Starting phenix.real_space_refine on Mon Jun 16 06:47:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8umr_42382/06_2025/8umr_42382.cif Found real_map, /net/cci-nas-00/data/ceres_data/8umr_42382/06_2025/8umr_42382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8umr_42382/06_2025/8umr_42382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8umr_42382/06_2025/8umr_42382.map" model { file = "/net/cci-nas-00/data/ceres_data/8umr_42382/06_2025/8umr_42382.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8umr_42382/06_2025/8umr_42382.cif" } resolution = 4.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 11952 2.51 5 N 3120 2.21 5 O 3522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18615 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "B" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Restraints were copied for chains: C, G, I, K, M, Q, U, W, D, F, H, J, L, N, P, R, T, V, X Time building chain proxies: 5.40, per 1000 atoms: 0.29 Number of scatterers: 18615 At special positions: 0 Unit cell: (141.9, 134.2, 105.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 3522 8.00 N 3120 7.00 C 11952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.79 Conformation dependent library (CDL) restraints added in 2.4 seconds 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4554 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 4 sheets defined 63.1% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 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: 5.21 Time building geometry restraints manager: 5.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5769 1.34 - 1.45: 2229 1.45 - 1.57: 10905 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 18933 Sorted by residual: bond pdb=" N ASN P 64 " pdb=" CA ASN P 64 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.83e+00 bond pdb=" N ASN H 64 " pdb=" CA ASN H 64 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.76e+00 bond pdb=" N ASN D 64 " pdb=" CA ASN D 64 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.76e+00 bond pdb=" N ASN T 64 " pdb=" CA ASN T 64 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.73e+00 bond pdb=" N ASN B 64 " pdb=" CA ASN B 64 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.68e+00 ... (remaining 18928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 24420 1.62 - 3.23: 1032 3.23 - 4.85: 252 4.85 - 6.47: 27 6.47 - 8.08: 30 Bond angle restraints: 25761 Sorted by residual: angle pdb=" N GLN M 62 " pdb=" CA GLN M 62 " pdb=" CB GLN M 62 " ideal model delta sigma weight residual 110.28 115.63 -5.35 1.55e+00 4.16e-01 1.19e+01 angle pdb=" N GLN C 62 " pdb=" CA GLN C 62 " pdb=" CB GLN C 62 " ideal model delta sigma weight residual 110.28 115.61 -5.33 1.55e+00 4.16e-01 1.18e+01 angle pdb=" N GLN A 62 " pdb=" CA GLN A 62 " pdb=" CB GLN A 62 " ideal model delta sigma weight residual 110.28 115.60 -5.32 1.55e+00 4.16e-01 1.18e+01 angle pdb=" N GLN W 62 " pdb=" CA GLN W 62 " pdb=" CB GLN W 62 " ideal model delta sigma weight residual 110.28 115.60 -5.32 1.55e+00 4.16e-01 1.18e+01 angle pdb=" N GLN G 62 " pdb=" CA GLN G 62 " pdb=" CB GLN G 62 " ideal model delta sigma weight residual 110.28 115.59 -5.31 1.55e+00 4.16e-01 1.17e+01 ... (remaining 25756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.42: 9504 10.42 - 20.83: 1098 20.83 - 31.25: 754 31.25 - 41.66: 137 41.66 - 52.08: 36 Dihedral angle restraints: 11529 sinusoidal: 4506 harmonic: 7023 Sorted by residual: dihedral pdb=" CA ASN G 53 " pdb=" C ASN G 53 " pdb=" N TYR G 54 " pdb=" CA TYR G 54 " ideal model delta harmonic sigma weight residual -180.00 -159.88 -20.12 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ASN U 53 " pdb=" C ASN U 53 " pdb=" N TYR U 54 " pdb=" CA TYR U 54 " ideal model delta harmonic sigma weight residual -180.00 -159.89 -20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ASN A 53 " pdb=" C ASN A 53 " pdb=" N TYR A 54 " pdb=" CA TYR A 54 " ideal model delta harmonic sigma weight residual -180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 11526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2056 0.037 - 0.075: 693 0.075 - 0.112: 222 0.112 - 0.149: 68 0.149 - 0.186: 12 Chirality restraints: 3051 Sorted by residual: chirality pdb=" CG LEU T 53 " pdb=" CB LEU T 53 " pdb=" CD1 LEU T 53 " pdb=" CD2 LEU T 53 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CG LEU H 53 " pdb=" CB LEU H 53 " pdb=" CD1 LEU H 53 " pdb=" CD2 LEU H 53 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CG LEU B 53 " pdb=" CB LEU B 53 " pdb=" CD1 LEU B 53 " pdb=" CD2 LEU B 53 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.18 2.00e-01 2.50e+01 8.56e-01 ... (remaining 3048 not shown) Planarity restraints: 3249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 38 " 0.007 2.00e-02 2.50e+03 1.46e-02 4.25e+00 pdb=" CG TYR J 38 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR J 38 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR J 38 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR J 38 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR J 38 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR J 38 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR J 38 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 38 " 0.007 2.00e-02 2.50e+03 1.45e-02 4.22e+00 pdb=" CG TYR R 38 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR R 38 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR R 38 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR R 38 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR R 38 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR R 38 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 38 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 38 " 0.007 2.00e-02 2.50e+03 1.45e-02 4.18e+00 pdb=" CG TYR F 38 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR F 38 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR F 38 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR F 38 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 38 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 38 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 38 " -0.001 2.00e-02 2.50e+03 ... (remaining 3246 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 484 2.62 - 3.19: 19027 3.19 - 3.76: 33025 3.76 - 4.33: 41605 4.33 - 4.90: 64594 Nonbonded interactions: 158735 Sorted by model distance: nonbonded pdb=" O ALA K 110 " pdb=" OH TYR L 38 " model vdw 2.052 3.040 nonbonded pdb=" O VAL N 52 " pdb=" NH2 ARG T 61 " model vdw 2.167 3.120 nonbonded pdb=" O ALA C 110 " pdb=" OH TYR D 38 " model vdw 2.172 3.040 nonbonded pdb=" NH2 ARG H 61 " pdb=" O VAL X 52 " model vdw 2.202 3.120 nonbonded pdb=" OH TYR A 54 " pdb=" NH1 ARG B 93 " model vdw 2.217 3.120 ... (remaining 158730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'Q' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 35.380 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18933 Z= 0.202 Angle : 0.822 8.084 25761 Z= 0.449 Chirality : 0.045 0.186 3051 Planarity : 0.007 0.048 3249 Dihedral : 12.523 52.077 6975 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 27.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2322 helix: 0.38 (0.13), residues: 1437 sheet: -0.07 (0.27), residues: 300 loop : -0.68 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 117 HIS 0.001 0.000 HIS F 95 PHE 0.017 0.003 PHE D 77 TYR 0.034 0.004 TYR R 38 ARG 0.012 0.001 ARG N 61 Details of bonding type rmsd hydrogen bonds : bond 0.14702 ( 1054) hydrogen bonds : angle 5.82419 ( 3162) covalent geometry : bond 0.00417 (18933) covalent geometry : angle 0.82212 (25761) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 775 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.9703 (tttt) cc_final: 0.9422 (mttt) REVERT: B 24 ARG cc_start: 0.9099 (mpt180) cc_final: 0.8192 (mmt-90) REVERT: B 52 VAL cc_start: 0.8383 (m) cc_final: 0.7415 (m) REVERT: B 103 LEU cc_start: 0.9333 (mt) cc_final: 0.8685 (mp) REVERT: C 14 GLU cc_start: 0.9508 (tp30) cc_final: 0.9006 (tp30) REVERT: C 80 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8243 (pt0) REVERT: D 26 LEU cc_start: 0.9624 (tp) cc_final: 0.9404 (tp) REVERT: D 28 THR cc_start: 0.8695 (m) cc_final: 0.8350 (m) REVERT: D 52 VAL cc_start: 0.9408 (m) cc_final: 0.9193 (m) REVERT: D 63 GLU cc_start: 0.8911 (tp30) cc_final: 0.8144 (pm20) REVERT: D 66 LYS cc_start: 0.8895 (mptt) cc_final: 0.8552 (mmmm) REVERT: D 68 VAL cc_start: 0.9536 (p) cc_final: 0.9192 (m) REVERT: D 80 THR cc_start: 0.9677 (p) cc_final: 0.9440 (p) REVERT: D 83 ARG cc_start: 0.8787 (tpp80) cc_final: 0.8415 (ttt180) REVERT: D 95 HIS cc_start: 0.7394 (t-90) cc_final: 0.6903 (t-170) REVERT: F 85 ASP cc_start: 0.9290 (m-30) cc_final: 0.8842 (t70) REVERT: F 116 ASP cc_start: 0.8510 (m-30) cc_final: 0.8229 (p0) REVERT: G 20 TYR cc_start: 0.8927 (m-10) cc_final: 0.8665 (m-10) REVERT: G 68 ASP cc_start: 0.8380 (t0) cc_final: 0.8099 (p0) REVERT: G 78 LEU cc_start: 0.9543 (tp) cc_final: 0.9243 (tp) REVERT: G 99 LEU cc_start: 0.9411 (pp) cc_final: 0.9202 (pp) REVERT: H 101 GLU cc_start: 0.8763 (tp30) cc_final: 0.8272 (tp30) REVERT: H 103 LEU cc_start: 0.9035 (mt) cc_final: 0.8583 (mp) REVERT: K 14 GLU cc_start: 0.9100 (tp30) cc_final: 0.8440 (tp30) REVERT: K 19 ASN cc_start: 0.8803 (m110) cc_final: 0.8165 (m110) REVERT: K 22 THR cc_start: 0.9438 (p) cc_final: 0.8988 (p) REVERT: L 26 LEU cc_start: 0.9592 (tp) cc_final: 0.9314 (tp) REVERT: L 39 LEU cc_start: 0.9530 (mm) cc_final: 0.9121 (pp) REVERT: L 73 TYR cc_start: 0.8900 (m-80) cc_final: 0.8490 (m-80) REVERT: L 75 LEU cc_start: 0.9606 (mt) cc_final: 0.9299 (mt) REVERT: L 77 PHE cc_start: 0.9171 (m-10) cc_final: 0.8508 (m-80) REVERT: L 90 TRP cc_start: 0.9342 (t60) cc_final: 0.9131 (t60) REVERT: N 75 LEU cc_start: 0.9408 (mt) cc_final: 0.8853 (tp) REVERT: P 24 ARG cc_start: 0.8405 (mpt180) cc_final: 0.8076 (mmt-90) REVERT: P 55 THR cc_start: 0.9046 (p) cc_final: 0.8819 (t) REVERT: P 94 ARG cc_start: 0.8511 (tpm170) cc_final: 0.7830 (tpm170) REVERT: P 100 PRO cc_start: 0.2611 (Cg_exo) cc_final: 0.2410 (Cg_endo) REVERT: R 25 LEU cc_start: 0.9542 (mm) cc_final: 0.9293 (mm) REVERT: R 71 ASP cc_start: 0.8662 (m-30) cc_final: 0.8049 (t0) REVERT: T 26 LEU cc_start: 0.9532 (tp) cc_final: 0.9129 (tp) REVERT: T 101 GLU cc_start: 0.8516 (tp30) cc_final: 0.8167 (mp0) REVERT: U 14 GLU cc_start: 0.9189 (tp30) cc_final: 0.8670 (tp30) REVERT: U 93 GLU cc_start: 0.9323 (mp0) cc_final: 0.9018 (mp0) REVERT: V 24 ARG cc_start: 0.8508 (mpt180) cc_final: 0.7834 (mmt-90) REVERT: V 52 VAL cc_start: 0.7939 (m) cc_final: 0.7430 (m) REVERT: V 87 LEU cc_start: 0.9576 (tt) cc_final: 0.9307 (pp) REVERT: W 39 GLU cc_start: 0.9375 (mp0) cc_final: 0.9075 (mp0) REVERT: X 24 ARG cc_start: 0.8700 (mpt180) cc_final: 0.8438 (mmt-90) REVERT: X 26 LEU cc_start: 0.9527 (tp) cc_final: 0.9222 (tp) REVERT: X 75 LEU cc_start: 0.9562 (mt) cc_final: 0.9286 (pp) REVERT: X 103 LEU cc_start: 0.9262 (mt) cc_final: 0.8843 (mt) outliers start: 0 outliers final: 0 residues processed: 775 average time/residue: 0.3659 time to fit residues: 396.4834 Evaluate side-chains 445 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 10.0000 chunk 172 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 43 ASN A 90 ASN C 19 ASN ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN G 19 ASN G 43 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 ASN ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 ASN K 43 ASN K 77 ASN K 90 ASN M 19 ASN ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 ASN Q 43 ASN U 19 ASN ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 77 ASN W 19 ASN ** W 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 90 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.057691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.043417 restraints weight = 109323.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.044778 restraints weight = 78221.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.045837 restraints weight = 60247.181| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18933 Z= 0.188 Angle : 0.735 10.578 25761 Z= 0.382 Chirality : 0.043 0.155 3051 Planarity : 0.006 0.072 3249 Dihedral : 4.528 23.185 2601 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.47 % Allowed : 7.62 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.17), residues: 2322 helix: 0.92 (0.13), residues: 1494 sheet: 0.17 (0.28), residues: 300 loop : -1.15 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 90 HIS 0.006 0.001 HIS T 95 PHE 0.020 0.003 PHE W 95 TYR 0.031 0.003 TYR L 73 ARG 0.010 0.001 ARG T 24 Details of bonding type rmsd hydrogen bonds : bond 0.04805 ( 1054) hydrogen bonds : angle 4.52448 ( 3162) covalent geometry : bond 0.00400 (18933) covalent geometry : angle 0.73505 (25761) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 556 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.8811 (t0) cc_final: 0.8547 (t0) REVERT: A 59 GLU cc_start: 0.9364 (pt0) cc_final: 0.9033 (pp20) REVERT: B 28 THR cc_start: 0.8231 (m) cc_final: 0.7354 (m) REVERT: B 38 TYR cc_start: 0.7470 (m-80) cc_final: 0.7120 (m-80) REVERT: B 45 GLU cc_start: 0.9458 (tp30) cc_final: 0.9205 (tm-30) REVERT: B 52 VAL cc_start: 0.8588 (m) cc_final: 0.8020 (m) REVERT: B 57 VAL cc_start: 0.9108 (t) cc_final: 0.8805 (m) REVERT: B 101 GLU cc_start: 0.9056 (tp30) cc_final: 0.8479 (tp30) REVERT: B 103 LEU cc_start: 0.9380 (mt) cc_final: 0.9153 (mp) REVERT: C 14 GLU cc_start: 0.9575 (tp30) cc_final: 0.9171 (tp30) REVERT: D 22 ASP cc_start: 0.7982 (t0) cc_final: 0.7712 (t0) REVERT: D 28 THR cc_start: 0.8881 (m) cc_final: 0.8546 (m) REVERT: D 63 GLU cc_start: 0.9161 (tp30) cc_final: 0.8943 (mp0) REVERT: D 94 ARG cc_start: 0.9337 (tpm170) cc_final: 0.9037 (tpm170) REVERT: D 118 LEU cc_start: 0.9602 (mp) cc_final: 0.9347 (pp) REVERT: F 38 TYR cc_start: 0.9018 (m-80) cc_final: 0.8727 (m-10) REVERT: F 78 LYS cc_start: 0.8028 (pttt) cc_final: 0.7822 (pttt) REVERT: F 79 THR cc_start: 0.9024 (m) cc_final: 0.8501 (m) REVERT: F 116 ASP cc_start: 0.8425 (m-30) cc_final: 0.8156 (p0) REVERT: G 7 MET cc_start: 0.8307 (ptt) cc_final: 0.8084 (ptm) REVERT: H 22 ASP cc_start: 0.9165 (t0) cc_final: 0.8901 (t0) REVERT: H 26 LEU cc_start: 0.9123 (tp) cc_final: 0.8853 (tp) REVERT: H 101 GLU cc_start: 0.9137 (tp30) cc_final: 0.8524 (tp30) REVERT: H 103 LEU cc_start: 0.9171 (mt) cc_final: 0.8936 (mt) REVERT: H 119 ARG cc_start: 0.9025 (tpm170) cc_final: 0.8272 (mtt180) REVERT: K 14 GLU cc_start: 0.9173 (tp30) cc_final: 0.8381 (tp30) REVERT: K 19 ASN cc_start: 0.8819 (m-40) cc_final: 0.8568 (t0) REVERT: K 22 THR cc_start: 0.9493 (p) cc_final: 0.9012 (p) REVERT: L 39 LEU cc_start: 0.9573 (mm) cc_final: 0.9218 (pp) REVERT: L 73 TYR cc_start: 0.8967 (m-80) cc_final: 0.8626 (m-10) REVERT: M 112 LEU cc_start: 0.9430 (mt) cc_final: 0.9126 (mt) REVERT: N 48 LEU cc_start: 0.9439 (mm) cc_final: 0.8638 (tt) REVERT: N 85 ASP cc_start: 0.9191 (p0) cc_final: 0.8984 (p0) REVERT: P 23 LEU cc_start: 0.9552 (mm) cc_final: 0.9348 (tt) REVERT: P 79 THR cc_start: 0.7992 (m) cc_final: 0.7387 (m) REVERT: P 80 THR cc_start: 0.8887 (p) cc_final: 0.8431 (t) REVERT: P 84 LEU cc_start: 0.8830 (tp) cc_final: 0.8464 (mt) REVERT: Q 95 PHE cc_start: 0.9001 (m-80) cc_final: 0.8503 (m-80) REVERT: R 45 GLU cc_start: 0.9213 (pp20) cc_final: 0.8682 (pp20) REVERT: R 46 LYS cc_start: 0.8877 (pttp) cc_final: 0.8650 (pttp) REVERT: R 60 VAL cc_start: 0.8773 (p) cc_final: 0.8487 (p) REVERT: R 71 ASP cc_start: 0.8927 (m-30) cc_final: 0.8200 (t0) REVERT: T 101 GLU cc_start: 0.9012 (tp30) cc_final: 0.8649 (mp0) REVERT: U 95 PHE cc_start: 0.9462 (m-80) cc_final: 0.9185 (m-10) REVERT: V 22 ASP cc_start: 0.7988 (t0) cc_final: 0.5713 (t0) REVERT: V 52 VAL cc_start: 0.8226 (m) cc_final: 0.8001 (m) REVERT: W 39 GLU cc_start: 0.9283 (mp0) cc_final: 0.9043 (mp0) REVERT: X 26 LEU cc_start: 0.9607 (tp) cc_final: 0.9390 (tp) REVERT: X 103 LEU cc_start: 0.9378 (mt) cc_final: 0.9110 (mt) outliers start: 9 outliers final: 6 residues processed: 562 average time/residue: 0.3121 time to fit residues: 260.4967 Evaluate side-chains 397 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 391 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 60 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 176 optimal weight: 6.9990 chunk 184 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 173 optimal weight: 0.7980 chunk 170 optimal weight: 8.9990 chunk 203 optimal weight: 1.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 ASN I 77 ASN I 90 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN M 43 ASN Q 43 ASN U 43 ASN ** 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 = 0.3252 r_free = 0.3252 target = 0.056601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.042143 restraints weight = 109616.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.043515 restraints weight = 76656.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.044568 restraints weight = 58380.928| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18933 Z= 0.161 Angle : 0.700 9.393 25761 Z= 0.359 Chirality : 0.042 0.141 3051 Planarity : 0.005 0.064 3249 Dihedral : 4.478 23.893 2601 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.16 % Allowed : 6.68 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.17), residues: 2322 helix: 0.94 (0.13), residues: 1494 sheet: -0.36 (0.28), residues: 276 loop : -1.15 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 117 HIS 0.007 0.002 HIS D 95 PHE 0.025 0.002 PHE K 95 TYR 0.034 0.003 TYR W 8 ARG 0.011 0.001 ARG T 61 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 1054) hydrogen bonds : angle 4.42717 ( 3162) covalent geometry : bond 0.00339 (18933) covalent geometry : angle 0.69980 (25761) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 508 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.9071 (t0) cc_final: 0.8847 (t0) REVERT: B 28 THR cc_start: 0.8185 (m) cc_final: 0.7544 (m) REVERT: B 45 GLU cc_start: 0.9448 (tp30) cc_final: 0.8749 (mm-30) REVERT: B 57 VAL cc_start: 0.9101 (t) cc_final: 0.8801 (m) REVERT: B 80 THR cc_start: 0.9205 (p) cc_final: 0.8963 (p) REVERT: B 101 GLU cc_start: 0.9151 (tp30) cc_final: 0.8508 (tp30) REVERT: B 103 LEU cc_start: 0.9338 (mt) cc_final: 0.9081 (mp) REVERT: B 104 VAL cc_start: 0.9491 (m) cc_final: 0.9269 (p) REVERT: C 14 GLU cc_start: 0.9640 (tp30) cc_final: 0.9183 (tp30) REVERT: C 61 TYR cc_start: 0.8529 (m-10) cc_final: 0.8219 (m-80) REVERT: D 22 ASP cc_start: 0.7987 (t0) cc_final: 0.6912 (t0) REVERT: D 28 THR cc_start: 0.8906 (m) cc_final: 0.8170 (m) REVERT: D 63 GLU cc_start: 0.9248 (tp30) cc_final: 0.8919 (mp0) REVERT: D 80 THR cc_start: 0.9575 (p) cc_final: 0.9277 (p) REVERT: D 94 ARG cc_start: 0.9295 (tpm170) cc_final: 0.8999 (tpm170) REVERT: D 101 GLU cc_start: 0.8975 (tp30) cc_final: 0.8194 (tp30) REVERT: D 103 LEU cc_start: 0.9640 (mt) cc_final: 0.9388 (mt) REVERT: D 118 LEU cc_start: 0.9646 (mp) cc_final: 0.9415 (pp) REVERT: F 38 TYR cc_start: 0.8855 (m-80) cc_final: 0.8602 (m-80) REVERT: F 71 ASP cc_start: 0.9031 (m-30) cc_final: 0.8338 (t0) REVERT: F 116 ASP cc_start: 0.8367 (m-30) cc_final: 0.8079 (p0) REVERT: G 7 MET cc_start: 0.8315 (ptt) cc_final: 0.7966 (ttp) REVERT: H 101 GLU cc_start: 0.9132 (tp30) cc_final: 0.8513 (mp0) REVERT: J 20 THR cc_start: 0.7094 (t) cc_final: 0.5801 (t) REVERT: J 22 ASP cc_start: 0.9076 (p0) cc_final: 0.8433 (t0) REVERT: K 7 MET cc_start: 0.9000 (ptp) cc_final: 0.8637 (ptp) REVERT: K 14 GLU cc_start: 0.9264 (tp30) cc_final: 0.8317 (tp30) REVERT: K 19 ASN cc_start: 0.8662 (m-40) cc_final: 0.8450 (t0) REVERT: K 22 THR cc_start: 0.9287 (p) cc_final: 0.8913 (p) REVERT: K 39 GLU cc_start: 0.9520 (mp0) cc_final: 0.9259 (mp0) REVERT: K 49 LEU cc_start: 0.9719 (tt) cc_final: 0.9501 (pp) REVERT: L 22 ASP cc_start: 0.7375 (t0) cc_final: 0.7081 (t0) REVERT: L 23 LEU cc_start: 0.9368 (mm) cc_final: 0.9007 (mm) REVERT: L 24 ARG cc_start: 0.8464 (mpt180) cc_final: 0.8221 (mpt90) REVERT: L 39 LEU cc_start: 0.9648 (mm) cc_final: 0.9331 (pp) REVERT: L 73 TYR cc_start: 0.9032 (m-80) cc_final: 0.8642 (m-10) REVERT: L 77 PHE cc_start: 0.9389 (m-80) cc_final: 0.8883 (m-80) REVERT: L 106 THR cc_start: 0.8220 (m) cc_final: 0.7722 (m) REVERT: M 112 LEU cc_start: 0.9446 (mt) cc_final: 0.9145 (mt) REVERT: P 38 TYR cc_start: 0.5934 (m-80) cc_final: 0.5721 (m-80) REVERT: P 63 GLU cc_start: 0.8623 (mp0) cc_final: 0.8398 (mp0) REVERT: Q 95 PHE cc_start: 0.9063 (m-80) cc_final: 0.8490 (m-80) REVERT: R 45 GLU cc_start: 0.9242 (pp20) cc_final: 0.8710 (pp20) REVERT: R 46 LYS cc_start: 0.8776 (pttp) cc_final: 0.8534 (pttp) REVERT: R 68 VAL cc_start: 0.9622 (m) cc_final: 0.9389 (p) REVERT: R 71 ASP cc_start: 0.9059 (m-30) cc_final: 0.8163 (t0) REVERT: T 101 GLU cc_start: 0.8977 (tp30) cc_final: 0.8662 (mt-10) REVERT: U 95 PHE cc_start: 0.9534 (m-80) cc_final: 0.9161 (m-10) REVERT: V 24 ARG cc_start: 0.8639 (mpt180) cc_final: 0.7686 (mmt-90) REVERT: V 52 VAL cc_start: 0.8438 (m) cc_final: 0.8219 (m) REVERT: V 87 LEU cc_start: 0.9627 (tt) cc_final: 0.9360 (pp) REVERT: V 104 VAL cc_start: 0.9681 (m) cc_final: 0.9444 (p) REVERT: W 39 GLU cc_start: 0.9375 (mp0) cc_final: 0.9149 (mp0) REVERT: W 76 TYR cc_start: 0.9452 (t80) cc_final: 0.9197 (t80) outliers start: 3 outliers final: 1 residues processed: 510 average time/residue: 0.3041 time to fit residues: 232.4737 Evaluate side-chains 380 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 191 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 180 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 149 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 C 90 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 W 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.055037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.040860 restraints weight = 112028.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.042255 restraints weight = 77580.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.043276 restraints weight = 58646.273| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18933 Z= 0.176 Angle : 0.703 10.147 25761 Z= 0.364 Chirality : 0.042 0.155 3051 Planarity : 0.006 0.073 3249 Dihedral : 4.642 23.867 2601 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.05 % Allowed : 6.47 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.17), residues: 2322 helix: 1.11 (0.13), residues: 1434 sheet: -0.68 (0.26), residues: 300 loop : -0.52 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 117 HIS 0.005 0.001 HIS D 95 PHE 0.024 0.002 PHE K 95 TYR 0.045 0.003 TYR K 48 ARG 0.026 0.001 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 1054) hydrogen bonds : angle 4.42364 ( 3162) covalent geometry : bond 0.00368 (18933) covalent geometry : angle 0.70306 (25761) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 475 time to evaluate : 2.117 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: A 82 TYR cc_start: 0.9230 (m-10) cc_final: 0.8737 (m-80) REVERT: B 45 GLU cc_start: 0.9434 (tp30) cc_final: 0.8746 (mm-30) REVERT: B 57 VAL cc_start: 0.9126 (t) cc_final: 0.8894 (m) REVERT: B 79 THR cc_start: 0.9216 (p) cc_final: 0.8951 (p) REVERT: B 101 GLU cc_start: 0.9269 (tp30) cc_final: 0.8622 (tp30) REVERT: C 14 GLU cc_start: 0.9642 (tp30) cc_final: 0.9172 (tp30) REVERT: D 28 THR cc_start: 0.8841 (m) cc_final: 0.8152 (p) REVERT: D 63 GLU cc_start: 0.9382 (tp30) cc_final: 0.8658 (pm20) REVERT: D 77 PHE cc_start: 0.9338 (m-80) cc_final: 0.8949 (m-80) REVERT: D 118 LEU cc_start: 0.9581 (mp) cc_final: 0.9361 (pp) REVERT: F 38 TYR cc_start: 0.8783 (m-80) cc_final: 0.8527 (m-10) REVERT: F 71 ASP cc_start: 0.9011 (m-30) cc_final: 0.8357 (t0) REVERT: F 116 ASP cc_start: 0.8417 (m-30) cc_final: 0.8081 (p0) REVERT: G 7 MET cc_start: 0.8342 (ptt) cc_final: 0.7940 (ttp) REVERT: G 61 TYR cc_start: 0.8079 (m-80) cc_final: 0.7781 (m-80) REVERT: G 114 LEU cc_start: 0.9195 (mt) cc_final: 0.8953 (mt) REVERT: H 101 GLU cc_start: 0.9197 (tp30) cc_final: 0.8800 (mp0) REVERT: J 20 THR cc_start: 0.7428 (t) cc_final: 0.6121 (t) REVERT: J 22 ASP cc_start: 0.9088 (p0) cc_final: 0.8347 (t0) REVERT: K 7 MET cc_start: 0.9004 (ptp) cc_final: 0.8693 (ptp) REVERT: K 39 GLU cc_start: 0.9543 (mp0) cc_final: 0.9297 (mp0) REVERT: K 68 ASP cc_start: 0.8422 (t0) cc_final: 0.8186 (t0) REVERT: L 22 ASP cc_start: 0.7260 (t0) cc_final: 0.7011 (t0) REVERT: L 23 LEU cc_start: 0.9383 (mm) cc_final: 0.9083 (mm) REVERT: L 24 ARG cc_start: 0.8565 (mpt180) cc_final: 0.8193 (mpt90) REVERT: L 39 LEU cc_start: 0.9685 (mm) cc_final: 0.9434 (pp) REVERT: L 45 GLU cc_start: 0.9001 (pp20) cc_final: 0.8799 (pp20) REVERT: L 73 TYR cc_start: 0.9053 (m-80) cc_final: 0.8623 (m-80) REVERT: L 80 THR cc_start: 0.9117 (t) cc_final: 0.8820 (t) REVERT: L 106 THR cc_start: 0.8215 (m) cc_final: 0.7826 (m) REVERT: M 112 LEU cc_start: 0.9487 (mt) cc_final: 0.9269 (mt) REVERT: N 48 LEU cc_start: 0.9414 (mm) cc_final: 0.8963 (tp) REVERT: N 75 LEU cc_start: 0.9488 (mm) cc_final: 0.9239 (mm) REVERT: P 63 GLU cc_start: 0.8597 (mp0) cc_final: 0.8352 (mp0) REVERT: Q 95 PHE cc_start: 0.9173 (m-80) cc_final: 0.8685 (m-80) REVERT: R 45 GLU cc_start: 0.9241 (pp20) cc_final: 0.8683 (pp20) REVERT: R 46 LYS cc_start: 0.8644 (pttp) cc_final: 0.8420 (pttp) REVERT: T 101 GLU cc_start: 0.8898 (tp30) cc_final: 0.8395 (mp0) REVERT: U 61 TYR cc_start: 0.9112 (m-80) cc_final: 0.8419 (m-80) REVERT: U 95 PHE cc_start: 0.9546 (m-80) cc_final: 0.9032 (m-10) REVERT: V 24 ARG cc_start: 0.8673 (mpt180) cc_final: 0.7584 (mmt-90) REVERT: W 33 LYS cc_start: 0.8675 (tttt) cc_final: 0.8433 (ttpt) REVERT: W 76 TYR cc_start: 0.9429 (t80) cc_final: 0.9190 (t80) REVERT: X 24 ARG cc_start: 0.8981 (mpt180) cc_final: 0.8585 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 475 average time/residue: 0.3142 time to fit residues: 222.7189 Evaluate side-chains 370 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 2 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 201 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 126 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 217 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 77 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 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 = 0.3168 r_free = 0.3168 target = 0.053361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.039520 restraints weight = 115009.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.040851 restraints weight = 80930.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.041848 restraints weight = 61423.506| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18933 Z= 0.197 Angle : 0.722 8.661 25761 Z= 0.376 Chirality : 0.042 0.150 3051 Planarity : 0.005 0.068 3249 Dihedral : 4.765 23.337 2601 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.42 % Allowed : 6.57 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2322 helix: 1.02 (0.13), residues: 1416 sheet: -0.95 (0.25), residues: 300 loop : -0.56 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 117 HIS 0.006 0.001 HIS X 95 PHE 0.035 0.003 PHE K 95 TYR 0.038 0.003 TYR B 38 ARG 0.018 0.001 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 1054) hydrogen bonds : angle 4.58095 ( 3162) covalent geometry : bond 0.00404 (18933) covalent geometry : angle 0.72175 (25761) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 449 time to evaluate : 2.233 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: B 18 ILE cc_start: 0.8796 (tp) cc_final: 0.8579 (mp) REVERT: B 45 GLU cc_start: 0.9377 (tp30) cc_final: 0.8678 (mm-30) REVERT: B 81 ARG cc_start: 0.8511 (ptt-90) cc_final: 0.8102 (ptt-90) REVERT: B 95 HIS cc_start: 0.7331 (t-170) cc_final: 0.6330 (t-170) REVERT: B 101 GLU cc_start: 0.9335 (tp30) cc_final: 0.9102 (mp0) REVERT: C 14 GLU cc_start: 0.9567 (tp30) cc_final: 0.9132 (tp30) REVERT: D 28 THR cc_start: 0.8880 (m) cc_final: 0.8145 (p) REVERT: D 63 GLU cc_start: 0.9556 (tp30) cc_final: 0.8879 (pm20) REVERT: D 74 ARG cc_start: 0.9364 (tmm-80) cc_final: 0.8771 (tmm-80) REVERT: D 75 LEU cc_start: 0.9717 (mt) cc_final: 0.9472 (mt) REVERT: D 94 ARG cc_start: 0.9252 (tpm170) cc_final: 0.8751 (tpp-160) REVERT: D 118 LEU cc_start: 0.9644 (mp) cc_final: 0.9407 (pp) REVERT: F 38 TYR cc_start: 0.8750 (m-80) cc_final: 0.8502 (m-80) REVERT: F 71 ASP cc_start: 0.8987 (m-30) cc_final: 0.8346 (t0) REVERT: F 116 ASP cc_start: 0.8323 (m-30) cc_final: 0.7978 (p0) REVERT: G 61 TYR cc_start: 0.8132 (m-80) cc_final: 0.7808 (m-80) REVERT: G 114 LEU cc_start: 0.9257 (mt) cc_final: 0.8963 (mt) REVERT: H 101 GLU cc_start: 0.9186 (tp30) cc_final: 0.8754 (mp0) REVERT: H 103 LEU cc_start: 0.9175 (mp) cc_final: 0.8938 (mp) REVERT: H 119 ARG cc_start: 0.9104 (tpm170) cc_final: 0.8859 (tpm170) REVERT: J 20 THR cc_start: 0.8072 (t) cc_final: 0.6638 (t) REVERT: J 22 ASP cc_start: 0.9003 (p0) cc_final: 0.8359 (t0) REVERT: K 39 GLU cc_start: 0.9499 (mp0) cc_final: 0.9226 (mp0) REVERT: K 49 LEU cc_start: 0.9694 (tt) cc_final: 0.9484 (pp) REVERT: L 39 LEU cc_start: 0.9683 (mm) cc_final: 0.9462 (pp) REVERT: L 73 TYR cc_start: 0.9002 (m-80) cc_final: 0.8594 (m-80) REVERT: N 48 LEU cc_start: 0.9398 (mm) cc_final: 0.8809 (tp) REVERT: P 63 GLU cc_start: 0.8578 (mp0) cc_final: 0.8365 (mp0) REVERT: Q 95 PHE cc_start: 0.9208 (m-80) cc_final: 0.8731 (m-80) REVERT: R 25 LEU cc_start: 0.9504 (mm) cc_final: 0.9289 (mm) REVERT: R 45 GLU cc_start: 0.9262 (pp20) cc_final: 0.8708 (pp20) REVERT: R 66 LYS cc_start: 0.9556 (mmmt) cc_final: 0.9288 (mmmm) REVERT: T 79 THR cc_start: 0.9352 (p) cc_final: 0.9133 (t) REVERT: U 61 TYR cc_start: 0.9108 (m-80) cc_final: 0.8421 (m-80) REVERT: U 95 PHE cc_start: 0.9528 (m-80) cc_final: 0.9069 (m-10) REVERT: W 61 TYR cc_start: 0.8893 (m-80) cc_final: 0.8517 (m-80) REVERT: W 76 TYR cc_start: 0.9478 (t80) cc_final: 0.9259 (t80) REVERT: X 24 ARG cc_start: 0.9002 (mpt180) cc_final: 0.8405 (mmt180) outliers start: 8 outliers final: 1 residues processed: 455 average time/residue: 0.3022 time to fit residues: 207.0193 Evaluate side-chains 350 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 349 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 107 optimal weight: 4.9990 chunk 208 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 L 92 GLN M 43 ASN Q 43 ASN U 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.054888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.040694 restraints weight = 115133.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.042105 restraints weight = 80424.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.043156 restraints weight = 60883.505| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.6041 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= 0.135 Angle : 0.712 10.339 25761 Z= 0.356 Chirality : 0.042 0.197 3051 Planarity : 0.005 0.054 3249 Dihedral : 4.576 24.629 2601 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.21 % Allowed : 4.17 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.17), residues: 2322 helix: 1.06 (0.13), residues: 1440 sheet: -0.48 (0.25), residues: 324 loop : -0.86 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 117 HIS 0.004 0.001 HIS D 95 PHE 0.014 0.002 PHE Q 15 TYR 0.042 0.003 TYR I 48 ARG 0.014 0.001 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 1054) hydrogen bonds : angle 4.37139 ( 3162) covalent geometry : bond 0.00297 (18933) covalent geometry : angle 0.71207 (25761) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 479 time to evaluate : 2.212 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: B 28 THR cc_start: 0.8645 (m) cc_final: 0.8375 (m) REVERT: B 45 GLU cc_start: 0.9376 (tp30) cc_final: 0.8611 (mm-30) REVERT: B 95 HIS cc_start: 0.7353 (t-170) cc_final: 0.6291 (t-170) REVERT: B 101 GLU cc_start: 0.9309 (tp30) cc_final: 0.9048 (mp0) REVERT: C 14 GLU cc_start: 0.9495 (tp30) cc_final: 0.9194 (tp30) REVERT: D 22 ASP cc_start: 0.8481 (t0) cc_final: 0.8059 (t0) REVERT: D 26 LEU cc_start: 0.9545 (tp) cc_final: 0.9254 (tp) REVERT: D 46 LYS cc_start: 0.8870 (ptpp) cc_final: 0.8665 (mttm) REVERT: D 63 GLU cc_start: 0.9548 (tp30) cc_final: 0.8849 (pm20) REVERT: D 74 ARG cc_start: 0.9324 (tmm-80) cc_final: 0.8700 (tmm-80) REVERT: D 78 LYS cc_start: 0.8597 (pttm) cc_final: 0.8249 (pttm) REVERT: D 94 ARG cc_start: 0.9299 (tpm170) cc_final: 0.8894 (tpp-160) REVERT: D 103 LEU cc_start: 0.9630 (mt) cc_final: 0.9430 (mp) REVERT: D 104 VAL cc_start: 0.9751 (m) cc_final: 0.9505 (p) REVERT: D 114 TYR cc_start: 0.8082 (m-80) cc_final: 0.7874 (m-80) REVERT: D 118 LEU cc_start: 0.9609 (mp) cc_final: 0.9355 (pp) REVERT: F 38 TYR cc_start: 0.8638 (m-80) cc_final: 0.8406 (m-80) REVERT: F 71 ASP cc_start: 0.9037 (m-30) cc_final: 0.8391 (t0) REVERT: F 116 ASP cc_start: 0.8373 (m-30) cc_final: 0.8031 (p0) REVERT: G 61 TYR cc_start: 0.7962 (m-80) cc_final: 0.7616 (m-80) REVERT: H 22 ASP cc_start: 0.9002 (t0) cc_final: 0.8717 (t0) REVERT: H 63 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8197 (mm-30) REVERT: H 101 GLU cc_start: 0.9116 (tp30) cc_final: 0.8770 (mp0) REVERT: H 103 LEU cc_start: 0.9123 (mp) cc_final: 0.8898 (mp) REVERT: J 20 THR cc_start: 0.7927 (t) cc_final: 0.6533 (t) REVERT: J 22 ASP cc_start: 0.8978 (p0) cc_final: 0.8555 (t0) REVERT: J 48 LEU cc_start: 0.9488 (mm) cc_final: 0.8695 (tp) REVERT: K 39 GLU cc_start: 0.9518 (mp0) cc_final: 0.9244 (mp0) REVERT: K 49 LEU cc_start: 0.9688 (tt) cc_final: 0.9465 (pp) REVERT: K 68 ASP cc_start: 0.8437 (t0) cc_final: 0.8115 (t0) REVERT: L 22 ASP cc_start: 0.7556 (t0) cc_final: 0.7203 (t0) REVERT: L 23 LEU cc_start: 0.9371 (mm) cc_final: 0.9059 (mm) REVERT: L 26 LEU cc_start: 0.9573 (tt) cc_final: 0.9301 (tp) REVERT: L 39 LEU cc_start: 0.9639 (mm) cc_final: 0.9396 (pp) REVERT: L 63 GLU cc_start: 0.9191 (mp0) cc_final: 0.8861 (mp0) REVERT: L 73 TYR cc_start: 0.9025 (m-80) cc_final: 0.8653 (m-80) REVERT: L 106 THR cc_start: 0.8463 (m) cc_final: 0.8136 (m) REVERT: M 112 LEU cc_start: 0.9499 (mt) cc_final: 0.9184 (pp) REVERT: N 45 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8868 (mm-30) REVERT: N 48 LEU cc_start: 0.9317 (mm) cc_final: 0.8755 (tp) REVERT: Q 95 PHE cc_start: 0.9216 (m-80) cc_final: 0.8712 (m-80) REVERT: R 33 GLU cc_start: 0.9189 (pm20) cc_final: 0.8966 (pp20) REVERT: R 45 GLU cc_start: 0.9203 (pp20) cc_final: 0.8648 (pp20) REVERT: R 66 LYS cc_start: 0.9558 (mmmt) cc_final: 0.9280 (mmmm) REVERT: T 81 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8229 (tpm170) REVERT: U 61 TYR cc_start: 0.9092 (m-80) cc_final: 0.8433 (m-80) REVERT: U 95 PHE cc_start: 0.9507 (m-80) cc_final: 0.8989 (m-10) REVERT: V 91 LEU cc_start: 0.9594 (tp) cc_final: 0.9385 (tp) REVERT: W 61 TYR cc_start: 0.8837 (m-80) cc_final: 0.8471 (m-80) REVERT: W 76 TYR cc_start: 0.9403 (t80) cc_final: 0.9192 (t80) REVERT: X 24 ARG cc_start: 0.8964 (mpt180) cc_final: 0.8727 (mmt90) outliers start: 4 outliers final: 1 residues processed: 483 average time/residue: 0.3176 time to fit residues: 231.5755 Evaluate side-chains 372 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 371 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 2 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 171 optimal weight: 3.9990 chunk 198 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 ASN ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.054411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.040463 restraints weight = 113886.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.041824 restraints weight = 79397.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.042862 restraints weight = 60588.928| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.6298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 18933 Z= 0.146 Angle : 0.727 12.413 25761 Z= 0.367 Chirality : 0.043 0.324 3051 Planarity : 0.005 0.083 3249 Dihedral : 4.513 22.519 2601 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.17), residues: 2322 helix: 0.99 (0.13), residues: 1440 sheet: -0.53 (0.27), residues: 300 loop : -0.94 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 90 HIS 0.005 0.001 HIS F 95 PHE 0.017 0.002 PHE K 95 TYR 0.047 0.003 TYR B 38 ARG 0.021 0.001 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 1054) hydrogen bonds : angle 4.55679 ( 3162) covalent geometry : bond 0.00320 (18933) covalent geometry : angle 0.72660 (25761) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.9303 (t0) cc_final: 0.9077 (t0) REVERT: B 28 THR cc_start: 0.8568 (m) cc_final: 0.8318 (m) REVERT: B 45 GLU cc_start: 0.9373 (tp30) cc_final: 0.8624 (mm-30) REVERT: B 78 LYS cc_start: 0.9048 (pttp) cc_final: 0.8738 (pttp) REVERT: B 95 HIS cc_start: 0.7406 (t-170) cc_final: 0.6494 (t-170) REVERT: B 101 GLU cc_start: 0.9357 (tp30) cc_final: 0.9005 (mp0) REVERT: C 14 GLU cc_start: 0.9490 (tp30) cc_final: 0.9226 (tp30) REVERT: D 28 THR cc_start: 0.8697 (m) cc_final: 0.7987 (p) REVERT: D 46 LYS cc_start: 0.8848 (ptpp) cc_final: 0.8587 (mttm) REVERT: D 63 GLU cc_start: 0.9547 (tp30) cc_final: 0.8826 (pm20) REVERT: D 74 ARG cc_start: 0.8529 (tmm-80) cc_final: 0.8064 (tmm-80) REVERT: D 75 LEU cc_start: 0.9667 (mt) cc_final: 0.9455 (mt) REVERT: D 94 ARG cc_start: 0.9234 (tpm170) cc_final: 0.8825 (tpp-160) REVERT: D 104 VAL cc_start: 0.9748 (m) cc_final: 0.9504 (p) REVERT: F 38 TYR cc_start: 0.8633 (m-80) cc_final: 0.8397 (m-80) REVERT: F 71 ASP cc_start: 0.9043 (m-30) cc_final: 0.8406 (t0) REVERT: F 116 ASP cc_start: 0.8385 (m-30) cc_final: 0.8029 (p0) REVERT: G 61 TYR cc_start: 0.8000 (m-80) cc_final: 0.7678 (m-80) REVERT: H 63 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8314 (mm-30) REVERT: H 101 GLU cc_start: 0.9210 (tp30) cc_final: 0.8694 (mp0) REVERT: H 119 ARG cc_start: 0.9185 (tpm170) cc_final: 0.8867 (mmp-170) REVERT: J 20 THR cc_start: 0.8181 (t) cc_final: 0.6851 (t) REVERT: J 22 ASP cc_start: 0.8906 (p0) cc_final: 0.8593 (t0) REVERT: J 46 LYS cc_start: 0.9081 (ptpp) cc_final: 0.8716 (pttt) REVERT: K 49 LEU cc_start: 0.9669 (tt) cc_final: 0.9447 (pp) REVERT: K 68 ASP cc_start: 0.8433 (t0) cc_final: 0.8096 (t0) REVERT: L 39 LEU cc_start: 0.9661 (mm) cc_final: 0.9427 (pp) REVERT: L 45 GLU cc_start: 0.8984 (pp20) cc_final: 0.8781 (pp20) REVERT: L 63 GLU cc_start: 0.9270 (mp0) cc_final: 0.8944 (mp0) REVERT: L 73 TYR cc_start: 0.9044 (m-80) cc_final: 0.8625 (m-80) REVERT: M 112 LEU cc_start: 0.9494 (mt) cc_final: 0.9260 (mt) REVERT: N 48 LEU cc_start: 0.9291 (mm) cc_final: 0.8717 (tp) REVERT: Q 95 PHE cc_start: 0.9236 (m-10) cc_final: 0.8792 (m-80) REVERT: R 33 GLU cc_start: 0.9215 (pm20) cc_final: 0.8984 (pp20) REVERT: R 45 GLU cc_start: 0.9162 (pp20) cc_final: 0.8582 (pp20) REVERT: R 46 LYS cc_start: 0.8740 (pttp) cc_final: 0.8502 (pttp) REVERT: R 66 LYS cc_start: 0.9522 (mmmt) cc_final: 0.9222 (mmmm) REVERT: T 81 ARG cc_start: 0.8494 (ttp80) cc_final: 0.8223 (tpm170) REVERT: U 95 PHE cc_start: 0.9476 (m-80) cc_final: 0.8979 (m-10) REVERT: V 28 THR cc_start: 0.8613 (m) cc_final: 0.8121 (m) REVERT: V 80 THR cc_start: 0.9116 (p) cc_final: 0.8890 (t) REVERT: W 61 TYR cc_start: 0.8838 (m-80) cc_final: 0.8518 (m-80) REVERT: X 24 ARG cc_start: 0.8938 (mpt180) cc_final: 0.8700 (mmt90) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.3162 time to fit residues: 216.4674 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 : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 99 optimal weight: 4.9990 chunk 192 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 ASN Q 43 ASN ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.053726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.039729 restraints weight = 115853.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.041098 restraints weight = 81444.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.042099 restraints weight = 61856.205| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.6562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18933 Z= 0.159 Angle : 0.725 10.388 25761 Z= 0.368 Chirality : 0.043 0.281 3051 Planarity : 0.006 0.079 3249 Dihedral : 4.567 22.730 2601 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.17), residues: 2322 helix: 0.95 (0.14), residues: 1440 sheet: -1.08 (0.26), residues: 300 loop : -1.10 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 117 HIS 0.002 0.001 HIS D 95 PHE 0.019 0.002 PHE K 95 TYR 0.038 0.003 TYR B 38 ARG 0.018 0.001 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.04245 ( 1054) hydrogen bonds : angle 4.61896 ( 3162) covalent geometry : bond 0.00340 (18933) covalent geometry : angle 0.72487 (25761) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.9376 (t0) cc_final: 0.9161 (t0) REVERT: B 38 TYR cc_start: 0.7375 (m-80) cc_final: 0.7077 (m-80) REVERT: B 45 GLU cc_start: 0.9375 (tp30) cc_final: 0.8870 (mm-30) REVERT: B 78 LYS cc_start: 0.9055 (pttp) cc_final: 0.8720 (pttp) REVERT: B 95 HIS cc_start: 0.7402 (t-170) cc_final: 0.6453 (t-170) REVERT: B 101 GLU cc_start: 0.9300 (tp30) cc_final: 0.9008 (mp0) REVERT: C 14 GLU cc_start: 0.9498 (tp30) cc_final: 0.9204 (tp30) REVERT: C 49 LEU cc_start: 0.9443 (mt) cc_final: 0.9029 (mt) REVERT: C 61 TYR cc_start: 0.8989 (m-10) cc_final: 0.8637 (m-80) REVERT: D 28 THR cc_start: 0.8752 (m) cc_final: 0.8050 (p) REVERT: D 46 LYS cc_start: 0.8895 (ptpp) cc_final: 0.8673 (mttm) REVERT: D 63 GLU cc_start: 0.9587 (tp30) cc_final: 0.8876 (pm20) REVERT: D 74 ARG cc_start: 0.8656 (tmm-80) cc_final: 0.8111 (tmm-80) REVERT: D 75 LEU cc_start: 0.9693 (mt) cc_final: 0.9469 (mt) REVERT: D 104 VAL cc_start: 0.9763 (m) cc_final: 0.9528 (p) REVERT: F 38 TYR cc_start: 0.8627 (m-80) cc_final: 0.8398 (m-80) REVERT: F 71 ASP cc_start: 0.9018 (m-30) cc_final: 0.8383 (t0) REVERT: F 116 ASP cc_start: 0.8299 (m-30) cc_final: 0.7960 (p0) REVERT: G 7 MET cc_start: 0.8705 (ppp) cc_final: 0.8405 (ppp) REVERT: G 61 TYR cc_start: 0.8105 (m-80) cc_final: 0.7742 (m-80) REVERT: H 57 VAL cc_start: 0.9404 (m) cc_final: 0.8931 (p) REVERT: H 63 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8505 (mm-30) REVERT: H 101 GLU cc_start: 0.9187 (tp30) cc_final: 0.8737 (mp0) REVERT: H 119 ARG cc_start: 0.9210 (tpm170) cc_final: 0.8946 (mmp-170) REVERT: J 20 THR cc_start: 0.8272 (t) cc_final: 0.6947 (t) REVERT: J 22 ASP cc_start: 0.8879 (p0) cc_final: 0.8529 (t0) REVERT: K 68 ASP cc_start: 0.8425 (t0) cc_final: 0.8077 (t0) REVERT: K 95 PHE cc_start: 0.9020 (m-80) cc_final: 0.8740 (m-10) REVERT: L 45 GLU cc_start: 0.9046 (pp20) cc_final: 0.8815 (pp20) REVERT: L 63 GLU cc_start: 0.9290 (mp0) cc_final: 0.8968 (mp0) REVERT: L 73 TYR cc_start: 0.9056 (m-80) cc_final: 0.8590 (m-80) REVERT: N 45 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8896 (mm-30) REVERT: Q 95 PHE cc_start: 0.9326 (m-10) cc_final: 0.8901 (m-80) REVERT: R 33 GLU cc_start: 0.9212 (pm20) cc_final: 0.8951 (pp20) REVERT: R 45 GLU cc_start: 0.9173 (pp20) cc_final: 0.8613 (pp20) REVERT: R 66 LYS cc_start: 0.9540 (mmmt) cc_final: 0.9324 (mtmm) REVERT: T 81 ARG cc_start: 0.8540 (ttp80) cc_final: 0.8262 (tpm170) REVERT: U 95 PHE cc_start: 0.9506 (m-80) cc_final: 0.8979 (m-10) REVERT: W 61 TYR cc_start: 0.8872 (m-80) cc_final: 0.8554 (m-80) REVERT: X 24 ARG cc_start: 0.8940 (mpt180) cc_final: 0.8707 (mmt90) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.3029 time to fit residues: 207.0813 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 : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.5428 > 50: distance: 48 - 73: 4.617 distance: 54 - 82: 12.164 distance: 58 - 61: 3.168 distance: 59 - 91: 14.064 distance: 61 - 62: 6.156 distance: 62 - 63: 5.011 distance: 62 - 65: 5.118 distance: 63 - 64: 10.556 distance: 63 - 73: 3.230 distance: 64 - 96: 8.570 distance: 65 - 66: 4.386 distance: 66 - 68: 5.300 distance: 67 - 69: 4.186 distance: 68 - 70: 4.440 distance: 70 - 71: 4.051 distance: 71 - 72: 3.089 distance: 73 - 74: 10.465 distance: 74 - 75: 7.655 distance: 74 - 77: 13.416 distance: 75 - 76: 14.116 distance: 75 - 82: 10.703 distance: 76 - 104: 27.696 distance: 77 - 78: 7.254 distance: 78 - 79: 12.908 distance: 79 - 80: 12.781 distance: 79 - 81: 7.418 distance: 82 - 83: 7.884 distance: 83 - 84: 3.907 distance: 83 - 86: 10.291 distance: 84 - 85: 4.322 distance: 84 - 91: 10.737 distance: 85 - 113: 14.048 distance: 86 - 87: 5.489 distance: 87 - 88: 4.193 distance: 88 - 89: 7.732 distance: 89 - 90: 12.615 distance: 91 - 92: 11.337 distance: 92 - 93: 3.110 distance: 92 - 95: 13.712 distance: 93 - 94: 4.480 distance: 93 - 96: 7.817 distance: 94 - 121: 13.631 distance: 96 - 97: 6.464 distance: 97 - 98: 8.098 distance: 97 - 100: 6.342 distance: 98 - 99: 27.959 distance: 98 - 104: 19.419 distance: 100 - 101: 4.486 distance: 101 - 102: 7.729 distance: 101 - 103: 5.152 distance: 104 - 105: 8.168 distance: 105 - 106: 10.662 distance: 105 - 108: 17.091 distance: 106 - 107: 25.097 distance: 106 - 113: 4.703 distance: 108 - 109: 5.521 distance: 109 - 110: 19.244 distance: 110 - 111: 9.432 distance: 110 - 112: 6.269 distance: 113 - 114: 16.996 distance: 114 - 115: 12.739 distance: 114 - 117: 21.929 distance: 115 - 116: 17.864 distance: 115 - 121: 14.415 distance: 117 - 118: 14.864 distance: 118 - 119: 15.239 distance: 118 - 120: 21.692 distance: 121 - 122: 10.820 distance: 122 - 123: 6.265 distance: 122 - 125: 10.854 distance: 123 - 124: 14.223 distance: 123 - 129: 11.131 distance: 125 - 126: 12.888 distance: 126 - 127: 19.440 distance: 126 - 128: 13.133 distance: 129 - 130: 13.287 distance: 129 - 135: 16.791 distance: 130 - 131: 12.394 distance: 130 - 133: 18.328 distance: 131 - 132: 19.486 distance: 131 - 136: 4.348 distance: 133 - 134: 16.535 distance: 134 - 135: 7.554 distance: 136 - 137: 3.130 distance: 137 - 138: 11.611 distance: 137 - 140: 4.113 distance: 138 - 139: 13.025 distance: 138 - 144: 17.654 distance: 140 - 141: 5.023 distance: 141 - 142: 11.623 distance: 141 - 143: 13.270