Starting phenix.real_space_refine on Mon May 19 09:53:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umr_42382/05_2025/8umr_42382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umr_42382/05_2025/8umr_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8umr_42382/05_2025/8umr_42382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umr_42382/05_2025/8umr_42382.map" model { file = "/net/cci-nas-00/data/ceres_data/8umr_42382/05_2025/8umr_42382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umr_42382/05_2025/8umr_42382.cif" } resolution = 4.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.94, per 1000 atoms: 0.27 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: 4.77 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.63 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: 4.85 Time building geometry restraints manager: 5.51 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: 0.16 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 33.370 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.070 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.050 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (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 TRP 0.007 0.001 TRP F 117 HIS 0.001 0.000 HIS F 95 PHE 0.017 0.003 PHE D 77 TYR 0.034 0.004 TYR R 38 ARG 0.012 0.001 ARG N 61 Details of bonding type rmsd hydrogen bonds : bond 0.14702 ( 1054) hydrogen bonds : angle 5.82419 ( 3162) covalent geometry : bond 0.00417 (18933) covalent geometry : angle 0.82212 (25761) *********************** 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 : 2.061 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: 0.8192 (mmt-90) REVERT: B 52 VAL cc_start: 0.8383 (m) cc_final: 0.7415 (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: 0.9006 (tp30) REVERT: C 80 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8243 (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: 0.9193 (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: 0.8415 (ttt180) REVERT: D 95 HIS cc_start: 0.7394 (t-90) cc_final: 0.6903 (t-170) REVERT: F 85 ASP cc_start: 0.9290 (m-30) cc_final: 0.8842 (t70) REVERT: F 116 ASP cc_start: 0.8510 (m-30) cc_final: 0.8229 (p0) 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: 0.8272 (tp30) REVERT: H 103 LEU cc_start: 0.9035 (mt) cc_final: 0.8583 (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: 0.9299 (mt) REVERT: L 77 PHE cc_start: 0.9171 (m-10) cc_final: 0.8508 (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: 0.8853 (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: P 100 PRO cc_start: 0.2611 (Cg_exo) cc_final: 0.2410 (Cg_endo) 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: 0.9129 (tp) REVERT: T 101 GLU cc_start: 0.8516 (tp30) cc_final: 0.8167 (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: 0.7834 (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: 0.8438 (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: 0.3657 time to fit residues: 399.3639 Evaluate side-chains 445 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 A 90 ASN C 19 ASN ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN G 19 ASN G 43 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 ASN ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 ASN K 43 ASN K 77 ASN K 90 ASN M 19 ASN ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 ASN Q 43 ASN U 19 ASN ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 77 ASN W 19 ASN ** W 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 90 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.057691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.043432 restraints weight = 109323.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.044776 restraints weight = 78135.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.045841 restraints weight = 60154.193| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18933 Z= 0.188 Angle : 0.735 10.578 25761 Z= 0.382 Chirality : 0.043 0.155 3051 Planarity : 0.006 0.072 3249 Dihedral : 4.528 23.185 2601 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.47 % Allowed : 7.62 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.17), residues: 2322 helix: 0.92 (0.13), residues: 1494 sheet: 0.17 (0.28), residues: 300 loop : -1.15 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 90 HIS 0.006 0.001 HIS T 95 PHE 0.020 0.003 PHE W 95 TYR 0.031 0.003 TYR L 73 ARG 0.010 0.001 ARG T 24 Details of bonding type rmsd hydrogen bonds : bond 0.04805 ( 1054) hydrogen bonds : angle 4.52448 ( 3162) covalent geometry : bond 0.00400 (18933) covalent geometry : angle 0.73505 (25761) *********************** 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 565 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 556 time to evaluate : 1.913 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: A 53 ASN cc_start: 0.8810 (t0) cc_final: 0.8546 (t0) REVERT: A 59 GLU cc_start: 0.9363 (pt0) cc_final: 0.9032 (pp20) REVERT: B 28 THR cc_start: 0.8234 (m) cc_final: 0.7360 (m) REVERT: B 38 TYR cc_start: 0.7469 (m-80) cc_final: 0.7119 (m-80) REVERT: B 45 GLU cc_start: 0.9458 (tp30) cc_final: 0.9206 (tm-30) REVERT: B 52 VAL cc_start: 0.8585 (m) cc_final: 0.8019 (m) REVERT: B 57 VAL cc_start: 0.9107 (t) cc_final: 0.8804 (m) REVERT: B 101 GLU cc_start: 0.9055 (tp30) cc_final: 0.8479 (tp30) REVERT: B 103 LEU cc_start: 0.9380 (mt) cc_final: 0.9154 (mp) REVERT: C 14 GLU cc_start: 0.9573 (tp30) cc_final: 0.9170 (tp30) REVERT: D 22 ASP cc_start: 0.7984 (t0) cc_final: 0.7715 (t0) REVERT: D 28 THR cc_start: 0.8883 (m) cc_final: 0.8546 (m) REVERT: D 63 GLU cc_start: 0.9162 (tp30) cc_final: 0.8944 (mp0) REVERT: D 94 ARG cc_start: 0.9336 (tpm170) cc_final: 0.9037 (tpm170) REVERT: D 118 LEU cc_start: 0.9603 (mp) cc_final: 0.9348 (pp) REVERT: F 38 TYR cc_start: 0.9017 (m-80) cc_final: 0.8727 (m-10) REVERT: F 78 LYS cc_start: 0.8028 (pttt) cc_final: 0.7821 (pttt) REVERT: F 79 THR cc_start: 0.9025 (m) cc_final: 0.8500 (m) REVERT: F 116 ASP cc_start: 0.8425 (m-30) cc_final: 0.8156 (p0) REVERT: G 7 MET cc_start: 0.8306 (ptt) cc_final: 0.8084 (ptm) REVERT: H 22 ASP cc_start: 0.9163 (t0) cc_final: 0.8901 (t0) REVERT: H 26 LEU cc_start: 0.9123 (tp) cc_final: 0.8854 (tp) REVERT: H 101 GLU cc_start: 0.9137 (tp30) cc_final: 0.8524 (tp30) REVERT: H 103 LEU cc_start: 0.9174 (mt) cc_final: 0.8939 (mt) REVERT: H 119 ARG cc_start: 0.9026 (tpm170) cc_final: 0.8273 (mtt180) REVERT: K 14 GLU cc_start: 0.9170 (tp30) cc_final: 0.8379 (tp30) REVERT: K 19 ASN cc_start: 0.8818 (m-40) cc_final: 0.8568 (t0) REVERT: K 22 THR cc_start: 0.9493 (p) cc_final: 0.9013 (p) REVERT: L 39 LEU cc_start: 0.9573 (mm) cc_final: 0.9218 (pp) REVERT: L 73 TYR cc_start: 0.8968 (m-80) cc_final: 0.8627 (m-10) REVERT: M 112 LEU cc_start: 0.9430 (mt) cc_final: 0.9125 (mt) REVERT: N 48 LEU cc_start: 0.9438 (mm) cc_final: 0.8636 (tt) REVERT: N 85 ASP cc_start: 0.9192 (p0) cc_final: 0.8985 (p0) REVERT: P 23 LEU cc_start: 0.9551 (mm) cc_final: 0.9348 (tt) REVERT: P 79 THR cc_start: 0.7994 (m) cc_final: 0.7389 (m) REVERT: P 80 THR cc_start: 0.8885 (p) cc_final: 0.8428 (t) REVERT: P 84 LEU cc_start: 0.8831 (tp) cc_final: 0.8464 (mt) REVERT: Q 95 PHE cc_start: 0.9000 (m-80) cc_final: 0.8502 (m-80) REVERT: R 45 GLU cc_start: 0.9212 (pp20) cc_final: 0.8683 (pp20) REVERT: R 46 LYS cc_start: 0.8879 (pttp) cc_final: 0.8651 (pttp) REVERT: R 60 VAL cc_start: 0.8771 (p) cc_final: 0.8486 (p) REVERT: R 71 ASP cc_start: 0.8928 (m-30) cc_final: 0.8200 (t0) REVERT: T 101 GLU cc_start: 0.9012 (tp30) cc_final: 0.8648 (mp0) REVERT: U 95 PHE cc_start: 0.9461 (m-80) cc_final: 0.9184 (m-10) REVERT: V 22 ASP cc_start: 0.7990 (t0) cc_final: 0.5718 (t0) REVERT: V 52 VAL cc_start: 0.8228 (m) cc_final: 0.8003 (m) REVERT: W 39 GLU cc_start: 0.9282 (mp0) cc_final: 0.9043 (mp0) REVERT: X 26 LEU cc_start: 0.9609 (tp) cc_final: 0.9392 (tp) REVERT: X 103 LEU cc_start: 0.9379 (mt) cc_final: 0.9112 (mt) outliers start: 9 outliers final: 6 residues processed: 562 average time/residue: 0.2923 time to fit residues: 243.7158 Evaluate side-chains 397 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 391 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 173 optimal weight: 0.5980 chunk 170 optimal weight: 8.9990 chunk 203 optimal weight: 2.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** 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 77 ASN I 90 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN M 43 ASN Q 43 ASN ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 90 ASN W 77 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 = 0.3237 r_free = 0.3237 target = 0.056082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.041955 restraints weight = 113439.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.043221 restraints weight = 80018.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.044256 restraints weight = 61696.230| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18933 Z= 0.175 Angle : 0.706 9.304 25761 Z= 0.365 Chirality : 0.042 0.143 3051 Planarity : 0.005 0.064 3249 Dihedral : 4.511 24.215 2601 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.10 % Allowed : 6.94 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2322 helix: 1.02 (0.13), residues: 1470 sheet: -0.43 (0.28), residues: 276 loop : -0.81 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 117 HIS 0.007 0.002 HIS D 95 PHE 0.028 0.002 PHE K 95 TYR 0.034 0.003 TYR W 8 ARG 0.010 0.001 ARG T 61 Details of bonding type rmsd hydrogen bonds : bond 0.04604 ( 1054) hydrogen bonds : angle 4.46850 ( 3162) covalent geometry : bond 0.00365 (18933) covalent geometry : angle 0.70572 (25761) *********************** 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 500 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 498 time to evaluate : 2.136 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 53 ASN cc_start: 0.9056 (t0) cc_final: 0.8827 (t0) REVERT: B 28 THR cc_start: 0.8235 (m) cc_final: 0.7616 (m) REVERT: B 57 VAL cc_start: 0.9120 (t) cc_final: 0.8874 (m) REVERT: B 79 THR cc_start: 0.9339 (p) cc_final: 0.8966 (p) REVERT: B 80 THR cc_start: 0.9193 (p) cc_final: 0.8767 (p) REVERT: B 101 GLU cc_start: 0.9191 (tp30) cc_final: 0.8602 (tp30) REVERT: B 103 LEU cc_start: 0.9343 (mt) cc_final: 0.9104 (mp) REVERT: C 14 GLU cc_start: 0.9611 (tp30) cc_final: 0.9194 (tp30) REVERT: C 61 TYR cc_start: 0.8533 (m-10) cc_final: 0.8102 (m-80) REVERT: D 22 ASP cc_start: 0.8010 (t0) cc_final: 0.6991 (t0) REVERT: D 28 THR cc_start: 0.8896 (m) cc_final: 0.8200 (m) REVERT: D 63 GLU cc_start: 0.9287 (tp30) cc_final: 0.8977 (mp0) REVERT: D 80 THR cc_start: 0.9545 (p) cc_final: 0.9254 (p) REVERT: D 94 ARG cc_start: 0.9253 (tpm170) cc_final: 0.8962 (tpm170) REVERT: D 101 GLU cc_start: 0.9001 (tp30) cc_final: 0.8266 (tp30) REVERT: D 103 LEU cc_start: 0.9674 (mt) cc_final: 0.9412 (mt) REVERT: D 118 LEU cc_start: 0.9630 (mp) cc_final: 0.9418 (pp) REVERT: F 38 TYR cc_start: 0.8849 (m-80) cc_final: 0.8580 (m-80) REVERT: F 71 ASP cc_start: 0.9035 (m-30) cc_final: 0.8363 (t0) REVERT: F 116 ASP cc_start: 0.8382 (m-30) cc_final: 0.8073 (p0) REVERT: G 7 MET cc_start: 0.8365 (ptt) cc_final: 0.7893 (ttp) REVERT: G 20 TYR cc_start: 0.8680 (m-80) cc_final: 0.8455 (m-10) REVERT: H 101 GLU cc_start: 0.9172 (tp30) cc_final: 0.8616 (mp0) REVERT: J 22 ASP cc_start: 0.9003 (p0) cc_final: 0.8392 (t0) REVERT: K 7 MET cc_start: 0.8986 (ptp) cc_final: 0.8609 (ptp) REVERT: K 14 GLU cc_start: 0.9223 (tp30) cc_final: 0.8317 (tp30) REVERT: K 19 ASN cc_start: 0.8696 (m-40) cc_final: 0.8467 (t0) REVERT: K 22 THR cc_start: 0.9332 (p) cc_final: 0.8900 (p) REVERT: K 39 GLU cc_start: 0.9489 (mp0) cc_final: 0.9224 (mp0) REVERT: K 49 LEU cc_start: 0.9723 (tt) cc_final: 0.9509 (pp) REVERT: L 22 ASP cc_start: 0.7287 (t0) cc_final: 0.6946 (t0) REVERT: L 23 LEU cc_start: 0.9376 (mm) cc_final: 0.8986 (mm) REVERT: L 24 ARG cc_start: 0.8469 (mpt180) cc_final: 0.8220 (mpt90) REVERT: L 39 LEU cc_start: 0.9625 (mm) cc_final: 0.9306 (pp) REVERT: L 73 TYR cc_start: 0.9032 (m-80) cc_final: 0.8570 (m-10) REVERT: L 106 THR cc_start: 0.8235 (m) cc_final: 0.7712 (m) REVERT: N 75 LEU cc_start: 0.9481 (mm) cc_final: 0.9163 (mm) REVERT: P 38 TYR cc_start: 0.5949 (m-80) cc_final: 0.5749 (m-80) REVERT: P 63 GLU cc_start: 0.8577 (mp0) cc_final: 0.8374 (mp0) REVERT: Q 95 PHE cc_start: 0.9073 (m-80) cc_final: 0.8526 (m-80) REVERT: R 45 GLU cc_start: 0.9268 (pp20) cc_final: 0.8748 (pp20) REVERT: R 46 LYS cc_start: 0.8823 (pttp) cc_final: 0.8594 (pttp) REVERT: R 68 VAL cc_start: 0.9622 (m) cc_final: 0.9362 (p) REVERT: R 70 GLU cc_start: 0.8624 (pm20) cc_final: 0.8397 (pm20) REVERT: R 71 ASP cc_start: 0.9064 (m-30) cc_final: 0.8158 (t0) REVERT: U 95 PHE cc_start: 0.9512 (m-80) cc_final: 0.9133 (m-10) REVERT: V 24 ARG cc_start: 0.8771 (mpt180) cc_final: 0.7741 (mmt-90) REVERT: V 52 VAL cc_start: 0.8395 (m) cc_final: 0.8187 (m) REVERT: V 104 VAL cc_start: 0.9658 (m) cc_final: 0.9435 (p) REVERT: W 39 GLU cc_start: 0.9326 (mp0) cc_final: 0.9108 (mp0) outliers start: 2 outliers final: 1 residues processed: 499 average time/residue: 0.3009 time to fit residues: 223.9165 Evaluate side-chains 374 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 191 optimal weight: 4.9990 chunk 30 optimal weight: 0.1980 chunk 54 optimal weight: 10.0000 chunk 137 optimal weight: 0.8980 chunk 190 optimal weight: 3.9990 chunk 180 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 157 optimal weight: 0.8980 chunk 165 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 G 43 ASN I 43 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.056530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.042086 restraints weight = 114604.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.043517 restraints weight = 80680.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.044600 restraints weight = 61423.631| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18933 Z= 0.139 Angle : 0.694 9.737 25761 Z= 0.351 Chirality : 0.042 0.170 3051 Planarity : 0.005 0.075 3249 Dihedral : 4.536 22.450 2601 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.05 % Allowed : 5.58 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.17), residues: 2322 helix: 1.08 (0.13), residues: 1458 sheet: -0.60 (0.26), residues: 300 loop : -0.84 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 117 HIS 0.004 0.001 HIS D 95 PHE 0.022 0.002 PHE K 95 TYR 0.035 0.002 TYR B 38 ARG 0.021 0.001 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 1054) hydrogen bonds : angle 4.29907 ( 3162) covalent geometry : bond 0.00302 (18933) covalent geometry : angle 0.69351 (25761) *********************** 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 501 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 500 time to evaluate : 2.275 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: B 24 ARG cc_start: 0.8694 (mpt180) cc_final: 0.8061 (mmt-90) REVERT: B 28 THR cc_start: 0.8280 (m) cc_final: 0.7718 (m) REVERT: B 38 TYR cc_start: 0.7421 (m-80) cc_final: 0.7221 (m-80) REVERT: B 57 VAL cc_start: 0.9099 (t) cc_final: 0.8838 (m) REVERT: B 79 THR cc_start: 0.9154 (p) cc_final: 0.8795 (p) REVERT: B 81 ARG cc_start: 0.8465 (ptt-90) cc_final: 0.8097 (ptt-90) REVERT: B 82 GLU cc_start: 0.9087 (mp0) cc_final: 0.8787 (mp0) REVERT: B 90 TRP cc_start: 0.9127 (t60) cc_final: 0.8915 (t60) REVERT: B 101 GLU cc_start: 0.9177 (tp30) cc_final: 0.8606 (tp30) REVERT: B 103 LEU cc_start: 0.9398 (mt) cc_final: 0.9188 (mp) REVERT: C 14 GLU cc_start: 0.9555 (tp30) cc_final: 0.9201 (tp30) REVERT: C 27 TYR cc_start: 0.9218 (m-10) cc_final: 0.8989 (m-80) REVERT: D 28 THR cc_start: 0.8696 (m) cc_final: 0.8028 (p) REVERT: D 63 GLU cc_start: 0.9315 (tp30) cc_final: 0.8446 (pp20) REVERT: D 77 PHE cc_start: 0.9315 (m-80) cc_final: 0.8921 (m-80) REVERT: D 118 LEU cc_start: 0.9503 (mp) cc_final: 0.9237 (pp) REVERT: F 38 TYR cc_start: 0.8807 (m-80) cc_final: 0.8582 (m-80) REVERT: F 71 ASP cc_start: 0.9020 (m-30) cc_final: 0.8273 (t0) REVERT: F 116 ASP cc_start: 0.8334 (m-30) cc_final: 0.7986 (p0) REVERT: G 7 MET cc_start: 0.8339 (ptt) cc_final: 0.7877 (ttp) REVERT: G 20 TYR cc_start: 0.8604 (m-80) cc_final: 0.8337 (m-10) REVERT: G 61 TYR cc_start: 0.7841 (m-80) cc_final: 0.7588 (m-80) REVERT: H 22 ASP cc_start: 0.8953 (t0) cc_final: 0.8505 (t0) REVERT: H 101 GLU cc_start: 0.9187 (tp30) cc_final: 0.8759 (mp0) REVERT: H 103 LEU cc_start: 0.9126 (mp) cc_final: 0.8918 (mp) REVERT: J 20 THR cc_start: 0.7454 (t) cc_final: 0.6165 (t) REVERT: J 22 ASP cc_start: 0.8934 (p0) cc_final: 0.8370 (t0) REVERT: K 39 GLU cc_start: 0.9500 (mp0) cc_final: 0.9232 (mp0) REVERT: L 22 ASP cc_start: 0.7260 (t0) cc_final: 0.7022 (t0) REVERT: L 23 LEU cc_start: 0.9402 (mm) cc_final: 0.9099 (mm) REVERT: L 24 ARG cc_start: 0.8476 (mpt180) cc_final: 0.8214 (mpt90) REVERT: L 39 LEU cc_start: 0.9647 (mm) cc_final: 0.9346 (pp) REVERT: L 73 TYR cc_start: 0.9016 (m-80) cc_final: 0.8574 (m-80) REVERT: L 106 THR cc_start: 0.8253 (m) cc_final: 0.7841 (m) REVERT: M 112 LEU cc_start: 0.9361 (mt) cc_final: 0.9127 (mt) REVERT: N 45 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8793 (mm-30) REVERT: N 48 LEU cc_start: 0.9368 (mm) cc_final: 0.8836 (tt) REVERT: P 38 TYR cc_start: 0.5915 (m-80) cc_final: 0.5689 (m-80) REVERT: P 63 GLU cc_start: 0.8653 (mp0) cc_final: 0.8416 (mp0) REVERT: P 119 ARG cc_start: 0.9311 (tpm170) cc_final: 0.8876 (tpt90) REVERT: Q 24 ILE cc_start: 0.9823 (mm) cc_final: 0.9599 (mm) REVERT: Q 95 PHE cc_start: 0.9065 (m-80) cc_final: 0.8520 (m-80) REVERT: R 45 GLU cc_start: 0.9218 (pp20) cc_final: 0.8678 (pp20) REVERT: R 46 LYS cc_start: 0.8755 (pttp) cc_final: 0.8531 (pttp) REVERT: R 71 ASP cc_start: 0.9056 (m-30) cc_final: 0.8100 (t0) REVERT: R 91 LEU cc_start: 0.9569 (tp) cc_final: 0.9358 (tp) REVERT: T 101 GLU cc_start: 0.8884 (tp30) cc_final: 0.8397 (mp0) REVERT: U 61 TYR cc_start: 0.9009 (m-80) cc_final: 0.8258 (m-80) REVERT: U 95 PHE cc_start: 0.9501 (m-80) cc_final: 0.9005 (m-10) REVERT: V 24 ARG cc_start: 0.8744 (mpt180) cc_final: 0.7685 (mmt-90) REVERT: W 8 TYR cc_start: 0.9013 (t80) cc_final: 0.8689 (t80) REVERT: W 33 LYS cc_start: 0.8643 (tttt) cc_final: 0.8436 (ttpt) REVERT: W 61 TYR cc_start: 0.8868 (m-80) cc_final: 0.8558 (m-80) REVERT: X 24 ARG cc_start: 0.8929 (mpt180) cc_final: 0.8482 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 500 average time/residue: 0.3006 time to fit residues: 225.9638 Evaluate side-chains 385 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 2 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 201 optimal weight: 9.9990 chunk 191 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 chunk 12 optimal weight: 30.0000 chunk 81 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 217 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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 G 43 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN M 43 ASN Q 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.053680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.040018 restraints weight = 116808.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.041336 restraints weight = 82039.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.042320 restraints weight = 62362.101| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18933 Z= 0.195 Angle : 0.731 9.415 25761 Z= 0.377 Chirality : 0.042 0.215 3051 Planarity : 0.005 0.068 3249 Dihedral : 4.677 26.122 2601 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.37 % Allowed : 6.10 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2322 helix: 1.07 (0.13), residues: 1416 sheet: -0.91 (0.25), residues: 300 loop : -0.50 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 117 HIS 0.006 0.001 HIS X 95 PHE 0.016 0.002 PHE G 95 TYR 0.043 0.003 TYR I 48 ARG 0.014 0.001 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 1054) hydrogen bonds : angle 4.57839 ( 3162) covalent geometry : bond 0.00405 (18933) covalent geometry : angle 0.73107 (25761) *********************** 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 456 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 449 time to evaluate : 2.323 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: A 53 ASN cc_start: 0.9356 (t0) cc_final: 0.9125 (t0) REVERT: A 82 TYR cc_start: 0.9231 (m-10) cc_final: 0.8699 (m-80) REVERT: B 28 THR cc_start: 0.8262 (m) cc_final: 0.7866 (m) REVERT: B 45 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8615 (mm-30) REVERT: B 78 LYS cc_start: 0.9094 (pttp) cc_final: 0.8791 (pttp) REVERT: B 81 ARG cc_start: 0.8519 (ptt-90) cc_final: 0.8124 (ptt-90) REVERT: B 101 GLU cc_start: 0.9271 (tp30) cc_final: 0.8689 (tp30) REVERT: B 104 VAL cc_start: 0.9534 (m) cc_final: 0.9297 (p) REVERT: C 14 GLU cc_start: 0.9602 (tp30) cc_final: 0.9185 (tp30) REVERT: C 49 LEU cc_start: 0.9646 (tt) cc_final: 0.9272 (mt) REVERT: C 61 TYR cc_start: 0.8569 (m-10) cc_final: 0.7930 (m-80) REVERT: D 28 THR cc_start: 0.8865 (m) cc_final: 0.8162 (p) REVERT: D 63 GLU cc_start: 0.9510 (tp30) cc_final: 0.8813 (pm20) REVERT: D 74 ARG cc_start: 0.9314 (tmm-80) cc_final: 0.8664 (tmm-80) REVERT: D 75 LEU cc_start: 0.9721 (mt) cc_final: 0.9506 (mt) REVERT: D 77 PHE cc_start: 0.9262 (m-80) cc_final: 0.8995 (m-80) REVERT: D 104 VAL cc_start: 0.9786 (m) cc_final: 0.9518 (p) REVERT: D 118 LEU cc_start: 0.9668 (mp) cc_final: 0.9463 (pp) REVERT: F 38 TYR cc_start: 0.8747 (m-80) cc_final: 0.8525 (m-80) REVERT: F 71 ASP cc_start: 0.9012 (m-30) cc_final: 0.8362 (t0) REVERT: F 116 ASP cc_start: 0.8423 (m-30) cc_final: 0.8067 (p0) REVERT: G 7 MET cc_start: 0.8350 (ptt) cc_final: 0.8149 (ptm) REVERT: G 61 TYR cc_start: 0.8097 (m-80) cc_final: 0.7788 (m-80) REVERT: G 114 LEU cc_start: 0.9250 (mt) cc_final: 0.9014 (mt) REVERT: H 85 ASP cc_start: 0.9524 (m-30) cc_final: 0.9322 (p0) REVERT: H 101 GLU cc_start: 0.9203 (tp30) cc_final: 0.8685 (mp0) REVERT: H 119 ARG cc_start: 0.9039 (tpm170) cc_final: 0.8808 (tpm170) REVERT: J 20 THR cc_start: 0.7886 (t) cc_final: 0.6437 (t) REVERT: J 22 ASP cc_start: 0.9043 (p0) cc_final: 0.8337 (t0) REVERT: K 68 ASP cc_start: 0.8418 (t0) cc_final: 0.8179 (t0) REVERT: L 39 LEU cc_start: 0.9675 (mm) cc_final: 0.9465 (pp) REVERT: L 73 TYR cc_start: 0.8995 (m-80) cc_final: 0.8680 (m-80) REVERT: L 77 PHE cc_start: 0.9423 (m-80) cc_final: 0.9035 (m-80) REVERT: M 112 LEU cc_start: 0.9497 (mt) cc_final: 0.9250 (mt) REVERT: N 45 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8756 (mm-30) REVERT: N 48 LEU cc_start: 0.9390 (mm) cc_final: 0.8820 (tp) REVERT: P 63 GLU cc_start: 0.8569 (mp0) cc_final: 0.8342 (mp0) REVERT: P 119 ARG cc_start: 0.9265 (tpm170) cc_final: 0.8834 (tpt90) REVERT: Q 95 PHE cc_start: 0.9217 (m-80) cc_final: 0.8751 (m-80) REVERT: R 25 LEU cc_start: 0.9492 (mm) cc_final: 0.9280 (mm) REVERT: R 45 GLU cc_start: 0.9270 (pp20) cc_final: 0.8726 (pp20) REVERT: R 66 LYS cc_start: 0.9570 (mmmt) cc_final: 0.9311 (mmmm) REVERT: U 95 PHE cc_start: 0.9518 (m-80) cc_final: 0.9083 (m-10) REVERT: V 22 ASP cc_start: 0.7924 (t0) cc_final: 0.6983 (t0) REVERT: W 27 TYR cc_start: 0.9431 (m-80) cc_final: 0.9228 (m-80) REVERT: W 61 TYR cc_start: 0.8802 (m-80) cc_final: 0.8544 (m-80) REVERT: X 24 ARG cc_start: 0.9014 (mpt180) cc_final: 0.8775 (mmt90) outliers start: 7 outliers final: 1 residues processed: 454 average time/residue: 0.2950 time to fit residues: 202.5148 Evaluate side-chains 364 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 107 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 GLN M 43 ASN Q 43 ASN ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.052459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.038890 restraints weight = 117148.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.040184 restraints weight = 81450.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.041168 restraints weight = 61755.241| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.6185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18933 Z= 0.209 Angle : 0.740 10.419 25761 Z= 0.382 Chirality : 0.043 0.175 3051 Planarity : 0.005 0.072 3249 Dihedral : 4.751 24.372 2601 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 25.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.17), residues: 2322 helix: 0.83 (0.13), residues: 1440 sheet: -1.14 (0.25), residues: 300 loop : -0.94 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP V 117 HIS 0.005 0.001 HIS D 95 PHE 0.015 0.002 PHE K 95 TYR 0.054 0.003 TYR K 48 ARG 0.011 0.001 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.04573 ( 1054) hydrogen bonds : angle 4.71255 ( 3162) covalent geometry : bond 0.00431 (18933) covalent geometry : angle 0.74024 (25761) *********************** 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 441 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 437 time to evaluate : 2.274 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: A 53 ASN cc_start: 0.9424 (t0) cc_final: 0.9186 (t0) REVERT: B 45 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8569 (mm-30) REVERT: B 78 LYS cc_start: 0.9059 (pttp) cc_final: 0.8738 (pttp) REVERT: B 81 ARG cc_start: 0.8561 (ptt-90) cc_final: 0.8147 (ptt-90) REVERT: B 95 HIS cc_start: 0.7369 (t-170) cc_final: 0.6398 (t-170) REVERT: B 101 GLU cc_start: 0.9293 (tp30) cc_final: 0.8996 (mp0) REVERT: B 104 VAL cc_start: 0.9545 (m) cc_final: 0.9279 (p) REVERT: C 14 GLU cc_start: 0.9537 (tp30) cc_final: 0.9206 (tp30) REVERT: C 49 LEU cc_start: 0.9575 (tt) cc_final: 0.9329 (mt) REVERT: C 61 TYR cc_start: 0.8811 (m-10) cc_final: 0.8357 (m-80) REVERT: D 22 ASP cc_start: 0.8318 (t0) cc_final: 0.7917 (t0) REVERT: D 26 LEU cc_start: 0.9571 (tp) cc_final: 0.9315 (tp) REVERT: D 63 GLU cc_start: 0.9589 (tp30) cc_final: 0.8893 (pm20) REVERT: D 74 ARG cc_start: 0.9303 (tmm-80) cc_final: 0.8754 (tmm-80) REVERT: D 75 LEU cc_start: 0.9726 (mt) cc_final: 0.9488 (mt) REVERT: D 80 THR cc_start: 0.9530 (p) cc_final: 0.9251 (t) REVERT: D 94 ARG cc_start: 0.9297 (tpm170) cc_final: 0.9069 (tpp-160) REVERT: D 104 VAL cc_start: 0.9774 (m) cc_final: 0.9530 (p) REVERT: D 118 LEU cc_start: 0.9630 (mp) cc_final: 0.9429 (pp) REVERT: F 38 TYR cc_start: 0.8709 (m-80) cc_final: 0.8482 (m-80) REVERT: F 71 ASP cc_start: 0.8997 (m-30) cc_final: 0.8364 (t0) REVERT: F 116 ASP cc_start: 0.8390 (m-30) cc_final: 0.8042 (p0) REVERT: G 61 TYR cc_start: 0.8105 (m-80) cc_final: 0.7784 (m-80) REVERT: H 85 ASP cc_start: 0.9554 (m-30) cc_final: 0.9309 (p0) REVERT: H 101 GLU cc_start: 0.9173 (tp30) cc_final: 0.8765 (mp0) REVERT: J 20 THR cc_start: 0.8287 (t) cc_final: 0.6882 (t) REVERT: J 22 ASP cc_start: 0.9029 (p0) cc_final: 0.8528 (t0) REVERT: K 19 ASN cc_start: 0.9125 (m-40) cc_final: 0.8847 (t0) REVERT: K 22 THR cc_start: 0.9701 (p) cc_final: 0.9337 (p) REVERT: L 22 ASP cc_start: 0.7412 (t0) cc_final: 0.7043 (t0) REVERT: L 23 LEU cc_start: 0.9457 (mm) cc_final: 0.9055 (mm) REVERT: L 24 ARG cc_start: 0.8716 (mpt180) cc_final: 0.8411 (mpt90) REVERT: L 39 LEU cc_start: 0.9685 (mm) cc_final: 0.9462 (pp) REVERT: L 73 TYR cc_start: 0.8998 (m-80) cc_final: 0.8554 (m-80) REVERT: L 77 PHE cc_start: 0.9504 (m-80) cc_final: 0.9297 (m-80) REVERT: L 106 THR cc_start: 0.8194 (m) cc_final: 0.7722 (m) REVERT: M 112 LEU cc_start: 0.9533 (mt) cc_final: 0.9304 (mt) REVERT: N 45 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8845 (mm-30) REVERT: N 48 LEU cc_start: 0.9384 (mm) cc_final: 0.8799 (tp) REVERT: P 119 ARG cc_start: 0.9281 (tpm170) cc_final: 0.8812 (tpt90) REVERT: Q 95 PHE cc_start: 0.9273 (m-10) cc_final: 0.8890 (m-80) REVERT: R 25 LEU cc_start: 0.9509 (mm) cc_final: 0.9286 (mm) REVERT: R 45 GLU cc_start: 0.9252 (pp20) cc_final: 0.8714 (pp20) REVERT: R 66 LYS cc_start: 0.9577 (mmmt) cc_final: 0.9295 (mmmm) REVERT: R 94 ARG cc_start: 0.8710 (tpm170) cc_final: 0.8363 (tpt90) REVERT: U 95 PHE cc_start: 0.9511 (m-80) cc_final: 0.9069 (m-10) REVERT: W 27 TYR cc_start: 0.9379 (m-80) cc_final: 0.9153 (m-80) REVERT: W 61 TYR cc_start: 0.8808 (m-80) cc_final: 0.8536 (m-80) REVERT: X 24 ARG cc_start: 0.9112 (mpt180) cc_final: 0.8373 (mpt90) outliers start: 4 outliers final: 2 residues processed: 441 average time/residue: 0.3029 time to fit residues: 201.6310 Evaluate side-chains 350 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 348 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 2 optimal weight: 3.9990 chunk 102 optimal weight: 0.0770 chunk 153 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 overall best weight: 2.5544 ------------------------------------------------------------------------------- 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 G 43 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.053886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.040084 restraints weight = 114082.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.041426 restraints weight = 79485.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.042417 restraints weight = 60313.401| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.6349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18933 Z= 0.148 Angle : 0.739 14.679 25761 Z= 0.372 Chirality : 0.043 0.311 3051 Planarity : 0.005 0.058 3249 Dihedral : 4.616 22.923 2601 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.17), residues: 2322 helix: 0.95 (0.13), residues: 1440 sheet: -1.09 (0.26), residues: 300 loop : -1.02 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 117 HIS 0.005 0.001 HIS D 95 PHE 0.016 0.002 PHE K 95 TYR 0.050 0.003 TYR Q 48 ARG 0.023 0.001 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 1054) hydrogen bonds : angle 4.60336 ( 3162) covalent geometry : bond 0.00320 (18933) covalent geometry : angle 0.73914 (25761) *********************** 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 467 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 467 time to evaluate : 1.977 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: 0.9348 (t0) cc_final: 0.9125 (t0) REVERT: B 24 ARG cc_start: 0.8723 (mpt180) cc_final: 0.7712 (mpt90) REVERT: B 45 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8570 (mm-30) REVERT: B 79 THR cc_start: 0.9109 (p) cc_final: 0.8713 (p) REVERT: B 81 ARG cc_start: 0.8560 (ptt-90) cc_final: 0.7963 (ptt-90) REVERT: B 95 HIS cc_start: 0.7383 (t-170) cc_final: 0.6373 (t-170) REVERT: B 101 GLU cc_start: 0.9288 (tp30) cc_final: 0.8965 (mp0) REVERT: C 14 GLU cc_start: 0.9535 (tp30) cc_final: 0.9217 (tp30) REVERT: C 49 LEU cc_start: 0.9569 (tt) cc_final: 0.9342 (mt) REVERT: C 61 TYR cc_start: 0.8744 (m-10) cc_final: 0.8408 (m-80) REVERT: C 65 LEU cc_start: 0.9612 (pp) cc_final: 0.9184 (mt) REVERT: D 26 LEU cc_start: 0.9577 (tp) cc_final: 0.9129 (tp) REVERT: D 28 THR cc_start: 0.8866 (m) cc_final: 0.7880 (p) REVERT: D 46 LYS cc_start: 0.8921 (ptpp) cc_final: 0.8626 (mttm) REVERT: D 63 GLU cc_start: 0.9570 (tp30) cc_final: 0.8848 (pm20) REVERT: D 74 ARG cc_start: 0.9297 (tmm-80) cc_final: 0.8665 (tmm-80) REVERT: D 77 PHE cc_start: 0.8999 (m-80) cc_final: 0.8533 (m-80) REVERT: D 80 THR cc_start: 0.9480 (p) cc_final: 0.9240 (p) REVERT: D 104 VAL cc_start: 0.9757 (m) cc_final: 0.9542 (p) REVERT: F 38 TYR cc_start: 0.8680 (m-80) cc_final: 0.8451 (m-80) REVERT: F 71 ASP cc_start: 0.9017 (m-30) cc_final: 0.8390 (t0) REVERT: F 116 ASP cc_start: 0.8303 (m-30) cc_final: 0.7969 (p0) REVERT: G 61 TYR cc_start: 0.7966 (m-80) cc_final: 0.7683 (m-80) REVERT: H 57 VAL cc_start: 0.9466 (m) cc_final: 0.9030 (p) REVERT: H 63 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8308 (mm-30) REVERT: H 85 ASP cc_start: 0.9523 (m-30) cc_final: 0.9307 (p0) REVERT: H 101 GLU cc_start: 0.9225 (tp30) cc_final: 0.8668 (mp0) REVERT: H 119 ARG cc_start: 0.9221 (tpm170) cc_final: 0.8947 (mmp-170) REVERT: J 20 THR cc_start: 0.8204 (t) cc_final: 0.6760 (t) REVERT: J 22 ASP cc_start: 0.8960 (p0) cc_final: 0.8537 (t0) REVERT: J 46 LYS cc_start: 0.9054 (ptpp) cc_final: 0.8728 (pttt) REVERT: J 48 LEU cc_start: 0.9489 (mm) cc_final: 0.8717 (tp) REVERT: K 68 ASP cc_start: 0.8439 (t0) cc_final: 0.8142 (t0) REVERT: L 22 ASP cc_start: 0.7539 (t0) cc_final: 0.7151 (t0) REVERT: L 23 LEU cc_start: 0.9512 (mm) cc_final: 0.9091 (mm) REVERT: L 24 ARG cc_start: 0.8795 (mpt180) cc_final: 0.8499 (mpt90) REVERT: L 28 THR cc_start: 0.8598 (m) cc_final: 0.8294 (p) REVERT: L 39 LEU cc_start: 0.9665 (mm) cc_final: 0.9428 (pp) REVERT: L 45 GLU cc_start: 0.9075 (pp20) cc_final: 0.8858 (pp20) REVERT: L 63 GLU cc_start: 0.9236 (mp0) cc_final: 0.8928 (mp0) REVERT: L 73 TYR cc_start: 0.8998 (m-80) cc_final: 0.8542 (m-80) REVERT: L 75 LEU cc_start: 0.9652 (mt) cc_final: 0.9370 (mt) REVERT: L 77 PHE cc_start: 0.9467 (m-80) cc_final: 0.8900 (m-80) REVERT: L 106 THR cc_start: 0.8363 (m) cc_final: 0.7974 (m) REVERT: M 112 LEU cc_start: 0.9524 (mt) cc_final: 0.9289 (mt) REVERT: N 45 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8856 (mm-30) REVERT: Q 95 PHE cc_start: 0.9241 (m-10) cc_final: 0.8758 (m-80) REVERT: R 25 LEU cc_start: 0.9542 (mm) cc_final: 0.9340 (mm) REVERT: R 33 GLU cc_start: 0.9215 (pm20) cc_final: 0.8999 (pp20) REVERT: R 45 GLU cc_start: 0.9202 (pp20) cc_final: 0.8594 (pp20) REVERT: R 46 LYS cc_start: 0.8742 (pttp) cc_final: 0.8525 (pttp) REVERT: R 66 LYS cc_start: 0.9556 (mmmt) cc_final: 0.9265 (mmmm) REVERT: R 94 ARG cc_start: 0.8777 (tpm170) cc_final: 0.8364 (tpt90) REVERT: U 95 PHE cc_start: 0.9495 (m-80) cc_final: 0.8971 (m-10) REVERT: V 22 ASP cc_start: 0.8097 (t70) cc_final: 0.5948 (t0) REVERT: W 61 TYR cc_start: 0.8890 (m-80) cc_final: 0.8562 (m-80) REVERT: X 24 ARG cc_start: 0.8981 (mpt180) cc_final: 0.8725 (mmt90) outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.2911 time to fit residues: 204.7760 Evaluate side-chains 367 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 99 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 200 optimal weight: 0.0170 chunk 20 optimal weight: 0.0570 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 145 optimal weight: 30.0000 chunk 135 optimal weight: 7.9990 chunk 227 optimal weight: 8.9990 overall best weight: 2.8142 ------------------------------------------------------------------------------- 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 G 43 ASN I 43 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3180 r_free = 0.3180 target = 0.053829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.040097 restraints weight = 115229.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.041440 restraints weight = 79708.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.042414 restraints weight = 60458.633| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.6603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18933 Z= 0.149 Angle : 0.738 12.415 25761 Z= 0.371 Chirality : 0.043 0.275 3051 Planarity : 0.005 0.080 3249 Dihedral : 4.605 26.353 2601 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.17), residues: 2322 helix: 0.95 (0.13), residues: 1440 sheet: -0.60 (0.26), residues: 300 loop : -0.99 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 117 HIS 0.004 0.001 HIS F 95 PHE 0.017 0.002 PHE K 95 TYR 0.052 0.002 TYR B 38 ARG 0.015 0.001 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 1054) hydrogen bonds : angle 4.61170 ( 3162) covalent geometry : bond 0.00323 (18933) covalent geometry : angle 0.73812 (25761) *********************** 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 453 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 2.127 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: 0.9350 (t0) cc_final: 0.9121 (t0) REVERT: B 28 THR cc_start: 0.8422 (m) cc_final: 0.8174 (m) REVERT: B 45 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8598 (mm-30) REVERT: B 78 LYS cc_start: 0.9066 (pttp) cc_final: 0.8784 (pttp) REVERT: B 81 ARG cc_start: 0.8727 (ptt-90) cc_final: 0.8264 (ptt90) REVERT: B 95 HIS cc_start: 0.7525 (t-170) cc_final: 0.6629 (t-170) REVERT: B 101 GLU cc_start: 0.9267 (tp30) cc_final: 0.8961 (mp0) REVERT: C 14 GLU cc_start: 0.9453 (tp30) cc_final: 0.9155 (tp30) REVERT: C 65 LEU cc_start: 0.9620 (pp) cc_final: 0.9198 (mt) REVERT: D 22 ASP cc_start: 0.8336 (t0) cc_final: 0.8097 (t0) REVERT: D 26 LEU cc_start: 0.9568 (tp) cc_final: 0.9298 (tp) REVERT: D 28 THR cc_start: 0.8871 (m) cc_final: 0.8268 (p) REVERT: D 46 LYS cc_start: 0.8889 (ptpp) cc_final: 0.8648 (mttm) REVERT: D 63 GLU cc_start: 0.9596 (tp30) cc_final: 0.8870 (pm20) REVERT: D 74 ARG cc_start: 0.9389 (tmm-80) cc_final: 0.8906 (tpp80) REVERT: D 75 LEU cc_start: 0.9618 (tp) cc_final: 0.9279 (tp) REVERT: D 80 THR cc_start: 0.9464 (p) cc_final: 0.9223 (p) REVERT: D 104 VAL cc_start: 0.9760 (m) cc_final: 0.9556 (p) REVERT: D 115 ARG cc_start: 0.9242 (tpp80) cc_final: 0.8878 (ttp80) REVERT: D 116 ASP cc_start: 0.9400 (m-30) cc_final: 0.9126 (m-30) REVERT: F 38 TYR cc_start: 0.8643 (m-80) cc_final: 0.8414 (m-80) REVERT: F 71 ASP cc_start: 0.9023 (m-30) cc_final: 0.8399 (t0) REVERT: F 116 ASP cc_start: 0.8309 (m-30) cc_final: 0.7979 (p0) REVERT: G 7 MET cc_start: 0.8762 (ppp) cc_final: 0.8415 (ppp) REVERT: G 61 TYR cc_start: 0.7998 (m-80) cc_final: 0.7667 (m-80) REVERT: H 85 ASP cc_start: 0.9539 (m-30) cc_final: 0.9330 (p0) REVERT: H 101 GLU cc_start: 0.9212 (tp30) cc_final: 0.8722 (mp0) REVERT: H 119 ARG cc_start: 0.9224 (tpm170) cc_final: 0.8975 (mmp-170) REVERT: J 20 THR cc_start: 0.8253 (t) cc_final: 0.6826 (t) REVERT: J 22 ASP cc_start: 0.9015 (p0) cc_final: 0.8512 (t0) REVERT: K 19 ASN cc_start: 0.9009 (m-40) cc_final: 0.8647 (m-40) REVERT: K 68 ASP cc_start: 0.8472 (t0) cc_final: 0.8179 (t0) REVERT: L 22 ASP cc_start: 0.7440 (t0) cc_final: 0.7146 (t0) REVERT: L 23 LEU cc_start: 0.9485 (mm) cc_final: 0.9077 (mm) REVERT: L 24 ARG cc_start: 0.8738 (mpt180) cc_final: 0.8457 (mpt90) REVERT: L 39 LEU cc_start: 0.9686 (mm) cc_final: 0.9458 (pp) REVERT: L 45 GLU cc_start: 0.9101 (pp20) cc_final: 0.8861 (pp20) REVERT: L 63 GLU cc_start: 0.9271 (mp0) cc_final: 0.8945 (mp0) REVERT: L 73 TYR cc_start: 0.9142 (m-80) cc_final: 0.8658 (m-80) REVERT: L 75 LEU cc_start: 0.9650 (mt) cc_final: 0.9421 (mt) REVERT: L 106 THR cc_start: 0.8279 (m) cc_final: 0.7839 (m) REVERT: M 112 LEU cc_start: 0.9558 (mt) cc_final: 0.9316 (mt) REVERT: N 54 ILE cc_start: 0.8687 (tt) cc_final: 0.8441 (tp) REVERT: P 24 ARG cc_start: 0.8935 (mpt180) cc_final: 0.8729 (mmt-90) REVERT: Q 95 PHE cc_start: 0.9305 (m-10) cc_final: 0.8866 (m-80) REVERT: R 33 GLU cc_start: 0.9207 (pm20) cc_final: 0.8982 (pp20) REVERT: R 45 GLU cc_start: 0.9166 (pp20) cc_final: 0.8590 (pp20) REVERT: R 66 LYS cc_start: 0.9568 (mmmt) cc_final: 0.9347 (mtmm) REVERT: U 95 PHE cc_start: 0.9495 (m-80) cc_final: 0.8975 (m-10) REVERT: V 23 LEU cc_start: 0.9433 (mm) cc_final: 0.9122 (mm) REVERT: V 81 ARG cc_start: 0.8989 (pmt170) cc_final: 0.8722 (ptt-90) REVERT: W 14 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8886 (tm-30) REVERT: W 61 TYR cc_start: 0.8810 (m-80) cc_final: 0.8568 (m-80) REVERT: X 24 ARG cc_start: 0.8885 (mpt180) cc_final: 0.8636 (mmt90) REVERT: X 66 LYS cc_start: 0.7247 (mmpt) cc_final: 0.7016 (mmmt) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.2901 time to fit residues: 199.2648 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 : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 22 optimal weight: 10.0000 chunk 74 optimal weight: 0.0470 chunk 45 optimal weight: 0.3980 chunk 126 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 chunk 221 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 overall best weight: 3.2884 ------------------------------------------------------------------------------- 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 G 43 ASN I 43 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3177 r_free = 0.3177 target = 0.053526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.039699 restraints weight = 116514.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.041055 restraints weight = 80548.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.042015 restraints weight = 60877.616| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.6811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 18933 Z= 0.159 Angle : 0.745 12.672 25761 Z= 0.375 Chirality : 0.043 0.183 3051 Planarity : 0.005 0.079 3249 Dihedral : 4.629 23.780 2601 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 21.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2322 helix: 0.87 (0.13), residues: 1440 sheet: -1.09 (0.26), residues: 300 loop : -1.07 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 117 HIS 0.002 0.001 HIS D 95 PHE 0.019 0.002 PHE K 95 TYR 0.045 0.003 TYR B 38 ARG 0.012 0.001 ARG R 61 Details of bonding type rmsd hydrogen bonds : bond 0.04245 ( 1054) hydrogen bonds : angle 4.71103 ( 3162) covalent geometry : bond 0.00347 (18933) covalent geometry : angle 0.74489 (25761) *********************** 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 448 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 2.262 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: A 53 ASN cc_start: 0.9341 (t0) cc_final: 0.9115 (t0) REVERT: B 45 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8602 (mm-30) REVERT: B 78 LYS cc_start: 0.9023 (pttp) cc_final: 0.8710 (pttp) REVERT: B 81 ARG cc_start: 0.8586 (ptt-90) cc_final: 0.8119 (ptt90) REVERT: B 101 GLU cc_start: 0.9285 (tp30) cc_final: 0.8759 (tt0) REVERT: C 14 GLU cc_start: 0.9429 (tp30) cc_final: 0.9053 (tp30) REVERT: D 22 ASP cc_start: 0.8271 (t0) cc_final: 0.8056 (t0) REVERT: D 28 THR cc_start: 0.8792 (m) cc_final: 0.8212 (p) REVERT: D 63 GLU cc_start: 0.9609 (tp30) cc_final: 0.8890 (pm20) REVERT: D 74 ARG cc_start: 0.8624 (tmm-80) cc_final: 0.7972 (ttp80) REVERT: D 75 LEU cc_start: 0.9605 (tp) cc_final: 0.9404 (tp) REVERT: D 80 THR cc_start: 0.9450 (p) cc_final: 0.9219 (p) REVERT: D 104 VAL cc_start: 0.9749 (m) cc_final: 0.9548 (p) REVERT: D 115 ARG cc_start: 0.9270 (tpp80) cc_final: 0.8900 (ttp80) REVERT: D 116 ASP cc_start: 0.9420 (m-30) cc_final: 0.9170 (m-30) REVERT: F 38 TYR cc_start: 0.8635 (m-80) cc_final: 0.8400 (m-80) REVERT: F 71 ASP cc_start: 0.9001 (m-30) cc_final: 0.8363 (t0) REVERT: F 116 ASP cc_start: 0.8324 (m-30) cc_final: 0.7977 (p0) REVERT: G 7 MET cc_start: 0.8663 (ppp) cc_final: 0.8378 (ppp) REVERT: G 61 TYR cc_start: 0.7995 (m-80) cc_final: 0.7634 (m-80) REVERT: H 57 VAL cc_start: 0.9425 (m) cc_final: 0.8990 (p) REVERT: H 101 GLU cc_start: 0.9227 (tp30) cc_final: 0.8784 (mp0) REVERT: H 119 ARG cc_start: 0.9230 (tpm170) cc_final: 0.8984 (mmp-170) REVERT: J 20 THR cc_start: 0.8447 (t) cc_final: 0.7036 (t) REVERT: J 22 ASP cc_start: 0.8951 (p0) cc_final: 0.8422 (t0) REVERT: K 19 ASN cc_start: 0.8937 (m-40) cc_final: 0.8571 (m-40) REVERT: K 68 ASP cc_start: 0.8535 (t0) cc_final: 0.8225 (t0) REVERT: L 22 ASP cc_start: 0.7419 (t0) cc_final: 0.7114 (t0) REVERT: L 23 LEU cc_start: 0.9407 (mm) cc_final: 0.9049 (mm) REVERT: L 45 GLU cc_start: 0.9096 (pp20) cc_final: 0.8850 (pp20) REVERT: L 63 GLU cc_start: 0.9278 (mp0) cc_final: 0.8958 (mp0) REVERT: L 73 TYR cc_start: 0.9083 (m-80) cc_final: 0.8582 (m-80) REVERT: L 106 THR cc_start: 0.8475 (m) cc_final: 0.8137 (m) REVERT: M 112 LEU cc_start: 0.9510 (mt) cc_final: 0.9237 (mt) REVERT: N 54 ILE cc_start: 0.8666 (tt) cc_final: 0.8406 (tp) REVERT: P 101 GLU cc_start: 0.8543 (tp30) cc_final: 0.7793 (mp0) REVERT: Q 95 PHE cc_start: 0.9324 (m-10) cc_final: 0.8874 (m-80) REVERT: R 33 GLU cc_start: 0.9197 (pm20) cc_final: 0.8958 (pp20) REVERT: R 45 GLU cc_start: 0.9148 (pp20) cc_final: 0.8557 (pp20) REVERT: R 66 LYS cc_start: 0.9558 (mmmt) cc_final: 0.9351 (mtmm) REVERT: U 61 TYR cc_start: 0.9124 (m-80) cc_final: 0.8526 (m-80) REVERT: U 95 PHE cc_start: 0.9483 (m-80) cc_final: 0.8974 (m-10) REVERT: V 22 ASP cc_start: 0.8118 (p0) cc_final: 0.7777 (p0) REVERT: W 61 TYR cc_start: 0.8773 (m-10) cc_final: 0.8530 (m-80) REVERT: X 24 ARG cc_start: 0.8879 (mpt180) cc_final: 0.8387 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 448 average time/residue: 0.2951 time to fit residues: 200.6450 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 : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 120 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 209 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 115 optimal weight: 20.0000 chunk 192 optimal weight: 6.9990 chunk 111 optimal weight: 0.0170 overall best weight: 1.3822 ------------------------------------------------------------------------------- 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 G 43 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3214 r_free = 0.3214 target = 0.055110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.040582 restraints weight = 113092.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.042030 restraints weight = 78899.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.043117 restraints weight = 59473.519| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.6947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18933 Z= 0.138 Angle : 0.771 15.136 25761 Z= 0.379 Chirality : 0.043 0.314 3051 Planarity : 0.005 0.071 3249 Dihedral : 4.553 22.541 2601 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2322 helix: 0.83 (0.13), residues: 1440 sheet: -1.04 (0.27), residues: 300 loop : -1.15 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 117 HIS 0.002 0.001 HIS B 95 PHE 0.020 0.001 PHE K 95 TYR 0.044 0.002 TYR B 38 ARG 0.009 0.001 ARG T 81 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 1054) hydrogen bonds : angle 4.64652 ( 3162) covalent geometry : bond 0.00303 (18933) covalent geometry : angle 0.77056 (25761) ********************** 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 461 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 2.019 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: A 53 ASN cc_start: 0.9361 (t0) cc_final: 0.9143 (t0) REVERT: B 38 TYR cc_start: 0.7496 (m-80) cc_final: 0.7201 (m-80) REVERT: B 45 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8545 (mm-30) REVERT: B 78 LYS cc_start: 0.8997 (pttp) cc_final: 0.8694 (pttp) REVERT: B 81 ARG cc_start: 0.8650 (ptt-90) cc_final: 0.8130 (ptt90) REVERT: B 90 TRP cc_start: 0.9067 (t60) cc_final: 0.8794 (t60) REVERT: B 95 HIS cc_start: 0.7267 (t-170) cc_final: 0.6397 (t-170) REVERT: B 101 GLU cc_start: 0.9263 (tp30) cc_final: 0.8968 (mp0) REVERT: C 14 GLU cc_start: 0.9412 (tp30) cc_final: 0.9207 (tp30) REVERT: C 65 LEU cc_start: 0.9630 (pp) cc_final: 0.9230 (mt) REVERT: D 28 THR cc_start: 0.8769 (m) cc_final: 0.8179 (p) REVERT: D 55 THR cc_start: 0.8604 (p) cc_final: 0.7473 (p) REVERT: D 63 GLU cc_start: 0.9592 (tp30) cc_final: 0.8871 (pm20) REVERT: D 74 ARG cc_start: 0.8597 (tmm-80) cc_final: 0.8092 (ttp80) REVERT: D 75 LEU cc_start: 0.9564 (tp) cc_final: 0.9338 (tp) REVERT: D 115 ARG cc_start: 0.9285 (tpp80) cc_final: 0.8931 (ttp80) REVERT: D 116 ASP cc_start: 0.9410 (m-30) cc_final: 0.9193 (m-30) REVERT: F 38 TYR cc_start: 0.8633 (m-80) cc_final: 0.8397 (m-80) REVERT: F 71 ASP cc_start: 0.9031 (m-30) cc_final: 0.8319 (t0) REVERT: F 116 ASP cc_start: 0.8234 (m-30) cc_final: 0.7873 (p0) REVERT: G 7 MET cc_start: 0.8584 (ppp) cc_final: 0.8299 (ppp) REVERT: G 58 ILE cc_start: 0.9620 (pt) cc_final: 0.9414 (pt) REVERT: G 61 TYR cc_start: 0.8021 (m-80) cc_final: 0.7699 (m-80) REVERT: H 57 VAL cc_start: 0.9299 (m) cc_final: 0.8828 (p) REVERT: H 101 GLU cc_start: 0.9138 (tp30) cc_final: 0.8711 (mp0) REVERT: H 119 ARG cc_start: 0.9231 (tpm170) cc_final: 0.8974 (mmp-170) REVERT: J 20 THR cc_start: 0.8404 (t) cc_final: 0.7020 (t) REVERT: J 22 ASP cc_start: 0.8932 (p0) cc_final: 0.8603 (t0) REVERT: K 19 ASN cc_start: 0.8822 (m-40) cc_final: 0.8469 (m-40) REVERT: K 68 ASP cc_start: 0.8467 (t0) cc_final: 0.8160 (t0) REVERT: L 45 GLU cc_start: 0.9126 (pp20) cc_final: 0.8827 (pp20) REVERT: L 63 GLU cc_start: 0.9327 (mp0) cc_final: 0.9037 (mp0) REVERT: L 73 TYR cc_start: 0.9168 (m-80) cc_final: 0.8706 (m-80) REVERT: M 112 LEU cc_start: 0.9515 (mt) cc_final: 0.9255 (mt) REVERT: N 45 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8844 (mm-30) REVERT: N 54 ILE cc_start: 0.8631 (tt) cc_final: 0.8350 (tp) REVERT: P 101 GLU cc_start: 0.8508 (tp30) cc_final: 0.7783 (mp0) REVERT: Q 95 PHE cc_start: 0.9317 (m-10) cc_final: 0.8901 (m-10) REVERT: R 33 GLU cc_start: 0.9191 (pm20) cc_final: 0.8959 (pp20) REVERT: R 45 GLU cc_start: 0.9138 (pp20) cc_final: 0.8504 (pp20) REVERT: T 75 LEU cc_start: 0.9340 (mp) cc_final: 0.9087 (tp) REVERT: U 61 TYR cc_start: 0.9166 (m-80) cc_final: 0.8492 (m-80) REVERT: U 95 PHE cc_start: 0.9479 (m-80) cc_final: 0.9001 (m-10) REVERT: V 20 THR cc_start: 0.7977 (t) cc_final: 0.7433 (t) REVERT: W 33 LYS cc_start: 0.9122 (ttmt) cc_final: 0.8893 (ttmt) REVERT: W 61 TYR cc_start: 0.8980 (m-10) cc_final: 0.8675 (m-80) REVERT: X 24 ARG cc_start: 0.8805 (mpt180) cc_final: 0.8329 (mmt-90) REVERT: X 53 LEU cc_start: 0.9613 (mm) cc_final: 0.9364 (mm) REVERT: X 66 LYS cc_start: 0.7289 (mmpt) cc_final: 0.7053 (mmmt) REVERT: X 73 TYR cc_start: 0.8328 (m-80) cc_final: 0.7753 (m-80) outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 0.2950 time to fit residues: 205.3121 Evaluate side-chains 361 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 107 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 116 optimal weight: 0.0370 chunk 29 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 191 optimal weight: 0.9980 overall best weight: 2.4064 ------------------------------------------------------------------------------- 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 G 43 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3200 r_free = 0.3200 target = 0.053930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.039980 restraints weight = 116118.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.041420 restraints weight = 80954.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.042473 restraints weight = 60945.681| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.7088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18933 Z= 0.146 Angle : 0.770 13.794 25761 Z= 0.383 Chirality : 0.043 0.295 3051 Planarity : 0.005 0.063 3249 Dihedral : 4.533 22.467 2601 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.17), residues: 2322 helix: 0.86 (0.13), residues: 1440 sheet: -0.75 (0.26), residues: 324 loop : -1.11 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 117 HIS 0.005 0.001 HIS F 95 PHE 0.019 0.002 PHE K 95 TYR 0.042 0.002 TYR B 38 ARG 0.009 0.001 ARG T 81 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 1054) hydrogen bonds : angle 4.69083 ( 3162) covalent geometry : bond 0.00321 (18933) covalent geometry : angle 0.76972 (25761) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6037.39 seconds wall clock time: 106 minutes 58.36 seconds (6418.36 seconds total)