Starting phenix.real_space_refine on Sun Aug 24 08:17:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umr_42382/08_2025/8umr_42382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umr_42382/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8umr_42382/08_2025/8umr_42382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umr_42382/08_2025/8umr_42382.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8umr_42382/08_2025/8umr_42382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umr_42382/08_2025/8umr_42382.map" } resolution = 4.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 11952 2.51 5 N 3120 2.21 5 O 3522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18615 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "B" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Restraints were copied for chains: C, G, I, K, M, Q, U, W, D, F, H, J, L, N, P, R, T, V, X Time building chain proxies: 2.35, per 1000 atoms: 0.13 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: 2.02 Conformation dependent library (CDL) restraints added in 822.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4554 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 4 sheets defined 63.1% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 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: 3.17 Time building geometry restraints manager: 2.53 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: 0.07 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: 0.900 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.440 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18933 Z= 0.202 Angle : 0.822 8.084 25761 Z= 0.449 Chirality : 0.045 0.186 3051 Planarity : 0.007 0.048 3249 Dihedral : 12.523 52.077 6975 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 27.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.16), residues: 2322 helix: 0.38 (0.13), residues: 1437 sheet: -0.07 (0.27), residues: 300 loop : -0.68 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 61 TYR 0.034 0.004 TYR R 38 PHE 0.017 0.003 PHE D 77 TRP 0.007 0.001 TRP F 117 HIS 0.001 0.000 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00417 (18933) covalent geometry : angle 0.82212 (25761) hydrogen bonds : bond 0.14702 ( 1054) hydrogen bonds : angle 5.82419 ( 3162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 775 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.9703 (tttt) cc_final: 0.9422 (mttt) REVERT: B 24 ARG cc_start: 0.9099 (mpt180) cc_final: 0.8193 (mmt-90) REVERT: B 52 VAL cc_start: 0.8383 (m) cc_final: 0.7413 (m) REVERT: B 103 LEU cc_start: 0.9333 (mt) cc_final: 0.8685 (mp) REVERT: C 14 GLU cc_start: 0.9508 (tp30) cc_final: 0.9005 (tp30) REVERT: C 80 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8244 (pt0) REVERT: D 26 LEU cc_start: 0.9624 (tp) cc_final: 0.9404 (tp) REVERT: D 28 THR cc_start: 0.8695 (m) cc_final: 0.8350 (m) REVERT: D 52 VAL cc_start: 0.9408 (m) cc_final: 0.9194 (m) REVERT: D 63 GLU cc_start: 0.8911 (tp30) cc_final: 0.8144 (pm20) REVERT: D 66 LYS cc_start: 0.8895 (mptt) cc_final: 0.8552 (mmmm) REVERT: D 68 VAL cc_start: 0.9536 (p) cc_final: 0.9192 (m) REVERT: D 80 THR cc_start: 0.9677 (p) cc_final: 0.9440 (p) REVERT: D 83 ARG cc_start: 0.8787 (tpp80) cc_final: 0.8414 (ttt180) REVERT: D 95 HIS cc_start: 0.7394 (t-90) cc_final: 0.6904 (t-170) REVERT: F 85 ASP cc_start: 0.9290 (m-30) cc_final: 0.8846 (t70) REVERT: F 116 ASP cc_start: 0.8510 (m-30) cc_final: 0.8226 (p0) REVERT: F 119 ARG cc_start: 0.5043 (tpm170) cc_final: 0.4475 (ptm-80) REVERT: G 20 TYR cc_start: 0.8927 (m-10) cc_final: 0.8665 (m-10) REVERT: G 68 ASP cc_start: 0.8380 (t0) cc_final: 0.8099 (p0) REVERT: G 78 LEU cc_start: 0.9543 (tp) cc_final: 0.9243 (tp) REVERT: G 99 LEU cc_start: 0.9411 (pp) cc_final: 0.9202 (pp) REVERT: H 101 GLU cc_start: 0.8763 (tp30) cc_final: 0.8271 (tp30) REVERT: H 103 LEU cc_start: 0.9035 (mt) cc_final: 0.8582 (mp) REVERT: K 14 GLU cc_start: 0.9100 (tp30) cc_final: 0.8440 (tp30) REVERT: K 19 ASN cc_start: 0.8803 (m110) cc_final: 0.8165 (m110) REVERT: K 22 THR cc_start: 0.9438 (p) cc_final: 0.8988 (p) REVERT: L 26 LEU cc_start: 0.9592 (tp) cc_final: 0.9314 (tp) REVERT: L 39 LEU cc_start: 0.9530 (mm) cc_final: 0.9121 (pp) REVERT: L 73 TYR cc_start: 0.8900 (m-80) cc_final: 0.8490 (m-80) REVERT: L 75 LEU cc_start: 0.9606 (mt) cc_final: 0.9300 (mt) REVERT: L 77 PHE cc_start: 0.9171 (m-10) cc_final: 0.8507 (m-80) REVERT: L 90 TRP cc_start: 0.9342 (t60) cc_final: 0.9131 (t60) REVERT: N 75 LEU cc_start: 0.9408 (mt) cc_final: 0.8854 (tp) REVERT: P 24 ARG cc_start: 0.8405 (mpt180) cc_final: 0.8076 (mmt-90) REVERT: P 55 THR cc_start: 0.9046 (p) cc_final: 0.8819 (t) REVERT: P 94 ARG cc_start: 0.8511 (tpm170) cc_final: 0.7830 (tpm170) REVERT: P 100 PRO cc_start: 0.2611 (Cg_exo) cc_final: 0.2411 (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: 0.9130 (tp) REVERT: T 101 GLU cc_start: 0.8516 (tp30) cc_final: 0.8166 (mp0) REVERT: U 14 GLU cc_start: 0.9189 (tp30) cc_final: 0.8670 (tp30) REVERT: U 93 GLU cc_start: 0.9323 (mp0) cc_final: 0.9018 (mp0) REVERT: V 24 ARG cc_start: 0.8508 (mpt180) cc_final: 0.7835 (mmt-90) REVERT: V 52 VAL cc_start: 0.7939 (m) cc_final: 0.7430 (m) REVERT: V 87 LEU cc_start: 0.9576 (tt) cc_final: 0.9307 (pp) REVERT: W 39 GLU cc_start: 0.9375 (mp0) cc_final: 0.9075 (mp0) REVERT: X 24 ARG cc_start: 0.8700 (mpt180) cc_final: 0.8439 (mmt-90) REVERT: X 26 LEU cc_start: 0.9527 (tp) cc_final: 0.9222 (tp) REVERT: X 75 LEU cc_start: 0.9562 (mt) cc_final: 0.9286 (pp) REVERT: X 103 LEU cc_start: 0.9262 (mt) cc_final: 0.8843 (mt) outliers start: 0 outliers final: 0 residues processed: 775 average time/residue: 0.1787 time to fit residues: 195.2669 Evaluate side-chains 446 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.0040 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.0870 overall best weight: 1.2374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 43 ASN C 19 ASN C 43 ASN G 19 ASN G 43 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 ASN I 43 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 ASN K 43 ASN K 77 ASN M 19 ASN M 43 ASN Q 19 ASN Q 43 ASN U 19 ASN U 43 ASN U 77 ASN W 19 ASN ** W 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.060913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.045657 restraints weight = 109350.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.047128 restraints weight = 78927.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.048280 restraints weight = 60984.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.049146 restraints weight = 49626.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.049825 restraints weight = 42096.756| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18933 Z= 0.152 Angle : 0.728 10.288 25761 Z= 0.369 Chirality : 0.043 0.154 3051 Planarity : 0.006 0.062 3249 Dihedral : 4.436 22.199 2601 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.47 % Allowed : 6.83 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.17), residues: 2322 helix: 0.94 (0.13), residues: 1494 sheet: 0.29 (0.28), residues: 300 loop : -1.11 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 24 TYR 0.034 0.003 TYR G 82 PHE 0.021 0.003 PHE W 95 TRP 0.018 0.001 TRP J 90 HIS 0.006 0.001 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00328 (18933) covalent geometry : angle 0.72770 (25761) hydrogen bonds : bond 0.04872 ( 1054) hydrogen bonds : angle 4.40099 ( 3162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 595 time to evaluate : 0.801 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: A 53 ASN cc_start: 0.8681 (t0) cc_final: 0.8456 (t0) REVERT: A 59 GLU cc_start: 0.9349 (pt0) cc_final: 0.8957 (pp20) REVERT: A 95 PHE cc_start: 0.8945 (m-80) cc_final: 0.8744 (m-10) REVERT: B 28 THR cc_start: 0.8342 (m) cc_final: 0.7654 (m) REVERT: B 38 TYR cc_start: 0.7469 (m-80) cc_final: 0.7062 (m-80) REVERT: B 52 VAL cc_start: 0.8269 (m) cc_final: 0.7546 (m) REVERT: B 57 VAL cc_start: 0.9059 (t) cc_final: 0.8679 (m) REVERT: B 79 THR cc_start: 0.9290 (p) cc_final: 0.8839 (p) REVERT: B 101 GLU cc_start: 0.9137 (tp30) cc_final: 0.8713 (tp30) REVERT: C 14 GLU cc_start: 0.9549 (tp30) cc_final: 0.9159 (tp30) REVERT: D 28 THR cc_start: 0.8756 (m) cc_final: 0.7979 (m) REVERT: D 80 THR cc_start: 0.9600 (p) cc_final: 0.9379 (p) REVERT: D 94 ARG cc_start: 0.9332 (tpm170) cc_final: 0.9003 (tpm170) REVERT: D 101 GLU cc_start: 0.8808 (tp30) cc_final: 0.7921 (tp30) REVERT: D 118 LEU cc_start: 0.9626 (mp) cc_final: 0.9371 (pp) REVERT: F 38 TYR cc_start: 0.8968 (m-80) cc_final: 0.8663 (m-80) REVERT: F 51 GLU cc_start: 0.8154 (tp30) cc_final: 0.7951 (mp0) REVERT: F 71 ASP cc_start: 0.9077 (m-30) cc_final: 0.8332 (t0) REVERT: F 119 ARG cc_start: 0.5373 (tpm170) cc_final: 0.4847 (ptm-80) REVERT: G 7 MET cc_start: 0.8251 (ptt) cc_final: 0.7980 (ptm) REVERT: H 101 GLU cc_start: 0.9156 (tp30) cc_final: 0.8545 (tp30) REVERT: J 46 LYS cc_start: 0.8931 (ptpp) cc_final: 0.8428 (pttt) REVERT: K 14 GLU cc_start: 0.9186 (tp30) cc_final: 0.8245 (tp30) REVERT: K 19 ASN cc_start: 0.8667 (m-40) cc_final: 0.8010 (m-40) REVERT: K 22 THR cc_start: 0.9440 (p) cc_final: 0.9149 (p) REVERT: L 39 LEU cc_start: 0.9569 (mm) cc_final: 0.9156 (pp) REVERT: L 48 LEU cc_start: 0.9003 (mt) cc_final: 0.8232 (tp) REVERT: L 73 TYR cc_start: 0.8883 (m-80) cc_final: 0.8462 (m-10) REVERT: M 112 LEU cc_start: 0.9375 (mt) cc_final: 0.9138 (mt) REVERT: N 29 THR cc_start: 0.9229 (t) cc_final: 0.9021 (t) REVERT: N 48 LEU cc_start: 0.9381 (mm) cc_final: 0.8640 (mm) REVERT: N 75 LEU cc_start: 0.9555 (mt) cc_final: 0.9117 (tp) REVERT: N 92 GLN cc_start: 0.9069 (mt0) cc_final: 0.8851 (pp30) REVERT: P 79 THR cc_start: 0.7542 (m) cc_final: 0.6882 (m) REVERT: Q 95 PHE cc_start: 0.8889 (m-80) cc_final: 0.8424 (m-80) REVERT: R 45 GLU cc_start: 0.9175 (pp20) cc_final: 0.8606 (pp20) REVERT: R 46 LYS cc_start: 0.8887 (pttp) cc_final: 0.8621 (pttp) REVERT: R 63 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8060 (mm-30) REVERT: R 70 GLU cc_start: 0.9282 (mp0) cc_final: 0.9055 (pm20) REVERT: R 71 ASP cc_start: 0.8862 (m-30) cc_final: 0.8181 (t0) REVERT: U 61 TYR cc_start: 0.8842 (m-80) cc_final: 0.8396 (m-80) REVERT: U 95 PHE cc_start: 0.9391 (m-80) cc_final: 0.9176 (m-10) REVERT: V 22 ASP cc_start: 0.7976 (t0) cc_final: 0.7515 (t0) REVERT: V 24 ARG cc_start: 0.8556 (mpt180) cc_final: 0.7884 (mmt-90) REVERT: V 52 VAL cc_start: 0.8016 (m) cc_final: 0.7790 (m) REVERT: W 76 TYR cc_start: 0.8867 (t80) cc_final: 0.8534 (t80) REVERT: X 26 LEU cc_start: 0.9642 (tp) cc_final: 0.9412 (tp) REVERT: X 103 LEU cc_start: 0.9376 (mt) cc_final: 0.9167 (mm) outliers start: 9 outliers final: 6 residues processed: 600 average time/residue: 0.1572 time to fit residues: 139.1871 Evaluate side-chains 426 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 420 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 33 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 207 optimal weight: 0.5980 chunk 193 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 104 optimal weight: 0.0980 chunk 91 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 I 77 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN M 43 ASN Q 43 ASN ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 ASN W 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.061144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.045974 restraints weight = 105504.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.047389 restraints weight = 75697.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.048516 restraints weight = 58691.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.049387 restraints weight = 47808.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.049923 restraints weight = 40518.178| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18933 Z= 0.139 Angle : 0.707 9.155 25761 Z= 0.351 Chirality : 0.042 0.151 3051 Planarity : 0.005 0.103 3249 Dihedral : 4.368 22.054 2601 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.05 % Allowed : 6.10 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.17), residues: 2322 helix: 0.99 (0.14), residues: 1458 sheet: 0.43 (0.29), residues: 300 loop : -0.82 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 24 TYR 0.033 0.003 TYR W 61 PHE 0.016 0.002 PHE W 95 TRP 0.011 0.001 TRP L 90 HIS 0.005 0.001 HIS T 95 Details of bonding type rmsd covalent geometry : bond 0.00301 (18933) covalent geometry : angle 0.70653 (25761) hydrogen bonds : bond 0.04439 ( 1054) hydrogen bonds : angle 4.31909 ( 3162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 544 time to evaluate : 0.780 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: A 53 ASN cc_start: 0.8450 (t0) cc_final: 0.8246 (t0) REVERT: B 24 ARG cc_start: 0.8747 (mpt180) cc_final: 0.7929 (mpt90) REVERT: B 38 TYR cc_start: 0.7385 (m-80) cc_final: 0.7120 (m-80) REVERT: B 57 VAL cc_start: 0.9085 (t) cc_final: 0.8746 (m) REVERT: B 79 THR cc_start: 0.9235 (p) cc_final: 0.8604 (p) REVERT: B 81 ARG cc_start: 0.8481 (ptt-90) cc_final: 0.8081 (ptt-90) REVERT: B 84 LEU cc_start: 0.9806 (mt) cc_final: 0.9444 (mt) REVERT: B 92 GLN cc_start: 0.9153 (pp30) cc_final: 0.8860 (pp30) REVERT: B 95 HIS cc_start: 0.6272 (t-170) cc_final: 0.5062 (t-170) REVERT: C 14 GLU cc_start: 0.9518 (tp30) cc_final: 0.9193 (tp30) REVERT: D 22 ASP cc_start: 0.7999 (t0) cc_final: 0.7663 (t0) REVERT: D 28 THR cc_start: 0.8606 (m) cc_final: 0.8273 (m) REVERT: D 45 GLU cc_start: 0.8504 (pp20) cc_final: 0.8295 (tm-30) REVERT: D 94 ARG cc_start: 0.9264 (tpm170) cc_final: 0.8886 (tpm170) REVERT: D 118 LEU cc_start: 0.9600 (mp) cc_final: 0.9371 (pp) REVERT: F 38 TYR cc_start: 0.9011 (m-80) cc_final: 0.8771 (m-10) REVERT: F 51 GLU cc_start: 0.8241 (tp30) cc_final: 0.8018 (mp0) REVERT: F 71 ASP cc_start: 0.9110 (m-30) cc_final: 0.8322 (t0) REVERT: F 116 ASP cc_start: 0.9052 (p0) cc_final: 0.8725 (m-30) REVERT: F 119 ARG cc_start: 0.5538 (tpm170) cc_final: 0.4808 (ptm-80) REVERT: G 7 MET cc_start: 0.8238 (ptt) cc_final: 0.7829 (ttp) REVERT: H 22 ASP cc_start: 0.8778 (t0) cc_final: 0.8548 (t0) REVERT: H 101 GLU cc_start: 0.9208 (tp30) cc_final: 0.8800 (mp0) REVERT: I 55 GLU cc_start: 0.9313 (mp0) cc_final: 0.8894 (pm20) REVERT: J 22 ASP cc_start: 0.8633 (p0) cc_final: 0.8099 (t0) REVERT: J 63 GLU cc_start: 0.8617 (pm20) cc_final: 0.8373 (pm20) REVERT: K 14 GLU cc_start: 0.9190 (tp30) cc_final: 0.8437 (tp30) REVERT: K 19 ASN cc_start: 0.8612 (m-40) cc_final: 0.7777 (m110) REVERT: K 22 THR cc_start: 0.9458 (p) cc_final: 0.9217 (p) REVERT: K 78 LEU cc_start: 0.9477 (tp) cc_final: 0.9267 (tp) REVERT: L 39 LEU cc_start: 0.9586 (mm) cc_final: 0.9193 (pp) REVERT: L 73 TYR cc_start: 0.9038 (m-80) cc_final: 0.8413 (m-80) REVERT: M 112 LEU cc_start: 0.9351 (mt) cc_final: 0.9071 (mt) REVERT: N 29 THR cc_start: 0.9347 (t) cc_final: 0.8885 (m) REVERT: N 45 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8707 (mm-30) REVERT: N 74 ARG cc_start: 0.9391 (tpt90) cc_final: 0.9116 (tpt170) REVERT: N 92 GLN cc_start: 0.9114 (mt0) cc_final: 0.8722 (tp40) REVERT: P 63 GLU cc_start: 0.8510 (mp0) cc_final: 0.8282 (mp0) REVERT: P 101 GLU cc_start: 0.7978 (tp30) cc_final: 0.7197 (mp0) REVERT: Q 95 PHE cc_start: 0.8784 (m-80) cc_final: 0.8240 (m-80) REVERT: R 45 GLU cc_start: 0.9191 (pp20) cc_final: 0.8664 (pp20) REVERT: R 60 VAL cc_start: 0.8760 (p) cc_final: 0.8550 (p) REVERT: R 70 GLU cc_start: 0.9261 (mp0) cc_final: 0.8970 (pm20) REVERT: R 71 ASP cc_start: 0.8977 (m-30) cc_final: 0.8121 (t0) REVERT: R 77 PHE cc_start: 0.9474 (m-10) cc_final: 0.9152 (m-10) REVERT: R 91 LEU cc_start: 0.9305 (tp) cc_final: 0.9042 (tp) REVERT: T 28 THR cc_start: 0.8640 (m) cc_final: 0.7760 (p) REVERT: T 75 LEU cc_start: 0.9210 (mp) cc_final: 0.8810 (tt) REVERT: U 61 TYR cc_start: 0.8820 (m-80) cc_final: 0.8197 (m-80) REVERT: U 95 PHE cc_start: 0.9368 (m-80) cc_final: 0.9013 (m-10) REVERT: V 22 ASP cc_start: 0.7930 (t0) cc_final: 0.7650 (t0) REVERT: V 24 ARG cc_start: 0.8602 (mpt180) cc_final: 0.7913 (mmt-90) REVERT: V 28 THR cc_start: 0.8633 (m) cc_final: 0.8154 (m) REVERT: V 52 VAL cc_start: 0.8193 (m) cc_final: 0.7886 (m) REVERT: V 91 LEU cc_start: 0.9388 (tp) cc_final: 0.9176 (tp) REVERT: X 26 LEU cc_start: 0.9621 (tp) cc_final: 0.9319 (tp) outliers start: 1 outliers final: 0 residues processed: 544 average time/residue: 0.1497 time to fit residues: 120.8193 Evaluate side-chains 408 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 146 optimal weight: 9.9990 chunk 194 optimal weight: 20.0000 chunk 17 optimal weight: 30.0000 chunk 67 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 181 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 161 optimal weight: 0.0050 chunk 203 optimal weight: 4.9990 overall best weight: 1.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN G 43 ASN H 92 GLN I 43 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN M 43 ASN Q 43 ASN U 43 ASN W 77 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.060378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.045337 restraints weight = 104226.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.046737 restraints weight = 74866.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.047802 restraints weight = 57842.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.048652 restraints weight = 47244.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.049301 restraints weight = 40167.696| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18933 Z= 0.130 Angle : 0.673 9.771 25761 Z= 0.335 Chirality : 0.041 0.190 3051 Planarity : 0.005 0.088 3249 Dihedral : 4.339 21.621 2601 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.05 % Allowed : 6.26 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.17), residues: 2322 helix: 1.05 (0.14), residues: 1458 sheet: 0.36 (0.28), residues: 300 loop : -0.81 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 24 TYR 0.045 0.002 TYR K 48 PHE 0.016 0.002 PHE A 95 TRP 0.010 0.001 TRP B 90 HIS 0.006 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00281 (18933) covalent geometry : angle 0.67341 (25761) hydrogen bonds : bond 0.04219 ( 1054) hydrogen bonds : angle 4.19338 ( 3162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 510 time to evaluate : 0.814 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: A 53 ASN cc_start: 0.8553 (t0) cc_final: 0.8347 (t0) REVERT: B 24 ARG cc_start: 0.8810 (mpt180) cc_final: 0.8358 (mmt-90) REVERT: B 38 TYR cc_start: 0.7443 (m-80) cc_final: 0.7230 (m-10) REVERT: B 45 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8448 (mm-30) REVERT: B 57 VAL cc_start: 0.9179 (t) cc_final: 0.8893 (m) REVERT: B 81 ARG cc_start: 0.8689 (ptt-90) cc_final: 0.8192 (ptt-90) REVERT: B 92 GLN cc_start: 0.9176 (pp30) cc_final: 0.8893 (pp30) REVERT: C 14 GLU cc_start: 0.9550 (tp30) cc_final: 0.9151 (tp30) REVERT: C 28 THR cc_start: 0.9647 (p) cc_final: 0.9420 (p) REVERT: D 77 PHE cc_start: 0.9370 (m-80) cc_final: 0.9087 (m-80) REVERT: D 118 LEU cc_start: 0.9617 (mp) cc_final: 0.9350 (pp) REVERT: F 38 TYR cc_start: 0.8852 (m-80) cc_final: 0.8646 (m-10) REVERT: F 71 ASP cc_start: 0.9126 (m-30) cc_final: 0.8362 (t0) REVERT: F 115 ARG cc_start: 0.7539 (tpp-160) cc_final: 0.7205 (tpp-160) REVERT: F 116 ASP cc_start: 0.9001 (p0) cc_final: 0.8680 (m-30) REVERT: F 119 ARG cc_start: 0.5313 (tpm170) cc_final: 0.4610 (ptm-80) REVERT: G 7 MET cc_start: 0.8276 (ptt) cc_final: 0.8067 (ptm) REVERT: G 61 TYR cc_start: 0.7676 (m-80) cc_final: 0.7453 (m-80) REVERT: G 114 LEU cc_start: 0.9091 (mt) cc_final: 0.8861 (mt) REVERT: H 22 ASP cc_start: 0.8826 (t0) cc_final: 0.8592 (t0) REVERT: H 101 GLU cc_start: 0.9120 (tp30) cc_final: 0.8660 (mp0) REVERT: I 55 GLU cc_start: 0.9315 (mp0) cc_final: 0.8898 (pm20) REVERT: J 20 THR cc_start: 0.7161 (t) cc_final: 0.5811 (t) REVERT: J 22 ASP cc_start: 0.8926 (p0) cc_final: 0.8195 (t0) REVERT: J 63 GLU cc_start: 0.8761 (pm20) cc_final: 0.8557 (pm20) REVERT: K 39 GLU cc_start: 0.9466 (mp0) cc_final: 0.9205 (mp0) REVERT: K 78 LEU cc_start: 0.9478 (tp) cc_final: 0.9278 (tp) REVERT: L 39 LEU cc_start: 0.9599 (mm) cc_final: 0.9202 (pp) REVERT: L 73 TYR cc_start: 0.9096 (m-80) cc_final: 0.8708 (m-80) REVERT: L 87 LEU cc_start: 0.9566 (tt) cc_final: 0.9313 (pp) REVERT: M 112 LEU cc_start: 0.9316 (mt) cc_final: 0.8784 (mt) REVERT: N 48 LEU cc_start: 0.9406 (mm) cc_final: 0.8815 (tt) REVERT: N 92 GLN cc_start: 0.9221 (mt0) cc_final: 0.8806 (tp40) REVERT: P 63 GLU cc_start: 0.8568 (mp0) cc_final: 0.8305 (mp0) REVERT: Q 95 PHE cc_start: 0.8839 (m-80) cc_final: 0.8215 (m-80) REVERT: R 45 GLU cc_start: 0.9182 (pp20) cc_final: 0.8631 (pp20) REVERT: R 46 LYS cc_start: 0.8900 (pttp) cc_final: 0.8615 (pttm) REVERT: R 60 VAL cc_start: 0.8643 (p) cc_final: 0.8396 (p) REVERT: R 70 GLU cc_start: 0.9312 (mp0) cc_final: 0.8890 (mp0) REVERT: R 71 ASP cc_start: 0.9067 (m-30) cc_final: 0.8136 (t0) REVERT: R 77 PHE cc_start: 0.9579 (m-10) cc_final: 0.9337 (m-10) REVERT: R 91 LEU cc_start: 0.9350 (tp) cc_final: 0.9129 (tp) REVERT: T 75 LEU cc_start: 0.9198 (mp) cc_final: 0.8964 (tp) REVERT: U 61 TYR cc_start: 0.8800 (m-80) cc_final: 0.8317 (m-80) REVERT: U 95 PHE cc_start: 0.9361 (m-80) cc_final: 0.9023 (m-10) REVERT: V 22 ASP cc_start: 0.8215 (t0) cc_final: 0.7571 (t0) REVERT: V 24 ARG cc_start: 0.8627 (mpt180) cc_final: 0.7934 (mmt-90) REVERT: V 52 VAL cc_start: 0.8127 (m) cc_final: 0.7923 (m) REVERT: V 64 ASN cc_start: 0.8985 (p0) cc_final: 0.8676 (p0) REVERT: V 91 LEU cc_start: 0.9475 (tp) cc_final: 0.9270 (tp) REVERT: W 27 TYR cc_start: 0.9321 (m-10) cc_final: 0.8999 (m-10) REVERT: X 26 LEU cc_start: 0.9673 (tp) cc_final: 0.9279 (tp) REVERT: X 77 PHE cc_start: 0.9611 (m-80) cc_final: 0.9115 (m-80) outliers start: 1 outliers final: 0 residues processed: 510 average time/residue: 0.1413 time to fit residues: 108.1387 Evaluate side-chains 400 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 36 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 142 optimal weight: 0.0970 chunk 199 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- 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 I 90 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN M 43 ASN Q 43 ASN Q 90 ASN U 43 ASN W 90 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 = 0.3266 r_free = 0.3266 target = 0.057546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.042695 restraints weight = 107062.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.044085 restraints weight = 75413.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.045155 restraints weight = 57241.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.045982 restraints weight = 46414.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.046609 restraints weight = 39238.063| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18933 Z= 0.157 Angle : 0.692 9.205 25761 Z= 0.352 Chirality : 0.041 0.150 3051 Planarity : 0.005 0.086 3249 Dihedral : 4.415 22.473 2601 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.21 % Allowed : 5.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.17), residues: 2322 helix: 1.17 (0.14), residues: 1434 sheet: -0.45 (0.27), residues: 300 loop : -0.44 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 24 TYR 0.026 0.002 TYR D 73 PHE 0.013 0.002 PHE G 95 TRP 0.016 0.001 TRP B 90 HIS 0.005 0.001 HIS X 95 Details of bonding type rmsd covalent geometry : bond 0.00331 (18933) covalent geometry : angle 0.69249 (25761) hydrogen bonds : bond 0.04221 ( 1054) hydrogen bonds : angle 4.33752 ( 3162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 468 time to evaluate : 0.526 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: B 24 ARG cc_start: 0.8724 (mpt180) cc_final: 0.7892 (mpt90) REVERT: B 45 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8555 (mm-30) REVERT: B 57 VAL cc_start: 0.9222 (t) cc_final: 0.8925 (m) REVERT: B 79 THR cc_start: 0.9251 (p) cc_final: 0.8880 (p) REVERT: B 81 ARG cc_start: 0.8521 (ptt-90) cc_final: 0.8185 (ptt-90) REVERT: C 14 GLU cc_start: 0.9578 (tp30) cc_final: 0.9209 (tp30) REVERT: D 24 ARG cc_start: 0.8960 (mpt180) cc_final: 0.8656 (mpt180) REVERT: D 28 THR cc_start: 0.8884 (m) cc_final: 0.8396 (m) REVERT: D 77 PHE cc_start: 0.9323 (m-80) cc_final: 0.9062 (m-80) REVERT: D 118 LEU cc_start: 0.9613 (mp) cc_final: 0.9376 (pp) REVERT: F 38 TYR cc_start: 0.8833 (m-80) cc_final: 0.8630 (m-80) REVERT: F 71 ASP cc_start: 0.9141 (m-30) cc_final: 0.8428 (t0) REVERT: F 115 ARG cc_start: 0.7602 (tpp-160) cc_final: 0.7346 (tpp-160) REVERT: F 116 ASP cc_start: 0.8960 (p0) cc_final: 0.8723 (m-30) REVERT: F 119 ARG cc_start: 0.4938 (tpm170) cc_final: 0.4307 (ttt90) REVERT: G 61 TYR cc_start: 0.7941 (m-80) cc_final: 0.7614 (m-80) REVERT: G 114 LEU cc_start: 0.9225 (mt) cc_final: 0.8969 (mt) REVERT: H 101 GLU cc_start: 0.9075 (tp30) cc_final: 0.8699 (mp0) REVERT: H 119 ARG cc_start: 0.8971 (tpm170) cc_final: 0.8681 (tpm170) REVERT: J 20 THR cc_start: 0.7405 (t) cc_final: 0.6084 (t) REVERT: J 22 ASP cc_start: 0.8955 (p0) cc_final: 0.8120 (t0) REVERT: L 22 ASP cc_start: 0.7529 (t0) cc_final: 0.7115 (t0) REVERT: L 23 LEU cc_start: 0.9398 (mm) cc_final: 0.9032 (mm) REVERT: L 24 ARG cc_start: 0.8361 (mpt180) cc_final: 0.8051 (mpt90) REVERT: L 39 LEU cc_start: 0.9644 (mm) cc_final: 0.9359 (pp) REVERT: L 73 TYR cc_start: 0.9086 (m-80) cc_final: 0.8622 (m-80) REVERT: L 106 THR cc_start: 0.8188 (m) cc_final: 0.7731 (m) REVERT: M 112 LEU cc_start: 0.9431 (mt) cc_final: 0.9156 (mt) REVERT: N 45 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8729 (mm-30) REVERT: N 48 LEU cc_start: 0.9401 (mm) cc_final: 0.8912 (tp) REVERT: N 92 GLN cc_start: 0.9272 (mt0) cc_final: 0.9067 (pp30) REVERT: P 63 GLU cc_start: 0.8619 (mp0) cc_final: 0.8359 (mp0) REVERT: P 79 THR cc_start: 0.8463 (m) cc_final: 0.8243 (m) REVERT: P 101 GLU cc_start: 0.8050 (tp30) cc_final: 0.7008 (mp0) REVERT: Q 95 PHE cc_start: 0.9042 (m-10) cc_final: 0.8554 (m-80) REVERT: R 45 GLU cc_start: 0.9180 (pp20) cc_final: 0.8613 (pp20) REVERT: R 46 LYS cc_start: 0.8722 (pttp) cc_final: 0.8502 (pttp) REVERT: T 28 THR cc_start: 0.8402 (m) cc_final: 0.7781 (m) REVERT: T 75 LEU cc_start: 0.9237 (mp) cc_final: 0.8955 (tp) REVERT: U 61 TYR cc_start: 0.8954 (m-80) cc_final: 0.8409 (m-80) REVERT: U 95 PHE cc_start: 0.9444 (m-80) cc_final: 0.8989 (m-10) REVERT: V 22 ASP cc_start: 0.8075 (t0) cc_final: 0.7405 (t0) REVERT: V 24 ARG cc_start: 0.8684 (mpt180) cc_final: 0.7707 (mmt-90) REVERT: V 82 GLU cc_start: 0.9082 (mp0) cc_final: 0.8868 (mp0) REVERT: V 104 VAL cc_start: 0.9691 (m) cc_final: 0.9485 (p) REVERT: W 44 LEU cc_start: 0.9782 (tp) cc_final: 0.9427 (pp) REVERT: W 61 TYR cc_start: 0.8737 (m-80) cc_final: 0.8522 (m-80) REVERT: X 26 LEU cc_start: 0.9685 (tp) cc_final: 0.9368 (tp) REVERT: X 77 PHE cc_start: 0.9662 (m-80) cc_final: 0.9267 (m-80) outliers start: 4 outliers final: 0 residues processed: 471 average time/residue: 0.1334 time to fit residues: 94.9702 Evaluate side-chains 363 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 176 optimal weight: 7.9990 chunk 217 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 U 90 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 = 0.3257 r_free = 0.3257 target = 0.057173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.042535 restraints weight = 110648.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.043948 restraints weight = 78538.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.044995 restraints weight = 59217.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.045773 restraints weight = 48080.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.046351 restraints weight = 40988.307| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18933 Z= 0.147 Angle : 0.692 10.455 25761 Z= 0.348 Chirality : 0.042 0.162 3051 Planarity : 0.005 0.057 3249 Dihedral : 4.439 24.448 2601 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.21 % Allowed : 4.75 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.17), residues: 2322 helix: 1.18 (0.14), residues: 1416 sheet: -0.45 (0.28), residues: 276 loop : -0.49 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 61 TYR 0.030 0.002 TYR B 38 PHE 0.012 0.002 PHE A 95 TRP 0.014 0.001 TRP V 117 HIS 0.003 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00315 (18933) covalent geometry : angle 0.69216 (25761) hydrogen bonds : bond 0.04188 ( 1054) hydrogen bonds : angle 4.37169 ( 3162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 456 time to evaluate : 0.728 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: A 95 PHE cc_start: 0.8928 (m-80) cc_final: 0.8658 (m-10) REVERT: B 45 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8458 (mm-30) REVERT: B 78 LYS cc_start: 0.9104 (pttp) cc_final: 0.8812 (pttp) REVERT: B 81 ARG cc_start: 0.8729 (ptt-90) cc_final: 0.8463 (ptt-90) REVERT: C 14 GLU cc_start: 0.9468 (tp30) cc_final: 0.9214 (tp30) REVERT: D 28 THR cc_start: 0.8868 (m) cc_final: 0.8494 (m) REVERT: F 38 TYR cc_start: 0.8840 (m-80) cc_final: 0.8628 (m-80) REVERT: F 71 ASP cc_start: 0.9187 (m-30) cc_final: 0.8482 (t0) REVERT: F 115 ARG cc_start: 0.7657 (tpp-160) cc_final: 0.7384 (tpp-160) REVERT: F 116 ASP cc_start: 0.8965 (p0) cc_final: 0.8685 (m-30) REVERT: F 119 ARG cc_start: 0.6031 (tpm170) cc_final: 0.5753 (ttt90) REVERT: G 61 TYR cc_start: 0.8038 (m-80) cc_final: 0.7647 (m-80) REVERT: G 114 LEU cc_start: 0.9277 (mt) cc_final: 0.9008 (mt) REVERT: H 101 GLU cc_start: 0.9080 (tp30) cc_final: 0.8575 (mp0) REVERT: H 119 ARG cc_start: 0.8973 (tpm170) cc_final: 0.8760 (tpm170) REVERT: J 20 THR cc_start: 0.7643 (t) cc_final: 0.6300 (t) REVERT: J 22 ASP cc_start: 0.9019 (p0) cc_final: 0.8466 (t0) REVERT: L 39 LEU cc_start: 0.9675 (mm) cc_final: 0.9390 (pp) REVERT: L 73 TYR cc_start: 0.9051 (m-80) cc_final: 0.8353 (m-80) REVERT: M 112 LEU cc_start: 0.9442 (mt) cc_final: 0.8999 (pp) REVERT: P 63 GLU cc_start: 0.8592 (mp0) cc_final: 0.8379 (mp0) REVERT: P 79 THR cc_start: 0.8378 (m) cc_final: 0.7701 (m) REVERT: P 119 ARG cc_start: 0.9211 (tpm170) cc_final: 0.8829 (tpt90) REVERT: Q 95 PHE cc_start: 0.9083 (m-10) cc_final: 0.8613 (m-80) REVERT: R 45 GLU cc_start: 0.9201 (pp20) cc_final: 0.8629 (pp20) REVERT: R 46 LYS cc_start: 0.8591 (pttp) cc_final: 0.8364 (pttp) REVERT: R 77 PHE cc_start: 0.9622 (m-10) cc_final: 0.9421 (m-10) REVERT: T 75 LEU cc_start: 0.9242 (mp) cc_final: 0.8935 (tp) REVERT: U 61 TYR cc_start: 0.8931 (m-80) cc_final: 0.8392 (m-80) REVERT: U 95 PHE cc_start: 0.9417 (m-80) cc_final: 0.8974 (m-10) REVERT: V 22 ASP cc_start: 0.7767 (t0) cc_final: 0.7432 (t0) REVERT: W 62 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8962 (mp10) REVERT: X 26 LEU cc_start: 0.9662 (tp) cc_final: 0.9275 (tp) REVERT: X 77 PHE cc_start: 0.9664 (m-80) cc_final: 0.9274 (m-80) outliers start: 4 outliers final: 2 residues processed: 460 average time/residue: 0.1400 time to fit residues: 97.8232 Evaluate side-chains 358 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 355 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 59 optimal weight: 0.9980 chunk 225 optimal weight: 6.9990 chunk 205 optimal weight: 20.0000 chunk 123 optimal weight: 0.8980 chunk 217 optimal weight: 5.9990 chunk 145 optimal weight: 30.0000 chunk 208 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- 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 = 0.3220 r_free = 0.3220 target = 0.055484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.041224 restraints weight = 112605.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.042556 restraints weight = 79284.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.043553 restraints weight = 60805.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.044351 restraints weight = 49088.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.044914 restraints weight = 41632.666| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.6061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18933 Z= 0.168 Angle : 0.727 9.889 25761 Z= 0.372 Chirality : 0.042 0.171 3051 Planarity : 0.006 0.131 3249 Dihedral : 4.511 22.516 2601 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.17), residues: 2322 helix: 0.96 (0.13), residues: 1440 sheet: -0.25 (0.27), residues: 324 loop : -0.84 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 93 TYR 0.052 0.003 TYR I 48 PHE 0.013 0.002 PHE K 95 TRP 0.015 0.001 TRP V 117 HIS 0.004 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00353 (18933) covalent geometry : angle 0.72733 (25761) hydrogen bonds : bond 0.04253 ( 1054) hydrogen bonds : angle 4.62362 ( 3162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 0.652 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: B 28 THR cc_start: 0.8727 (m) cc_final: 0.8200 (m) REVERT: B 45 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8463 (mm-30) REVERT: B 78 LYS cc_start: 0.9146 (pttp) cc_final: 0.8869 (pttp) REVERT: B 104 VAL cc_start: 0.9623 (m) cc_final: 0.9373 (p) REVERT: C 14 GLU cc_start: 0.9429 (tp30) cc_final: 0.9149 (tp30) REVERT: D 26 LEU cc_start: 0.9668 (tp) cc_final: 0.9331 (tp) REVERT: D 28 THR cc_start: 0.8888 (m) cc_final: 0.8377 (m) REVERT: D 77 PHE cc_start: 0.9223 (m-80) cc_final: 0.8749 (m-80) REVERT: F 71 ASP cc_start: 0.9192 (m-30) cc_final: 0.8531 (t0) REVERT: G 61 TYR cc_start: 0.8281 (m-10) cc_final: 0.7813 (m-80) REVERT: H 22 ASP cc_start: 0.8848 (t0) cc_final: 0.8627 (t0) REVERT: H 101 GLU cc_start: 0.9126 (tp30) cc_final: 0.8747 (mp0) REVERT: J 20 THR cc_start: 0.7970 (t) cc_final: 0.6544 (t) REVERT: J 22 ASP cc_start: 0.8997 (p0) cc_final: 0.8446 (t0) REVERT: L 22 ASP cc_start: 0.7517 (t0) cc_final: 0.7064 (t0) REVERT: L 23 LEU cc_start: 0.9432 (mm) cc_final: 0.9088 (mm) REVERT: L 24 ARG cc_start: 0.8457 (mpt180) cc_final: 0.8099 (mpt90) REVERT: L 39 LEU cc_start: 0.9695 (mm) cc_final: 0.9413 (pp) REVERT: L 73 TYR cc_start: 0.9098 (m-80) cc_final: 0.8626 (m-80) REVERT: L 106 THR cc_start: 0.8188 (m) cc_final: 0.7715 (m) REVERT: M 92 ILE cc_start: 0.9406 (mm) cc_final: 0.9204 (mm) REVERT: M 112 LEU cc_start: 0.9508 (mt) cc_final: 0.9015 (pp) REVERT: N 45 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8827 (mm-30) REVERT: P 63 GLU cc_start: 0.8653 (mp0) cc_final: 0.8446 (mp0) REVERT: P 119 ARG cc_start: 0.9154 (tpm170) cc_final: 0.8789 (tpt90) REVERT: Q 95 PHE cc_start: 0.9207 (m-10) cc_final: 0.8706 (m-80) REVERT: R 45 GLU cc_start: 0.9165 (pp20) cc_final: 0.8643 (pp20) REVERT: T 75 LEU cc_start: 0.9238 (mp) cc_final: 0.8958 (tp) REVERT: U 61 TYR cc_start: 0.8919 (m-80) cc_final: 0.8437 (m-80) REVERT: U 95 PHE cc_start: 0.9428 (m-80) cc_final: 0.8971 (m-10) REVERT: V 24 ARG cc_start: 0.8819 (mpt180) cc_final: 0.8028 (mmt-90) REVERT: W 44 LEU cc_start: 0.9705 (tp) cc_final: 0.9288 (pp) REVERT: W 76 TYR cc_start: 0.9256 (t80) cc_final: 0.8995 (t80) REVERT: X 24 ARG cc_start: 0.8977 (mpt180) cc_final: 0.8625 (mmt90) REVERT: X 26 LEU cc_start: 0.9649 (tp) cc_final: 0.9298 (tp) REVERT: X 77 PHE cc_start: 0.9661 (m-80) cc_final: 0.9333 (m-80) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.1397 time to fit residues: 94.4641 Evaluate side-chains 337 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 226 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 169 optimal weight: 0.5980 chunk 134 optimal weight: 7.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN ** H 92 GLN ** 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 = 0.3213 r_free = 0.3213 target = 0.054991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.040797 restraints weight = 112134.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.042162 restraints weight = 78757.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.043209 restraints weight = 59254.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.043942 restraints weight = 48195.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.044531 restraints weight = 41152.000| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.6377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18933 Z= 0.161 Angle : 0.731 14.191 25761 Z= 0.367 Chirality : 0.043 0.348 3051 Planarity : 0.005 0.089 3249 Dihedral : 4.512 22.058 2601 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.17), residues: 2322 helix: 0.91 (0.13), residues: 1440 sheet: -0.25 (0.28), residues: 300 loop : -0.91 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG T 81 TYR 0.039 0.003 TYR B 38 PHE 0.015 0.002 PHE K 95 TRP 0.017 0.001 TRP V 117 HIS 0.002 0.001 HIS X 95 Details of bonding type rmsd covalent geometry : bond 0.00339 (18933) covalent geometry : angle 0.73050 (25761) hydrogen bonds : bond 0.04172 ( 1054) hydrogen bonds : angle 4.59536 ( 3162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 0.793 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: A 95 PHE cc_start: 0.8866 (m-80) cc_final: 0.8646 (m-10) REVERT: B 18 ILE cc_start: 0.8854 (tp) cc_final: 0.8639 (mp) REVERT: B 28 THR cc_start: 0.8834 (m) cc_final: 0.8366 (m) REVERT: B 45 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8538 (mm-30) REVERT: B 78 LYS cc_start: 0.9074 (pttp) cc_final: 0.8793 (pttp) REVERT: B 104 VAL cc_start: 0.9621 (m) cc_final: 0.9390 (p) REVERT: C 14 GLU cc_start: 0.9417 (tp30) cc_final: 0.9207 (tp30) REVERT: D 26 LEU cc_start: 0.9646 (tp) cc_final: 0.9285 (tp) REVERT: D 77 PHE cc_start: 0.9223 (m-80) cc_final: 0.8526 (m-80) REVERT: D 95 HIS cc_start: 0.7962 (t-170) cc_final: 0.7726 (t-170) REVERT: F 71 ASP cc_start: 0.9232 (m-30) cc_final: 0.8587 (t0) REVERT: F 102 CYS cc_start: 0.9058 (t) cc_final: 0.8819 (t) REVERT: F 116 ASP cc_start: 0.8518 (m-30) cc_final: 0.8174 (p0) REVERT: G 7 MET cc_start: 0.8796 (ppp) cc_final: 0.8487 (ppp) REVERT: G 61 TYR cc_start: 0.8382 (m-10) cc_final: 0.7940 (m-80) REVERT: H 22 ASP cc_start: 0.8825 (t0) cc_final: 0.8562 (t0) REVERT: H 101 GLU cc_start: 0.9166 (tp30) cc_final: 0.8677 (mp0) REVERT: H 119 ARG cc_start: 0.9183 (tpm170) cc_final: 0.8862 (mmp-170) REVERT: J 20 THR cc_start: 0.8233 (t) cc_final: 0.6813 (t) REVERT: J 22 ASP cc_start: 0.8904 (p0) cc_final: 0.8364 (t0) REVERT: K 19 ASN cc_start: 0.8903 (m-40) cc_final: 0.8532 (m-40) REVERT: L 22 ASP cc_start: 0.7364 (t0) cc_final: 0.6902 (t0) REVERT: L 23 LEU cc_start: 0.9449 (mm) cc_final: 0.9077 (mm) REVERT: L 24 ARG cc_start: 0.8557 (mpt180) cc_final: 0.8153 (mpt90) REVERT: L 39 LEU cc_start: 0.9715 (mm) cc_final: 0.9491 (pp) REVERT: L 73 TYR cc_start: 0.9067 (m-80) cc_final: 0.8567 (m-80) REVERT: L 78 LYS cc_start: 0.8878 (ptpp) cc_final: 0.8606 (ptpp) REVERT: L 106 THR cc_start: 0.8181 (m) cc_final: 0.7713 (m) REVERT: M 92 ILE cc_start: 0.9437 (mm) cc_final: 0.9202 (mm) REVERT: M 112 LEU cc_start: 0.9524 (mt) cc_final: 0.9007 (pp) REVERT: P 101 GLU cc_start: 0.8275 (tp30) cc_final: 0.7321 (mp0) REVERT: P 119 ARG cc_start: 0.9116 (tpm170) cc_final: 0.8740 (tpt90) REVERT: Q 95 PHE cc_start: 0.9289 (m-10) cc_final: 0.8820 (m-80) REVERT: R 25 LEU cc_start: 0.9499 (mm) cc_final: 0.9286 (mm) REVERT: R 45 GLU cc_start: 0.9169 (pp20) cc_final: 0.8623 (pp20) REVERT: R 46 LYS cc_start: 0.8639 (pttp) cc_final: 0.8257 (pttm) REVERT: R 66 LYS cc_start: 0.9510 (mmmm) cc_final: 0.9280 (mmmm) REVERT: T 75 LEU cc_start: 0.9276 (mp) cc_final: 0.8991 (tp) REVERT: U 61 TYR cc_start: 0.8913 (m-80) cc_final: 0.8484 (m-80) REVERT: U 95 PHE cc_start: 0.9405 (m-80) cc_final: 0.8954 (m-10) REVERT: V 28 THR cc_start: 0.8545 (m) cc_final: 0.7905 (m) REVERT: W 61 TYR cc_start: 0.8764 (m-80) cc_final: 0.8529 (m-80) REVERT: W 76 TYR cc_start: 0.9282 (t80) cc_final: 0.9080 (t80) REVERT: X 24 ARG cc_start: 0.9001 (mpt180) cc_final: 0.8674 (mmt90) REVERT: X 26 LEU cc_start: 0.9648 (tp) cc_final: 0.9253 (tp) REVERT: X 77 PHE cc_start: 0.9646 (m-80) cc_final: 0.9239 (m-80) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.1421 time to fit residues: 94.5301 Evaluate side-chains 341 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 66 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 148 optimal weight: 9.9990 chunk 219 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 213 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.055065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.040929 restraints weight = 113669.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.042284 restraints weight = 79760.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.043343 restraints weight = 59998.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.044071 restraints weight = 48843.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.044624 restraints weight = 41699.834| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18933 Z= 0.153 Angle : 0.723 10.359 25761 Z= 0.365 Chirality : 0.043 0.268 3051 Planarity : 0.005 0.073 3249 Dihedral : 4.534 23.088 2601 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.17), residues: 2322 helix: 0.95 (0.13), residues: 1428 sheet: -0.41 (0.27), residues: 300 loop : -0.74 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 61 TYR 0.052 0.003 TYR B 38 PHE 0.028 0.002 PHE X 77 TRP 0.015 0.001 TRP B 90 HIS 0.005 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00330 (18933) covalent geometry : angle 0.72340 (25761) hydrogen bonds : bond 0.04126 ( 1054) hydrogen bonds : angle 4.59096 ( 3162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 436 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8862 (m-80) cc_final: 0.8658 (m-10) REVERT: B 18 ILE cc_start: 0.8899 (tp) cc_final: 0.8696 (mp) REVERT: B 28 THR cc_start: 0.8831 (m) cc_final: 0.8373 (m) REVERT: B 45 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8555 (mm-30) REVERT: B 78 LYS cc_start: 0.9004 (pttp) cc_final: 0.8748 (pttp) REVERT: B 104 VAL cc_start: 0.9608 (m) cc_final: 0.9365 (p) REVERT: C 14 GLU cc_start: 0.9432 (tp30) cc_final: 0.9205 (tp30) REVERT: D 26 LEU cc_start: 0.9651 (tp) cc_final: 0.9227 (tp) REVERT: D 28 THR cc_start: 0.8832 (m) cc_final: 0.8249 (m) REVERT: D 77 PHE cc_start: 0.9184 (m-80) cc_final: 0.8491 (m-80) REVERT: D 78 LYS cc_start: 0.8675 (pttm) cc_final: 0.8417 (pttm) REVERT: D 95 HIS cc_start: 0.7928 (t-170) cc_final: 0.7578 (t-170) REVERT: F 71 ASP cc_start: 0.9242 (m-30) cc_final: 0.8590 (t0) REVERT: F 102 CYS cc_start: 0.8973 (t) cc_final: 0.8694 (t) REVERT: F 116 ASP cc_start: 0.8481 (m-30) cc_final: 0.8177 (p0) REVERT: G 7 MET cc_start: 0.8717 (ppp) cc_final: 0.8408 (ppp) REVERT: G 61 TYR cc_start: 0.8379 (m-10) cc_final: 0.7903 (m-80) REVERT: H 80 THR cc_start: 0.9626 (p) cc_final: 0.9405 (p) REVERT: H 101 GLU cc_start: 0.9219 (tp30) cc_final: 0.8753 (mp0) REVERT: H 119 ARG cc_start: 0.9058 (tpm170) cc_final: 0.8740 (mmp-170) REVERT: J 22 ASP cc_start: 0.8878 (p0) cc_final: 0.8384 (t0) REVERT: K 19 ASN cc_start: 0.8928 (m-40) cc_final: 0.8583 (m-40) REVERT: K 68 ASP cc_start: 0.8266 (t0) cc_final: 0.8063 (t0) REVERT: L 39 LEU cc_start: 0.9722 (mm) cc_final: 0.9493 (pp) REVERT: L 73 TYR cc_start: 0.9094 (m-80) cc_final: 0.8682 (m-80) REVERT: M 92 ILE cc_start: 0.9376 (mm) cc_final: 0.9148 (mm) REVERT: M 112 LEU cc_start: 0.9506 (mt) cc_final: 0.8990 (pp) REVERT: N 28 THR cc_start: 0.9326 (t) cc_final: 0.8340 (m) REVERT: N 45 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8844 (mm-30) REVERT: P 101 GLU cc_start: 0.8343 (tp30) cc_final: 0.7393 (mp0) REVERT: Q 95 PHE cc_start: 0.9314 (m-10) cc_final: 0.8856 (m-10) REVERT: R 25 LEU cc_start: 0.9511 (mm) cc_final: 0.9296 (mm) REVERT: R 45 GLU cc_start: 0.9184 (pp20) cc_final: 0.8626 (pp20) REVERT: R 46 LYS cc_start: 0.8496 (pttp) cc_final: 0.8154 (pttp) REVERT: R 66 LYS cc_start: 0.9504 (mmmm) cc_final: 0.9272 (mmmm) REVERT: R 75 LEU cc_start: 0.9826 (mt) cc_final: 0.9398 (pp) REVERT: T 75 LEU cc_start: 0.9282 (mp) cc_final: 0.9000 (tp) REVERT: U 61 TYR cc_start: 0.8932 (m-80) cc_final: 0.8502 (m-80) REVERT: U 95 PHE cc_start: 0.9393 (m-80) cc_final: 0.8980 (m-10) REVERT: V 28 THR cc_start: 0.8654 (m) cc_final: 0.8103 (m) REVERT: W 14 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8767 (tm-30) REVERT: W 61 TYR cc_start: 0.8719 (m-80) cc_final: 0.8462 (m-80) REVERT: X 24 ARG cc_start: 0.9067 (mpt180) cc_final: 0.8841 (mmt90) REVERT: X 26 LEU cc_start: 0.9639 (tp) cc_final: 0.9355 (tp) REVERT: X 77 PHE cc_start: 0.9583 (m-80) cc_final: 0.9204 (m-80) outliers start: 0 outliers final: 0 residues processed: 436 average time/residue: 0.1383 time to fit residues: 94.2968 Evaluate side-chains 345 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.7757 > 50: distance: 51 - 70: 31.033 distance: 55 - 82: 31.672 distance: 63 - 91: 35.436 distance: 67 - 70: 28.719 distance: 68 - 100: 31.277 distance: 70 - 71: 36.229 distance: 71 - 72: 42.708 distance: 71 - 74: 37.857 distance: 72 - 73: 44.190 distance: 72 - 82: 6.220 distance: 73 - 105: 55.476 distance: 74 - 75: 40.765 distance: 75 - 77: 21.332 distance: 77 - 79: 18.872 distance: 82 - 83: 42.244 distance: 83 - 86: 19.553 distance: 84 - 91: 39.522 distance: 85 - 113: 40.934 distance: 86 - 87: 17.638 distance: 88 - 89: 39.893 distance: 88 - 90: 43.404 distance: 93 - 94: 38.989 distance: 93 - 100: 40.232 distance: 94 - 122: 49.221 distance: 95 - 96: 3.241 distance: 96 - 97: 40.040 distance: 97 - 98: 42.446 distance: 98 - 99: 39.333 distance: 100 - 101: 63.411 distance: 101 - 102: 63.187 distance: 101 - 104: 30.205 distance: 102 - 103: 40.380 distance: 103 - 130: 56.314 distance: 105 - 106: 40.710 distance: 106 - 107: 56.187 distance: 107 - 113: 57.016 distance: 113 - 114: 14.381 distance: 114 - 115: 51.559 distance: 114 - 117: 43.700 distance: 115 - 116: 47.848 distance: 115 - 122: 32.558 distance: 117 - 118: 57.134 distance: 118 - 119: 40.316 distance: 119 - 120: 3.029 distance: 119 - 121: 21.366 distance: 122 - 123: 26.359 distance: 123 - 124: 33.387 distance: 123 - 126: 32.546 distance: 124 - 130: 39.726 distance: 127 - 129: 40.470 distance: 130 - 131: 40.882 distance: 131 - 134: 41.030 distance: 132 - 138: 40.000 distance: 134 - 135: 56.278 distance: 135 - 136: 39.974 distance: 135 - 137: 40.864 distance: 139 - 140: 40.231 distance: 140 - 141: 39.788 distance: 140 - 145: 20.852 distance: 142 - 143: 38.708 distance: 143 - 144: 40.116 distance: 145 - 146: 44.789 distance: 146 - 147: 40.282 distance: 147 - 153: 34.169