0.8396 (mpt180) cc_final: 0.8074 (mpt90) REVERT: L 39 LEU cc_start: 0.9651 (mm) cc_final: 0.9398 (pp) REVERT: L 73 TYR cc_start: 0.9045 (m-80) cc_final: 0.8553 (m-80) REVERT: L 77 PHE cc_start: 0.9247 (m-80) cc_final: 0.8844 (m-80) REVERT: L 106 THR cc_start: 0.8290 (m) cc_final: 0.7867 (m) REVERT: M 112 LEU cc_start: 0.9388 (mt) cc_final: 0.9143 (mt) REVERT: N 29 THR cc_start: 0.9271 (t) cc_final: 0.8971 (m) REVERT: N 45 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8836 (mm-30) REVERT: N 48 LEU cc_start: 0.9288 (mm) cc_final: 0.8487 (tt) REVERT: N 74 ARG cc_start: 0.9501 (tpt90) cc_final: 0.9206 (tpt170) REVERT: P 63 GLU cc_start: 0.8624 (mp0) cc_final: 0.8402 (mp0) REVERT: P 101 GLU cc_start: 0.8185 (tp30) cc_final: 0.7199 (mp0) REVERT: P 119 ARG cc_start: 0.9248 (tpm170) cc_final: 0.8770 (tpt90) REVERT: Q 68 ASP cc_start: 0.9188 (t0) cc_final: 0.8931 (t0) REVERT: Q 95 PHE cc_start: 0.9081 (m-80) cc_final: 0.8626 (m-80) REVERT: R 45 GLU cc_start: 0.9231 (pp20) cc_final: 0.8688 (pp20) REVERT: R 46 LYS cc_start: 0.8856 (pttp) cc_final: 0.8652 (pttm) REVERT: U 95 PHE cc_start: 0.9423 (m-80) cc_final: 0.8906 (m-10) REVERT: V 22 ASP cc_start: 0.8139 (t0) cc_final: 0.6794 (t0) REVERT: W 33 LYS cc_start: 0.8547 (tttt) cc_final: 0.8342 (ttpt) REVERT: W 44 LEU cc_start: 0.9738 (tp) cc_final: 0.9361 (pp) REVERT: X 77 PHE cc_start: 0.9666 (m-80) cc_final: 0.9361 (m-80) outliers start: 5 outliers final: 0 residues processed: 467 average time/residue: 0.1187 time to fit residues: 85.0325 Evaluate side-chains 368 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 176 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 174 optimal weight: 0.0270 chunk 102 optimal weight: 0.8980 chunk 81 optimal weight: 0.0170 chunk 154 optimal weight: 1.9990 chunk 133 optimal weight: 8.9990 overall best weight: 1.3880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN F 92 GLN G 43 ASN I 43 ASN K 43 ASN M 43 ASN Q 43 ASN U 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.057481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.042861 restraints weight = 106953.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.044233 restraints weight = 75231.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.045341 restraints weight = 57187.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.046166 restraints weight = 46162.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.046782 restraints weight = 38984.027| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18933 Z= 0.131 Angle : 0.705 11.887 25761 Z= 0.349 Chirality : 0.042 0.157 3051 Planarity : 0.005 0.064 3249 Dihedral : 4.441 24.147 2601 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.21 % Allowed : 4.59 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.58 (0.17), residues: 2322 helix: 1.07 (0.13), residues: 1452 sheet: -0.05 (0.28), residues: 300 loop : -0.97 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 94 TYR 0.049 0.002 TYR I 48 PHE 0.012 0.001 PHE K 95 TRP 0.022 0.001 TRP B 90 HIS 0.004 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00283 (18933) covalent geometry : angle 0.70460 (25761) hydrogen bonds : bond 0.04054 ( 1054) hydrogen bonds : angle 4.29429 ( 3162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 480 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ARG cc_start: 0.8796 (mpt180) cc_final: 0.8346 (mmt-90) REVERT: B 45 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8547 (mm-30) REVERT: B 78 LYS cc_start: 0.9124 (pttp) cc_final: 0.8888 (pttp) REVERT: B 88 VAL cc_start: 0.9811 (p) cc_final: 0.9431 (p) REVERT: B 91 LEU cc_start: 0.9512 (tp) cc_final: 0.9153 (pp) REVERT: B 92 GLN cc_start: 0.9203 (pp30) cc_final: 0.8809 (pp30) REVERT: C 14 GLU cc_start: 0.9515 (tp30) cc_final: 0.9227 (tp30) REVERT: C 61 TYR cc_start: 0.8729 (m-10) cc_final: 0.8409 (m-80) REVERT: D 22 ASP cc_start: 0.8670 (t0) cc_final: 0.7961 (t0) REVERT: D 28 THR cc_start: 0.8762 (m) cc_final: 0.8267 (p) REVERT: D 80 THR cc_start: 0.9609 (p) cc_final: 0.9271 (t) REVERT: D 82 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8947 (mt-10) REVERT: D 114 TYR cc_start: 0.8276 (m-80) cc_final: 0.7992 (m-80) REVERT: D 118 LEU cc_start: 0.9639 (mp) cc_final: 0.9360 (pp) REVERT: F 38 TYR cc_start: 0.8843 (m-80) cc_final: 0.8631 (m-80) REVERT: F 71 ASP cc_start: 0.9233 (m-30) cc_final: 0.8531 (t0) REVERT: F 116 ASP cc_start: 0.8960 (p0) cc_final: 0.8604 (m-30) REVERT: F 119 ARG cc_start: 0.6056 (tpm170) cc_final: 0.5604 (ptm-80) REVERT: G 7 MET cc_start: 0.8227 (ptt) cc_final: 0.7995 (ptm) REVERT: G 61 TYR cc_start: 0.8021 (m-80) cc_final: 0.7719 (m-80) REVERT: G 82 TYR cc_start: 0.8630 (m-80) cc_final: 0.8418 (m-80) REVERT: H 101 GLU cc_start: 0.9107 (tp30) cc_final: 0.8582 (mp0) REVERT: H 119 ARG cc_start: 0.8967 (tpm170) cc_final: 0.8728 (tpm170) REVERT: J 20 THR cc_start: 0.7729 (t) cc_final: 0.6378 (t) REVERT: J 22 ASP cc_start: 0.8995 (p0) cc_final: 0.8498 (t0) REVERT: J 46 LYS cc_start: 0.8942 (ptpp) cc_final: 0.8699 (pttt) REVERT: K 68 ASP cc_start: 0.8370 (t0) cc_final: 0.8070 (t0) REVERT: L 22 ASP cc_start: 0.7467 (t0) cc_final: 0.7149 (t0) REVERT: L 23 LEU cc_start: 0.9429 (mm) cc_final: 0.9061 (mm) REVERT: L 24 ARG cc_start: 0.8404 (mpt180) cc_final: 0.8075 (mpt90) REVERT: L 39 LEU cc_start: 0.9642 (mm) cc_final: 0.9375 (pp) REVERT: L 73 TYR cc_start: 0.9049 (m-80) cc_final: 0.8330 (m-80) REVERT: L 75 LEU cc_start: 0.9665 (mt) cc_final: 0.9456 (mt) REVERT: L 77 PHE cc_start: 0.9236 (m-80) cc_final: 0.8786 (m-80) REVERT: L 106 THR cc_start: 0.8280 (m) cc_final: 0.7876 (m) REVERT: M 112 LEU cc_start: 0.9408 (mt) cc_final: 0.9153 (mt) REVERT: N 29 THR cc_start: 0.9290 (t) cc_final: 0.8856 (m) REVERT: N 48 LEU cc_start: 0.9229 (mm) cc_final: 0.8367 (tt) REVERT: N 74 ARG cc_start: 0.9524 (tpt90) cc_final: 0.9203 (tpt170) REVERT: N 115 ARG cc_start: 0.9156 (ppt170) cc_final: 0.8953 (ttp80) REVERT: P 35 GLU cc_start: 0.9169 (pm20) cc_final: 0.8954 (pm20) REVERT: P 63 GLU cc_start: 0.8624 (mp0) cc_final: 0.8411 (mp0) REVERT: Q 95 PHE cc_start: 0.9056 (m-10) cc_final: 0.8601 (m-80) REVERT: R 45 GLU cc_start: 0.9195 (pp20) cc_final: 0.8622 (pp20) REVERT: R 46 LYS cc_start: 0.8822 (pttp) cc_final: 0.8598 (pttm) REVERT: T 101 GLU cc_start: 0.9067 (tp30) cc_final: 0.8382 (mp0) REVERT: U 95 PHE cc_start: 0.9361 (m-80) cc_final: 0.8926 (m-10) REVERT: W 44 LEU cc_start: 0.9736 (tp) cc_final: 0.9249 (pp) REVERT: W 61 TYR cc_start: 0.8790 (m-80) cc_final: 0.8573 (m-80) REVERT: W 76 TYR cc_start: 0.9253 (t80) cc_final: 0.8913 (t80) REVERT: X 77 PHE cc_start: 0.9612 (m-80) cc_final: 0.9286 (m-80) outliers start: 4 outliers final: 1 residues processed: 484 average time/residue: 0.1227 time to fit residues: 90.7005 Evaluate side-chains 385 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 384 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 59 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 205 optimal weight: 10.0000 chunk 123 optimal weight: 0.0060 chunk 217 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN F 92 GLN G 43 ASN I 43 ASN K 43 ASN M 43 ASN Q 43 ASN U 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.055666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.041406 restraints weight = 110609.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.042738 restraints weight = 77556.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.043784 restraints weight = 58763.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.044594 restraints weight = 47795.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.045177 restraints weight = 40562.864| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 18933 Z= 0.162 Angle : 0.740 13.530 25761 Z= 0.376 Chirality : 0.043 0.281 3051 Planarity : 0.005 0.073 3249 Dihedral : 4.482 22.690 2601 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: 0.37 (0.17), residues: 2322 helix: 0.91 (0.13), residues: 1452 sheet: -0.26 (0.27), residues: 300 loop : -0.98 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG T 81 TYR 0.050 0.003 TYR B 38 PHE 0.023 0.002 PHE K 95 TRP 0.014 0.001 TRP P 117 HIS 0.004 0.001 HIS X 95 Details of bonding type rmsd covalent geometry : bond 0.00348 (18933) covalent geometry : angle 0.73956 (25761) hydrogen bonds : bond 0.04325 ( 1054) hydrogen bonds : angle 4.68061 ( 3162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 ILE cc_start: 0.8849 (tp) cc_final: 0.8639 (mp) REVERT: B 24 ARG cc_start: 0.8803 (mpt180) cc_final: 0.8041 (mpt90) REVERT: B 45 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8607 (mm-30) REVERT: B 78 LYS cc_start: 0.9122 (pttp) cc_final: 0.8839 (pttp) REVERT: B 79 THR cc_start: 0.9206 (p) cc_final: 0.8940 (p) REVERT: C 14 GLU cc_start: 0.9509 (tp30) cc_final: 0.9201 (tp30) REVERT: D 22 ASP cc_start: 0.8712 (t0) cc_final: 0.7694 (t0) REVERT: D 28 THR cc_start: 0.8699 (m) cc_final: 0.8266 (p) REVERT: D 77 PHE cc_start: 0.9336 (m-10) cc_final: 0.8983 (m-10) REVERT: D 80 THR cc_start: 0.9613 (p) cc_final: 0.8932 (p) REVERT: D 82 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8981 (mp0) REVERT: D 95 HIS cc_start: 0.7942 (t-170) cc_final: 0.7665 (t-170) REVERT: D 118 LEU cc_start: 0.9612 (mp) cc_final: 0.9395 (pp) REVERT: F 71 ASP cc_start: 0.9196 (m-30) cc_final: 0.8511 (t0) REVERT: F 116 ASP cc_start: 0.8920 (p0) cc_final: 0.8571 (m-30) REVERT: F 119 ARG cc_start: 0.5834 (tpm170) cc_final: 0.5370 (ptm-80) REVERT: G 7 MET cc_start: 0.8287 (ptt) cc_final: 0.7921 (ttp) REVERT: G 61 TYR cc_start: 0.8168 (m-80) cc_final: 0.7795 (m-80) REVERT: H 101 GLU cc_start: 0.9118 (tp30) cc_final: 0.8672 (mp0) REVERT: J 20 THR cc_start: 0.7909 (t) cc_final: 0.6480 (t) REVERT: J 22 ASP cc_start: 0.9006 (p0) cc_final: 0.8547 (t0) REVERT: K 68 ASP cc_start: 0.8373 (t0) cc_final: 0.8061 (t0) REVERT: L 22 ASP cc_start: 0.7308 (t0) cc_final: 0.6982 (t0) REVERT: L 23 LEU cc_start: 0.9399 (mm) cc_final: 0.9005 (mm) REVERT: L 24 ARG cc_start: 0.8410 (mpt180) cc_final: 0.8109 (mpt90) REVERT: L 39 LEU cc_start: 0.9685 (mm) cc_final: 0.9420 (pp) REVERT: L 73 TYR cc_start: 0.9021 (m-80) cc_final: 0.8523 (m-80) REVERT: L 75 LEU cc_start: 0.9652 (mt) cc_final: 0.9435 (mt) REVERT: L 77 PHE cc_start: 0.9289 (m-80) cc_final: 0.8767 (m-80) REVERT: L 106 THR cc_start: 0.8235 (m) cc_final: 0.7839 (m) REVERT: M 112 LEU cc_start: 0.9494 (mt) cc_final: 0.9261 (mt) REVERT: N 45 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8811 (mm-30) REVERT: N 48 LEU cc_start: 0.9220 (mm) cc_final: 0.8474 (tp) REVERT: P 24 ARG cc_start: 0.8792 (mpt180) cc_final: 0.8589 (mmt-90) REVERT: P 63 GLU cc_start: 0.8620 (mp0) cc_final: 0.8413 (mp0) REVERT: Q 95 PHE cc_start: 0.9177 (m-10) cc_final: 0.8718 (m-80) REVERT: R 45 GLU cc_start: 0.9211 (pp20) cc_final: 0.8641 (pp20) REVERT: R 46 LYS cc_start: 0.8699 (pttp) cc_final: 0.8480 (pttm) REVERT: U 95 PHE cc_start: 0.9378 (m-80) cc_final: 0.8915 (m-10) REVERT: V 28 THR cc_start: 0.8732 (m) cc_final: 0.8236 (m) REVERT: V 73 TYR cc_start: 0.9326 (m-80) cc_final: 0.9083 (m-10) REVERT: W 14 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8832 (tm-30) REVERT: W 61 TYR cc_start: 0.8812 (m-80) cc_final: 0.8599 (m-80) REVERT: W 76 TYR cc_start: 0.9268 (t80) cc_final: 0.9026 (t80) REVERT: X 77 PHE cc_start: 0.9650 (m-80) cc_final: 0.9397 (m-80) outliers start: 0 outliers final: 0 residues processed: 447 average time/residue: 0.1302 time to fit residues: 88.3634 Evaluate side-chains 352 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 226 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN D 92 GLN G 43 ASN I 43 ASN K 43 ASN M 43 ASN Q 43 ASN U 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.054526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.040478 restraints weight = 111959.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.041814 restraints weight = 78064.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.042874 restraints weight = 59280.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.043672 restraints weight = 47628.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.044255 restraints weight = 40310.332| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.6395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18933 Z= 0.167 Angle : 0.733 12.130 25761 Z= 0.372 Chirality : 0.043 0.277 3051 Planarity : 0.005 0.062 3249 Dihedral : 4.543 22.895 2601 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.44 (0.17), residues: 2322 helix: 1.02 (0.13), residues: 1416 sheet: -0.79 (0.28), residues: 276 loop : -0.66 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG V 61 TYR 0.040 0.003 TYR B 38 PHE 0.015 0.002 PHE K 95 TRP 0.016 0.001 TRP V 117 HIS 0.006 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00357 (18933) covalent geometry : angle 0.73297 (25761) hydrogen bonds : bond 0.04206 ( 1054) hydrogen bonds : angle 4.62863 ( 3162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 449 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.9152 (t0) cc_final: 0.8896 (t0) REVERT: A 82 TYR cc_start: 0.9132 (m-10) cc_final: 0.8517 (m-80) REVERT: B 18 ILE cc_start: 0.8867 (tp) cc_final: 0.8653 (mp) REVERT: B 45 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8544 (mm-30) REVERT: B 78 LYS cc_start: 0.9145 (pttp) cc_final: 0.8872 (pttp) REVERT: C 14 GLU cc_start: 0.9475 (tp30) cc_final: 0.9158 (tp30) REVERT: D 22 ASP cc_start: 0.8595 (t0) cc_final: 0.7731 (t0) REVERT: D 26 LEU cc_start: 0.9598 (tp) cc_final: 0.9381 (tp) REVERT: D 28 THR cc_start: 0.8772 (m) cc_final: 0.8148 (m) REVERT: D 77 PHE cc_start: 0.9315 (m-10) cc_final: 0.9017 (m-10) REVERT: D 80 THR cc_start: 0.9563 (p) cc_final: 0.8847 (p) REVERT: D 82 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8881 (mp0) REVERT: D 95 HIS cc_start: 0.8074 (t-170) cc_final: 0.7780 (t-170) REVERT: D 118 LEU cc_start: 0.9593 (mp) cc_final: 0.9387 (pp) REVERT: F 71 ASP cc_start: 0.9229 (m-30) cc_final: 0.8588 (t0) REVERT: F 102 CYS cc_start: 0.8979 (t) cc_final: 0.8699 (t) REVERT: F 116 ASP cc_start: 0.8929 (p0) cc_final: 0.8569 (m-30) REVERT: F 119 ARG cc_start: 0.6109 (tpm170) cc_final: 0.5359 (ptm-80) REVERT: G 61 TYR cc_start: 0.8244 (m-80) cc_final: 0.7846 (m-80) REVERT: H 101 GLU cc_start: 0.9093 (tp30) cc_final: 0.8587 (mp0) REVERT: H 119 ARG cc_start: 0.9189 (tpm170) cc_final: 0.8888 (mmp-170) REVERT: J 20 THR cc_start: 0.8177 (t) cc_final: 0.6738 (t) REVERT: J 22 ASP cc_start: 0.8985 (p0) cc_final: 0.8400 (t0) REVERT: J 95 HIS cc_start: 0.5829 (t-90) cc_final: 0.5536 (t-90) REVERT: K 19 ASN cc_start: 0.8974 (m-40) cc_final: 0.8618 (m-40) REVERT: K 68 ASP cc_start: 0.8332 (t0) cc_final: 0.7993 (t0) REVERT: L 22 ASP cc_start: 0.7330 (t0) cc_final: 0.7032 (t0) REVERT: L 23 LEU cc_start: 0.9382 (mm) cc_final: 0.8939 (mm) REVERT: L 24 ARG cc_start: 0.8623 (mpt180) cc_final: 0.8237 (mpt90) REVERT: L 39 LEU cc_start: 0.9704 (mm) cc_final: 0.9496 (pp) REVERT: L 73 TYR cc_start: 0.9070 (m-80) cc_final: 0.8540 (m-80) REVERT: L 77 PHE cc_start: 0.9337 (m-80) cc_final: 0.8832 (m-80) REVERT: L 106 THR cc_start: 0.8252 (m) cc_final: 0.7830 (m) REVERT: M 112 LEU cc_start: 0.9509 (mt) cc_final: 0.9231 (mt) REVERT: N 48 LEU cc_start: 0.9183 (mm) cc_final: 0.8403 (tp) REVERT: P 101 GLU cc_start: 0.8292 (tp30) cc_final: 0.7441 (mp0) REVERT: Q 95 PHE cc_start: 0.9255 (m-10) cc_final: 0.8812 (m-10) REVERT: R 45 GLU cc_start: 0.9205 (pp20) cc_final: 0.8669 (pp20) REVERT: R 66 LYS cc_start: 0.9519 (mmmm) cc_final: 0.9294 (mmmm) REVERT: U 61 TYR cc_start: 0.9059 (m-80) cc_final: 0.8390 (m-80) REVERT: U 95 PHE cc_start: 0.9364 (m-80) cc_final: 0.8908 (m-10) REVERT: W 14 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8833 (tm-30) REVERT: W 44 LEU cc_start: 0.9736 (tp) cc_final: 0.9338 (pp) REVERT: X 24 ARG cc_start: 0.8953 (mpt180) cc_final: 0.8620 (mmt90) REVERT: X 77 PHE cc_start: 0.9644 (m-80) cc_final: 0.9419 (m-80) outliers start: 1 outliers final: 0 residues processed: 449 average time/residue: 0.1281 time to fit residues: 88.0129 Evaluate side-chains 349 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 66 optimal weight: 5.9990 chunk 175 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 219 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 213 optimal weight: 0.0970 chunk 107 optimal weight: 0.9980 chunk 113 optimal weight: 20.0000 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN I 43 ASN K 43 ASN M 43 ASN Q 43 ASN U 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.054643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.040614 restraints weight = 112236.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.041995 restraints weight = 77829.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.042998 restraints weight = 58974.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.043812 restraints weight = 47502.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.044449 restraints weight = 40060.432| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.6595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 18933 Z= 0.157 Angle : 0.741 12.833 25761 Z= 0.371 Chirality : 0.042 0.182 3051 Planarity : 0.005 0.060 3249 Dihedral : 4.511 22.775 2601 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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: 0.20 (0.17), residues: 2322 helix: 0.88 (0.13), residues: 1440 sheet: -0.91 (0.27), residues: 300 loop : -0.96 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 94 TYR 0.057 0.003 TYR B 38 PHE 0.025 0.002 PHE K 95 TRP 0.023 0.001 TRP D 90 HIS 0.004 0.001 HIS D 95 Details of bonding type rmsd covalent geometry : bond 0.00342 (18933) covalent geometry : angle 0.74148 (25761) hydrogen bonds : bond 0.04147 ( 1054) hydrogen bonds : angle 4.62738 ( 3162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.9148 (t0) cc_final: 0.8900 (t0) REVERT: B 24 ARG cc_start: 0.8818 (mpt180) cc_final: 0.8146 (mmt-90) REVERT: B 28 THR cc_start: 0.8952 (m) cc_final: 0.8631 (m) REVERT: B 45 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8592 (mm-30) REVERT: B 78 LYS cc_start: 0.9111 (pttp) cc_final: 0.8794 (pttp) REVERT: C 14 GLU cc_start: 0.9425 (tp30) cc_final: 0.9115 (tp30) REVERT: C 65 LEU cc_start: 0.9608 (pp) cc_final: 0.9164 (mt) REVERT: D 22 ASP cc_start: 0.8608 (t0) cc_final: 0.8019 (t0) REVERT: D 26 LEU cc_start: 0.9655 (tp) cc_final: 0.9436 (tp) REVERT: D 74 ARG cc_start: 0.9171 (ttt-90) cc_final: 0.8917 (tmm-80) REVERT: D 77 PHE cc_start: 0.9303 (m-10) cc_final: 0.8962 (m-10) REVERT: D 80 THR cc_start: 0.9587 (p) cc_final: 0.9180 (t) REVERT: D 82 GLU cc_start: 0.9172 (mt-10) cc_final: 0.8946 (mt-10) REVERT: D 118 LEU cc_start: 0.9583 (mp) cc_final: 0.9372 (pp) REVERT: F 71 ASP cc_start: 0.9233 (m-30) cc_final: 0.8572 (t0) REVERT: F 116 ASP cc_start: 0.8954 (p0) cc_final: 0.8605 (m-30) REVERT: F 119 ARG cc_start: 0.5962 (tpm170) cc_final: 0.5253 (ptm-80) REVERT: G 61 TYR cc_start: 0.8301 (m-80) cc_final: 0.7870 (m-80) REVERT: H 101 GLU cc_start: 0.9130 (tp30) cc_final: 0.8601 (mp0) REVERT: H 119 ARG cc_start: 0.9218 (tpm170) cc_final: 0.8928 (mmp-170) REVERT: J 20 THR cc_start: 0.8356 (t) cc_final: 0.6946 (t) REVERT: J 22 ASP cc_start: 0.8917 (p0) cc_final: 0.8390 (t0) REVERT: K 19 ASN cc_start: 0.8901 (m-40) cc_final: 0.8554 (m-40) REVERT: K 68 ASP cc_start: 0.8369 (t0) cc_final: 0.8027 (t0) REVERT: L 22 ASP cc_start: 0.7319 (t0) cc_final: 0.6943 (t0) REVERT: L 23 LEU cc_start: 0.9393 (mm) cc_final: 0.8952 (mm) REVERT: L 24 ARG cc_start: 0.8635 (mpt180) cc_final: 0.8253 (mpt90) REVERT: L 39 LEU cc_start: 0.9700 (mm) cc_final: 0.9473 (pp) REVERT: L 73 TYR cc_start: 0.9052 (m-80) cc_final: 0.8539 (m-80) REVERT: L 106 THR cc_start: 0.8215 (m) cc_final: 0.7856 (m) REVERT: M 112 LEU cc_start: 0.9526 (mt) cc_final: 0.9247 (mt) REVERT: N 45 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8841 (mm-30) REVERT: N 75 LEU cc_start: 0.9453 (mm) cc_final: 0.9155 (mm) REVERT: P 101 GLU cc_start: 0.8443 (tp30) cc_final: 0.7942 (tp30) REVERT: Q 95 PHE cc_start: 0.9283 (m-10) cc_final: 0.8857 (m-10) REVERT: R 45 GLU cc_start: 0.9258 (pp20) cc_final: 0.8682 (pp20) REVERT: R 46 LYS cc_start: 0.8907 (pttm) cc_final: 0.8639 (pttp) REVERT: R 66 LYS cc_start: 0.9518 (mmmm) cc_final: 0.9299 (mmmm) REVERT: R 75 LEU cc_start: 0.9823 (mt) cc_final: 0.9313 (pp) REVERT: R 92 GLN cc_start: 0.8878 (pp30) cc_final: 0.8673 (pp30) REVERT: U 61 TYR cc_start: 0.9036 (m-80) cc_final: 0.8395 (m-80) REVERT: U 95 PHE cc_start: 0.9373 (m-80) cc_final: 0.8936 (m-10) REVERT: V 28 THR cc_start: 0.8784 (m) cc_final: 0.8294 (m) REVERT: W 14 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8805 (tm-30) REVERT: W 49 LEU cc_start: 0.9192 (tp) cc_final: 0.8957 (mt) REVERT: X 24 ARG cc_start: 0.8950 (mpt180) cc_final: 0.8610 (mmt90) REVERT: X 77 PHE cc_start: 0.9643 (m-80) cc_final: 0.9437 (m-80) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.1423 time to fit residues: 95.6601 Evaluate side-chains 346 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 163 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 212 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN I 43 ASN K 43 ASN M 43 ASN ** P 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 ASN U 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.055534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.041357 restraints weight = 109370.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.042767 restraints weight = 75718.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.043771 restraints weight = 57501.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.044646 restraints weight = 46215.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.045301 restraints weight = 38808.755| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.6744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18933 Z= 0.138 Angle : 0.756 14.484 25761 Z= 0.374 Chirality : 0.043 0.301 3051 Planarity : 0.005 0.058 3249 Dihedral : 4.497 22.645 2601 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % 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: 0.18 (0.17), residues: 2322 helix: 0.84 (0.13), residues: 1452 sheet: -0.61 (0.26), residues: 324 loop : -1.11 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG T 81 TYR 0.049 0.003 TYR B 38 PHE 0.012 0.002 PHE K 95 TRP 0.023 0.001 TRP D 90 HIS 0.003 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00302 (18933) covalent geometry : angle 0.75599 (25761) hydrogen bonds : bond 0.04059 ( 1054) hydrogen bonds : angle 4.59064 ( 3162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ARG cc_start: 0.8676 (mpt180) cc_final: 0.8226 (mmt-90) REVERT: B 28 THR cc_start: 0.9042 (m) cc_final: 0.8521 (m) REVERT: B 78 LYS cc_start: 0.9117 (pttp) cc_final: 0.8855 (pttp) REVERT: B 92 GLN cc_start: 0.9242 (pp30) cc_final: 0.8972 (pp30) REVERT: C 14 GLU cc_start: 0.9430 (tp30) cc_final: 0.9109 (tp30) REVERT: C 65 LEU cc_start: 0.9596 (pp) cc_final: 0.9170 (mt) REVERT: D 22 ASP cc_start: 0.8544 (t0) cc_final: 0.8008 (t0) REVERT: D 80 THR cc_start: 0.9581 (p) cc_final: 0.9158 (t) REVERT: D 81 ARG cc_start: 0.9215 (mtp-110) cc_final: 0.8817 (mtp85) REVERT: D 82 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8908 (mt-10) REVERT: D 101 GLU cc_start: 0.8858 (tp30) cc_final: 0.7686 (tp30) REVERT: F 71 ASP cc_start: 0.9246 (m-30) cc_final: 0.8562 (t0) REVERT: F 85 ASP cc_start: 0.9491 (m-30) cc_final: 0.9260 (t70) REVERT: F 116 ASP cc_start: 0.8948 (p0) cc_final: 0.8564 (m-30) REVERT: F 119 ARG cc_start: 0.5679 (tpm170) cc_final: 0.5181 (ptm160) REVERT: G 7 MET cc_start: 0.8724 (ppp) cc_final: 0.8440 (ppp) REVERT: G 61 TYR cc_start: 0.8239 (m-80) cc_final: 0.7809 (m-80) REVERT: H 22 ASP cc_start: 0.8811 (t0) cc_final: 0.8558 (t0) REVERT: H 101 GLU cc_start: 0.9143 (tp30) cc_final: 0.8655 (mp0) REVERT: H 119 ARG cc_start: 0.9235 (tpm170) cc_final: 0.8948 (mmp-170) REVERT: J 20 THR cc_start: 0.8357 (t) cc_final: 0.6947 (t) REVERT: J 22 ASP cc_start: 0.8913 (p0) cc_final: 0.8538 (t0) REVERT: K 19 ASN cc_start: 0.8845 (m-40) cc_final: 0.8482 (m-40) REVERT: K 68 ASP cc_start: 0.8421 (t0) cc_final: 0.8096 (t0) REVERT: L 39 LEU cc_start: 0.9694 (mm) cc_final: 0.9453 (pp) REVERT: L 73 TYR cc_start: 0.9065 (m-80) cc_final: 0.8565 (m-80) REVERT: L 77 PHE cc_start: 0.9402 (m-10) cc_final: 0.9164 (m-10) REVERT: M 112 LEU cc_start: 0.9508 (mt) cc_final: 0.9223 (mt) REVERT: N 45 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8808 (mm-30) REVERT: N 54 ILE cc_start: 0.8590 (tt) cc_final: 0.8327 (tp) REVERT: P 101 GLU cc_start: 0.8574 (tp30) cc_final: 0.7822 (mp0) REVERT: Q 95 PHE cc_start: 0.9254 (m-10) cc_final: 0.8774 (m-80) REVERT: R 45 GLU cc_start: 0.9230 (pp20) cc_final: 0.8639 (pp20) REVERT: R 46 LYS cc_start: 0.8897 (pttm) cc_final: 0.8636 (pttp) REVERT: R 66 LYS cc_start: 0.9480 (mmmm) cc_final: 0.9245 (mtmm) REVERT: R 75 LEU cc_start: 0.9794 (mt) cc_final: 0.9264 (pp) REVERT: R 92 GLN cc_start: 0.8874 (pp30) cc_final: 0.8662 (pp30) REVERT: T 24 ARG cc_start: 0.8961 (mmp-170) cc_final: 0.8737 (mmm160) REVERT: T 75 LEU cc_start: 0.9347 (mp) cc_final: 0.9106 (tp) REVERT: U 95 PHE cc_start: 0.9343 (m-80) cc_final: 0.8916 (m-10) REVERT: V 28 THR cc_start: 0.8777 (m) cc_final: 0.8345 (m) REVERT: V 114 TYR cc_start: 0.7622 (m-10) cc_final: 0.6656 (m-10) REVERT: W 44 LEU cc_start: 0.9691 (tp) cc_final: 0.9388 (pp) REVERT: W 49 LEU cc_start: 0.9174 (tp) cc_final: 0.8927 (mt) REVERT: X 24 ARG cc_start: 0.8948 (mpt180) cc_final: 0.8644 (mmt90) REVERT: X 66 LYS cc_start: 0.7317 (mmpt) cc_final: 0.7109 (mmmt) REVERT: X 77 PHE cc_start: 0.9621 (m-80) cc_final: 0.9413 (m-80) outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.1372 time to fit residues: 96.2620 Evaluate side-chains 355 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 34 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 28 optimal weight: 0.0270 chunk 137 optimal weight: 6.9990 chunk 138 optimal weight: 0.0000 chunk 65 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 196 optimal weight: 0.3980 chunk 180 optimal weight: 7.9990 overall best weight: 2.0846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN ** F 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN I 43 ASN ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 ASN P 92 GLN Q 43 ASN U 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.055210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.040803 restraints weight = 114395.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.042238 restraints weight = 80199.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.043381 restraints weight = 60453.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.044233 restraints weight = 48497.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.044840 restraints weight = 40676.811| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.6890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18933 Z= 0.140 Angle : 0.756 13.770 25761 Z= 0.376 Chirality : 0.043 0.288 3051 Planarity : 0.005 0.058 3249 Dihedral : 4.489 23.348 2601 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: 0.19 (0.17), residues: 2322 helix: 0.87 (0.13), residues: 1452 sheet: -0.60 (0.26), residues: 324 loop : -1.20 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 74 TYR 0.049 0.003 TYR B 38 PHE 0.018 0.002 PHE K 95 TRP 0.024 0.001 TRP D 90 HIS 0.002 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00305 (18933) covalent geometry : angle 0.75614 (25761) hydrogen bonds : bond 0.04071 ( 1054) hydrogen bonds : angle 4.56811 ( 3162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2942.06 seconds wall clock time: 51 minutes 59.35 seconds (3119.35 seconds total)