Starting phenix.real_space_refine on Mon Oct 14 16:36:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umr_42382/10_2024/8umr_42382.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umr_42382/10_2024/8umr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umr_42382/10_2024/8umr_42382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umr_42382/10_2024/8umr_42382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umr_42382/10_2024/8umr_42382.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umr_42382/10_2024/8umr_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-5477/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: 5.62, per 1000 atoms: 0.30 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: 4.98 Conformation dependent library (CDL) restraints added in 2.7 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: 1.59 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: 5.67 Time building geometry restraints manager: 5.66 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: 0.00 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 35.300 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.120 ------------------------------------------------------------------------------- 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= 0.274 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 775 time to evaluate : 2.060 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: 0.3954 time to fit residues: 427.7656 Evaluate side-chains 445 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 2.100 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 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= 0.260 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 *********************** 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 fitting. rotamer outliers: 9 poor density : 556 time to evaluate : 2.222 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: 0.8602 (t0) cc_final: 0.8344 (t0) REVERT: A 59 GLU cc_start: 0.9296 (pt0) cc_final: 0.8902 (pp20) REVERT: B 28 THR cc_start: 0.8004 (m) cc_final: 0.7283 (m) REVERT: B 38 TYR cc_start: 0.7456 (m-80) cc_final: 0.7090 (m-80) REVERT: B 45 GLU cc_start: 0.9446 (tp30) cc_final: 0.9226 (tm-30) REVERT: B 52 VAL cc_start: 0.8622 (m) cc_final: 0.8166 (m) REVERT: B 57 VAL cc_start: 0.8683 (t) cc_final: 0.8376 (m) REVERT: B 103 LEU cc_start: 0.9432 (mt) cc_final: 0.9136 (mp) REVERT: C 14 GLU cc_start: 0.9542 (tp30) cc_final: 0.9067 (tp30) REVERT: D 22 ASP cc_start: 0.7878 (t0) cc_final: 0.7626 (t0) REVERT: D 28 THR cc_start: 0.8914 (m) cc_final: 0.8590 (m) REVERT: D 63 GLU cc_start: 0.9066 (tp30) cc_final: 0.8852 (mp0) REVERT: D 80 THR cc_start: 0.9569 (p) cc_final: 0.9355 (p) REVERT: D 94 ARG cc_start: 0.9286 (tpm170) cc_final: 0.9025 (tpm170) REVERT: D 118 LEU cc_start: 0.9695 (mp) cc_final: 0.9449 (pp) REVERT: F 38 TYR cc_start: 0.8825 (m-80) cc_final: 0.8616 (m-10) REVERT: F 79 THR cc_start: 0.8918 (m) cc_final: 0.8613 (m) REVERT: F 116 ASP cc_start: 0.8510 (m-30) cc_final: 0.8156 (p0) REVERT: H 22 ASP cc_start: 0.8974 (t0) cc_final: 0.8763 (t0) REVERT: H 26 LEU cc_start: 0.9290 (tp) cc_final: 0.9008 (tp) REVERT: H 101 GLU cc_start: 0.8845 (tp30) cc_final: 0.8527 (tp30) REVERT: H 103 LEU cc_start: 0.9386 (mt) cc_final: 0.9014 (mt) REVERT: H 119 ARG cc_start: 0.8918 (tpm170) cc_final: 0.8308 (mtt180) REVERT: K 14 GLU cc_start: 0.9131 (tp30) cc_final: 0.8299 (tp30) REVERT: K 19 ASN cc_start: 0.8718 (m-40) cc_final: 0.8513 (t0) REVERT: K 22 THR cc_start: 0.9499 (p) cc_final: 0.8899 (p) REVERT: L 39 LEU cc_start: 0.9561 (mm) cc_final: 0.9220 (pp) REVERT: L 73 TYR cc_start: 0.8957 (m-80) cc_final: 0.8586 (m-10) REVERT: M 112 LEU cc_start: 0.9449 (mt) cc_final: 0.9154 (mt) REVERT: N 48 LEU cc_start: 0.9198 (mm) cc_final: 0.8498 (tt) REVERT: N 92 GLN cc_start: 0.9124 (mt0) cc_final: 0.8856 (pp30) REVERT: P 80 THR cc_start: 0.8673 (p) cc_final: 0.8301 (t) REVERT: P 84 LEU cc_start: 0.8767 (tp) cc_final: 0.8452 (mt) REVERT: Q 95 PHE cc_start: 0.8901 (m-80) cc_final: 0.8409 (m-80) REVERT: R 45 GLU cc_start: 0.9188 (pp20) cc_final: 0.8755 (pp20) REVERT: R 60 VAL cc_start: 0.8693 (p) cc_final: 0.8440 (p) REVERT: R 71 ASP cc_start: 0.8906 (m-30) cc_final: 0.8180 (t0) REVERT: T 26 LEU cc_start: 0.9296 (tp) cc_final: 0.9068 (tp) REVERT: T 101 GLU cc_start: 0.8434 (tp30) cc_final: 0.8123 (mp0) REVERT: V 22 ASP cc_start: 0.8068 (t0) cc_final: 0.5939 (t0) REVERT: V 52 VAL cc_start: 0.8331 (m) cc_final: 0.8029 (m) REVERT: W 14 GLU cc_start: 0.9324 (tp30) cc_final: 0.9080 (tp30) REVERT: W 39 GLU cc_start: 0.9390 (mp0) cc_final: 0.9151 (mp0) REVERT: X 26 LEU cc_start: 0.9326 (tp) cc_final: 0.9023 (tp) REVERT: X 66 LYS cc_start: 0.7424 (mmtt) cc_final: 0.7175 (mmmt) REVERT: X 103 LEU cc_start: 0.9023 (mt) cc_final: 0.8730 (mt) outliers start: 9 outliers final: 6 residues processed: 562 average time/residue: 0.3205 time to fit residues: 267.1471 Evaluate side-chains 395 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 389 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 172 optimal weight: 40.0000 chunk 140 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 205 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 ASN I 90 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN M 43 ASN Q 43 ASN ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 77 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18933 Z= 0.283 Angle : 0.728 9.425 25761 Z= 0.379 Chirality : 0.043 0.143 3051 Planarity : 0.005 0.065 3249 Dihedral : 4.598 24.610 2601 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 24.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.05 % Allowed : 6.83 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2322 helix: 1.01 (0.13), residues: 1452 sheet: -0.54 (0.27), residues: 276 loop : -0.64 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 117 HIS 0.006 0.002 HIS D 95 PHE 0.026 0.002 PHE K 95 TYR 0.031 0.003 TYR W 8 ARG 0.010 0.001 ARG T 61 *********************** 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 481 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 480 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 THR cc_start: 0.8052 (m) cc_final: 0.7625 (m) REVERT: B 79 THR cc_start: 0.9383 (p) cc_final: 0.9079 (p) REVERT: B 80 THR cc_start: 0.9068 (p) cc_final: 0.8754 (p) REVERT: C 14 GLU cc_start: 0.9561 (tp30) cc_final: 0.9080 (tp30) REVERT: D 22 ASP cc_start: 0.8055 (t0) cc_final: 0.7704 (t0) REVERT: D 28 THR cc_start: 0.8925 (m) cc_final: 0.8533 (m) REVERT: D 63 GLU cc_start: 0.9239 (tp30) cc_final: 0.8933 (mp0) REVERT: D 80 THR cc_start: 0.9515 (p) cc_final: 0.9284 (p) REVERT: D 94 ARG cc_start: 0.9157 (tpm170) cc_final: 0.8942 (tpm170) REVERT: D 118 LEU cc_start: 0.9650 (mp) cc_final: 0.9446 (pp) REVERT: F 38 TYR cc_start: 0.8737 (m-80) cc_final: 0.8527 (m-80) REVERT: F 71 ASP cc_start: 0.8981 (m-30) cc_final: 0.8279 (t0) REVERT: F 116 ASP cc_start: 0.8500 (m-30) cc_final: 0.8037 (p0) REVERT: H 101 GLU cc_start: 0.9061 (tp30) cc_final: 0.8657 (mp0) REVERT: J 22 ASP cc_start: 0.8926 (p0) cc_final: 0.8266 (t0) REVERT: J 46 LYS cc_start: 0.8897 (ptpp) cc_final: 0.8673 (pttt) REVERT: K 14 GLU cc_start: 0.9193 (tp30) cc_final: 0.8257 (tp30) REVERT: K 22 THR cc_start: 0.9354 (p) cc_final: 0.8817 (p) REVERT: K 39 GLU cc_start: 0.9492 (mp0) cc_final: 0.9220 (mp0) REVERT: K 68 ASP cc_start: 0.8243 (t0) cc_final: 0.7999 (t0) REVERT: L 39 LEU cc_start: 0.9656 (mm) cc_final: 0.9359 (pp) REVERT: L 73 TYR cc_start: 0.9016 (m-80) cc_final: 0.8603 (m-10) REVERT: N 48 LEU cc_start: 0.9150 (mm) cc_final: 0.8846 (tt) REVERT: N 92 GLN cc_start: 0.9237 (mt0) cc_final: 0.9020 (pp30) REVERT: P 63 GLU cc_start: 0.8705 (mp0) cc_final: 0.8461 (mp0) REVERT: Q 95 PHE cc_start: 0.9040 (m-80) cc_final: 0.8513 (m-80) REVERT: R 45 GLU cc_start: 0.9237 (pp20) cc_final: 0.8812 (pp20) REVERT: R 68 VAL cc_start: 0.9639 (m) cc_final: 0.9332 (p) REVERT: R 71 ASP cc_start: 0.9153 (m-30) cc_final: 0.8243 (t0) REVERT: T 26 LEU cc_start: 0.9420 (tp) cc_final: 0.9217 (tp) REVERT: T 78 LYS cc_start: 0.9552 (ptpp) cc_final: 0.9341 (ptpp) REVERT: V 52 VAL cc_start: 0.8599 (m) cc_final: 0.8321 (m) REVERT: W 14 GLU cc_start: 0.9419 (tp30) cc_final: 0.9002 (tp30) REVERT: W 39 GLU cc_start: 0.9416 (mp0) cc_final: 0.9188 (mp0) REVERT: W 76 TYR cc_start: 0.9462 (t80) cc_final: 0.9237 (t80) REVERT: W 97 LYS cc_start: 0.9572 (mtpt) cc_final: 0.9366 (mmmt) REVERT: X 26 LEU cc_start: 0.9451 (tp) cc_final: 0.9159 (tp) REVERT: X 103 LEU cc_start: 0.9030 (mt) cc_final: 0.8810 (mm) outliers start: 1 outliers final: 0 residues processed: 480 average time/residue: 0.3189 time to fit residues: 229.3915 Evaluate side-chains 366 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN M 43 ASN Q 43 ASN ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 90 ASN ** W 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18933 Z= 0.252 Angle : 0.705 9.834 25761 Z= 0.366 Chirality : 0.042 0.157 3051 Planarity : 0.006 0.075 3249 Dihedral : 4.666 22.438 2601 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 23.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.16 % Allowed : 6.21 % Favored : 93.64 % 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: 0.48 (0.17), residues: 2322 helix: 1.06 (0.13), residues: 1440 sheet: -0.85 (0.25), residues: 300 loop : -0.70 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 117 HIS 0.005 0.001 HIS X 95 PHE 0.025 0.002 PHE K 95 TYR 0.033 0.003 TYR B 38 ARG 0.022 0.001 ARG D 61 *********************** 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 470 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 467 time to evaluate : 2.096 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: B 59 ARG cc_start: 0.8439 (ttt90) cc_final: 0.8222 (ttt90) REVERT: B 81 ARG cc_start: 0.8797 (ptt-90) cc_final: 0.8415 (ptt-90) REVERT: B 101 GLU cc_start: 0.8897 (tp30) cc_final: 0.8655 (tp30) REVERT: B 103 LEU cc_start: 0.9572 (tt) cc_final: 0.9119 (mp) REVERT: C 14 GLU cc_start: 0.9576 (tp30) cc_final: 0.9086 (tp30) REVERT: C 31 LEU cc_start: 0.9652 (pp) cc_final: 0.9440 (mt) REVERT: D 22 ASP cc_start: 0.8011 (t0) cc_final: 0.7543 (t0) REVERT: D 28 THR cc_start: 0.8853 (m) cc_final: 0.8203 (p) REVERT: D 63 GLU cc_start: 0.9417 (tp30) cc_final: 0.8722 (pm20) REVERT: D 77 PHE cc_start: 0.9308 (m-80) cc_final: 0.8993 (m-80) REVERT: D 80 THR cc_start: 0.9482 (p) cc_final: 0.9135 (p) REVERT: F 71 ASP cc_start: 0.8994 (m-30) cc_final: 0.8205 (t0) REVERT: F 116 ASP cc_start: 0.8487 (m-30) cc_final: 0.8034 (p0) REVERT: G 61 TYR cc_start: 0.8089 (m-80) cc_final: 0.7795 (m-80) REVERT: G 114 LEU cc_start: 0.9187 (mt) cc_final: 0.8935 (mt) REVERT: H 103 LEU cc_start: 0.9349 (mp) cc_final: 0.9131 (mp) REVERT: H 119 ARG cc_start: 0.8913 (tpm170) cc_final: 0.8623 (tpm170) REVERT: J 20 THR cc_start: 0.7809 (t) cc_final: 0.6441 (t) REVERT: J 22 ASP cc_start: 0.8914 (p0) cc_final: 0.8349 (t0) REVERT: K 14 GLU cc_start: 0.9115 (tp30) cc_final: 0.8288 (tp30) REVERT: K 19 ASN cc_start: 0.8663 (t0) cc_final: 0.8374 (t0) REVERT: K 22 THR cc_start: 0.9315 (p) cc_final: 0.8880 (p) REVERT: K 39 GLU cc_start: 0.9482 (mp0) cc_final: 0.9205 (mp0) REVERT: K 68 ASP cc_start: 0.8410 (t0) cc_final: 0.8141 (t0) REVERT: L 23 LEU cc_start: 0.9271 (mm) cc_final: 0.8852 (mm) REVERT: L 24 ARG cc_start: 0.8561 (mpt180) cc_final: 0.8308 (mpt90) REVERT: L 39 LEU cc_start: 0.9695 (mm) cc_final: 0.9455 (pp) REVERT: L 73 TYR cc_start: 0.9037 (m-80) cc_final: 0.8661 (m-80) REVERT: L 106 THR cc_start: 0.8043 (m) cc_final: 0.7684 (m) REVERT: M 112 LEU cc_start: 0.9516 (mt) cc_final: 0.9283 (mt) REVERT: N 48 LEU cc_start: 0.9189 (mm) cc_final: 0.8787 (tt) REVERT: N 75 LEU cc_start: 0.9481 (mm) cc_final: 0.9202 (mm) REVERT: P 63 GLU cc_start: 0.8635 (mp0) cc_final: 0.8377 (mp0) REVERT: P 108 ILE cc_start: 0.8871 (pt) cc_final: 0.8445 (mp) REVERT: Q 95 PHE cc_start: 0.9066 (m-80) cc_final: 0.8546 (m-80) REVERT: R 26 LEU cc_start: 0.9558 (tp) cc_final: 0.9354 (tp) REVERT: R 45 GLU cc_start: 0.9200 (pp20) cc_final: 0.8739 (pp20) REVERT: R 66 LYS cc_start: 0.9554 (mmmt) cc_final: 0.9288 (mmmm) REVERT: R 71 ASP cc_start: 0.9178 (m-30) cc_final: 0.8179 (t0) REVERT: U 61 TYR cc_start: 0.9244 (m-80) cc_final: 0.8489 (m-80) REVERT: V 52 VAL cc_start: 0.8261 (m) cc_final: 0.8032 (m) REVERT: W 14 GLU cc_start: 0.9448 (tp30) cc_final: 0.9016 (tp30) REVERT: W 39 GLU cc_start: 0.9464 (mp0) cc_final: 0.9192 (mp0) REVERT: W 76 TYR cc_start: 0.9415 (t80) cc_final: 0.9197 (t80) REVERT: W 97 LYS cc_start: 0.9635 (mtpt) cc_final: 0.9212 (mmmm) REVERT: X 24 ARG cc_start: 0.9053 (mpt180) cc_final: 0.8381 (mmt180) REVERT: X 26 LEU cc_start: 0.9441 (tp) cc_final: 0.9160 (tp) REVERT: X 103 LEU cc_start: 0.9003 (mt) cc_final: 0.8773 (mt) outliers start: 3 outliers final: 1 residues processed: 469 average time/residue: 0.3293 time to fit residues: 232.4692 Evaluate side-chains 380 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 379 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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** K 43 ASN M 43 ASN Q 43 ASN U 43 ASN W 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18933 Z= 0.249 Angle : 0.711 9.164 25761 Z= 0.369 Chirality : 0.042 0.164 3051 Planarity : 0.005 0.069 3249 Dihedral : 4.672 25.149 2601 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 22.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.37 % Allowed : 6.21 % Favored : 93.43 % 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: 0.31 (0.17), residues: 2322 helix: 0.98 (0.13), residues: 1440 sheet: -1.08 (0.25), residues: 300 loop : -0.81 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 117 HIS 0.005 0.001 HIS X 95 PHE 0.014 0.002 PHE C 95 TYR 0.041 0.003 TYR I 48 ARG 0.012 0.001 ARG D 61 *********************** 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 473 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 466 time to evaluate : 2.005 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: A 53 ASN cc_start: 0.9285 (t0) cc_final: 0.9026 (t0) REVERT: A 82 TYR cc_start: 0.9302 (m-80) cc_final: 0.8712 (m-80) REVERT: B 18 ILE cc_start: 0.8930 (tp) cc_final: 0.8710 (mp) REVERT: B 59 ARG cc_start: 0.8309 (ttt90) cc_final: 0.8098 (ttt90) REVERT: B 78 LYS cc_start: 0.8903 (pttp) cc_final: 0.8424 (pttp) REVERT: C 14 GLU cc_start: 0.9532 (tp30) cc_final: 0.9090 (tp30) REVERT: C 49 LEU cc_start: 0.9388 (mt) cc_final: 0.9149 (mt) REVERT: D 22 ASP cc_start: 0.7917 (t0) cc_final: 0.7463 (t0) REVERT: D 28 THR cc_start: 0.8885 (m) cc_final: 0.8250 (p) REVERT: D 63 GLU cc_start: 0.9506 (tp30) cc_final: 0.8755 (pm20) REVERT: D 80 THR cc_start: 0.9426 (p) cc_final: 0.9132 (p) REVERT: D 94 ARG cc_start: 0.9186 (tpm170) cc_final: 0.8606 (tpp-160) REVERT: D 104 VAL cc_start: 0.9690 (m) cc_final: 0.9406 (p) REVERT: F 71 ASP cc_start: 0.9071 (m-30) cc_final: 0.8343 (t0) REVERT: F 116 ASP cc_start: 0.8420 (m-30) cc_final: 0.7967 (p0) REVERT: G 7 MET cc_start: 0.8851 (ppp) cc_final: 0.8523 (ppp) REVERT: G 61 TYR cc_start: 0.8108 (m-80) cc_final: 0.7752 (m-80) REVERT: G 114 LEU cc_start: 0.9242 (mt) cc_final: 0.8951 (mt) REVERT: H 119 ARG cc_start: 0.9019 (tpm170) cc_final: 0.8671 (tpm170) REVERT: J 20 THR cc_start: 0.8007 (t) cc_final: 0.6568 (t) REVERT: J 22 ASP cc_start: 0.8900 (p0) cc_final: 0.8229 (t0) REVERT: J 95 HIS cc_start: 0.5545 (t-90) cc_final: 0.5329 (t-90) REVERT: K 39 GLU cc_start: 0.9488 (mp0) cc_final: 0.9232 (mp0) REVERT: L 23 LEU cc_start: 0.9316 (mm) cc_final: 0.8791 (mm) REVERT: L 26 LEU cc_start: 0.9496 (tp) cc_final: 0.9286 (tp) REVERT: L 39 LEU cc_start: 0.9706 (mm) cc_final: 0.9494 (pp) REVERT: L 73 TYR cc_start: 0.8972 (m-80) cc_final: 0.8521 (m-80) REVERT: L 106 THR cc_start: 0.8161 (m) cc_final: 0.7777 (m) REVERT: M 112 LEU cc_start: 0.9580 (mt) cc_final: 0.9327 (mt) REVERT: N 48 LEU cc_start: 0.9189 (mm) cc_final: 0.8726 (tp) REVERT: Q 95 PHE cc_start: 0.9105 (m-80) cc_final: 0.8619 (m-80) REVERT: R 25 LEU cc_start: 0.9550 (mm) cc_final: 0.9333 (mm) REVERT: R 26 LEU cc_start: 0.9597 (tp) cc_final: 0.9391 (tp) REVERT: R 45 GLU cc_start: 0.9200 (pp20) cc_final: 0.8746 (pp20) REVERT: R 66 LYS cc_start: 0.9562 (mmmt) cc_final: 0.9282 (mmmm) REVERT: T 26 LEU cc_start: 0.9477 (tp) cc_final: 0.9256 (tp) REVERT: U 61 TYR cc_start: 0.9262 (m-80) cc_final: 0.8603 (m-80) REVERT: V 52 VAL cc_start: 0.8342 (m) cc_final: 0.8091 (m) REVERT: V 104 VAL cc_start: 0.9641 (m) cc_final: 0.9430 (p) REVERT: W 14 GLU cc_start: 0.9445 (tp30) cc_final: 0.8988 (tp30) REVERT: X 24 ARG cc_start: 0.9075 (mpt180) cc_final: 0.8380 (mmt180) outliers start: 7 outliers final: 1 residues processed: 471 average time/residue: 0.3134 time to fit residues: 220.7222 Evaluate side-chains 368 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 367 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 220 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN M 43 ASN Q 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18933 Z= 0.279 Angle : 0.741 10.355 25761 Z= 0.384 Chirality : 0.044 0.179 3051 Planarity : 0.006 0.095 3249 Dihedral : 4.763 22.834 2601 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 25.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.21 % Allowed : 5.53 % Favored : 94.26 % 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: 0.34 (0.17), residues: 2322 helix: 0.99 (0.13), residues: 1416 sheet: -1.18 (0.26), residues: 276 loop : -0.66 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP V 117 HIS 0.005 0.001 HIS D 95 PHE 0.015 0.002 PHE K 95 TYR 0.045 0.003 TYR F 38 ARG 0.027 0.001 ARG L 24 *********************** 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 456 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 452 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.9317 (t0) cc_final: 0.9070 (t0) REVERT: B 18 ILE cc_start: 0.8929 (tp) cc_final: 0.8704 (mp) REVERT: B 78 LYS cc_start: 0.8887 (pttp) cc_final: 0.8418 (pttp) REVERT: B 81 ARG cc_start: 0.9033 (ptt-90) cc_final: 0.8768 (ptt-90) REVERT: C 14 GLU cc_start: 0.9550 (tp30) cc_final: 0.9099 (tp30) REVERT: D 22 ASP cc_start: 0.8200 (t0) cc_final: 0.7821 (t0) REVERT: D 26 LEU cc_start: 0.9570 (tp) cc_final: 0.9360 (tp) REVERT: D 63 GLU cc_start: 0.9540 (tp30) cc_final: 0.8815 (pm20) REVERT: D 74 ARG cc_start: 0.9331 (tmm-80) cc_final: 0.8638 (tmm-80) REVERT: D 94 ARG cc_start: 0.9170 (tpm170) cc_final: 0.8925 (tpp-160) REVERT: F 71 ASP cc_start: 0.9067 (m-30) cc_final: 0.8416 (t0) REVERT: F 116 ASP cc_start: 0.8490 (m-30) cc_final: 0.8041 (p0) REVERT: G 7 MET cc_start: 0.8883 (ppp) cc_final: 0.8613 (ppp) REVERT: G 61 TYR cc_start: 0.8226 (m-80) cc_final: 0.7948 (m-80) REVERT: H 63 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8558 (mm-30) REVERT: H 119 ARG cc_start: 0.9027 (tpm170) cc_final: 0.8825 (tpm170) REVERT: J 20 THR cc_start: 0.8262 (t) cc_final: 0.6778 (t) REVERT: J 22 ASP cc_start: 0.8958 (p0) cc_final: 0.8442 (t0) REVERT: J 95 HIS cc_start: 0.5609 (t-90) cc_final: 0.5301 (t-90) REVERT: L 39 LEU cc_start: 0.9720 (mm) cc_final: 0.9504 (pp) REVERT: L 73 TYR cc_start: 0.9029 (m-80) cc_final: 0.8573 (m-80) REVERT: L 77 PHE cc_start: 0.9466 (m-10) cc_final: 0.9242 (m-80) REVERT: L 84 LEU cc_start: 0.9228 (tt) cc_final: 0.8710 (pp) REVERT: M 112 LEU cc_start: 0.9607 (mt) cc_final: 0.9402 (mt) REVERT: Q 12 GLN cc_start: 0.9243 (pt0) cc_final: 0.9005 (pt0) REVERT: Q 95 PHE cc_start: 0.9242 (m-80) cc_final: 0.8842 (m-80) REVERT: R 25 LEU cc_start: 0.9531 (mm) cc_final: 0.9295 (mm) REVERT: R 26 LEU cc_start: 0.9628 (tp) cc_final: 0.9406 (tp) REVERT: R 33 GLU cc_start: 0.9231 (pm20) cc_final: 0.8961 (pp20) REVERT: R 45 GLU cc_start: 0.9264 (pp20) cc_final: 0.8800 (pp20) REVERT: R 64 ASN cc_start: 0.9487 (p0) cc_final: 0.9275 (p0) REVERT: R 66 LYS cc_start: 0.9584 (mmmt) cc_final: 0.9303 (mmmm) REVERT: T 26 LEU cc_start: 0.9514 (tp) cc_final: 0.9281 (tp) REVERT: U 61 TYR cc_start: 0.9309 (m-80) cc_final: 0.8620 (m-80) REVERT: V 52 VAL cc_start: 0.8283 (m) cc_final: 0.8020 (m) REVERT: V 104 VAL cc_start: 0.9651 (m) cc_final: 0.9438 (p) REVERT: W 14 GLU cc_start: 0.9466 (tp30) cc_final: 0.8987 (tp30) REVERT: W 76 TYR cc_start: 0.9438 (t80) cc_final: 0.9088 (t80) REVERT: X 24 ARG cc_start: 0.9112 (mpt180) cc_final: 0.8350 (mmt180) outliers start: 4 outliers final: 1 residues processed: 456 average time/residue: 0.2899 time to fit residues: 200.6604 Evaluate side-chains 355 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 354 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 161 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 185 optimal weight: 9.9990 chunk 123 optimal weight: 0.9990 chunk 219 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 G 77 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.6507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18933 Z= 0.228 Angle : 0.753 11.757 25761 Z= 0.387 Chirality : 0.044 0.289 3051 Planarity : 0.005 0.051 3249 Dihedral : 4.652 24.324 2601 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: 0.09 (0.17), residues: 2322 helix: 0.86 (0.13), residues: 1440 sheet: -1.24 (0.25), residues: 300 loop : -0.99 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP V 117 HIS 0.006 0.001 HIS D 95 PHE 0.018 0.002 PHE D 77 TYR 0.049 0.003 TYR B 38 ARG 0.022 0.001 ARG D 61 *********************** 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 463 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 2.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.9272 (t0) cc_final: 0.9046 (t0) REVERT: B 28 THR cc_start: 0.8242 (m) cc_final: 0.8018 (m) REVERT: C 14 GLU cc_start: 0.9533 (tp30) cc_final: 0.9099 (tp30) REVERT: C 49 LEU cc_start: 0.9422 (mt) cc_final: 0.8968 (mt) REVERT: C 61 TYR cc_start: 0.9281 (m-10) cc_final: 0.8640 (m-10) REVERT: C 65 LEU cc_start: 0.9557 (pp) cc_final: 0.9138 (mt) REVERT: D 22 ASP cc_start: 0.8054 (t0) cc_final: 0.7667 (t0) REVERT: D 26 LEU cc_start: 0.9597 (tp) cc_final: 0.9305 (tp) REVERT: D 28 THR cc_start: 0.8975 (m) cc_final: 0.8446 (m) REVERT: D 63 GLU cc_start: 0.9561 (tp30) cc_final: 0.8792 (pm20) REVERT: D 74 ARG cc_start: 0.9301 (tmm-80) cc_final: 0.8558 (tmm-80) REVERT: D 75 LEU cc_start: 0.9727 (mt) cc_final: 0.9480 (mt) REVERT: D 80 THR cc_start: 0.9417 (p) cc_final: 0.9007 (p) REVERT: D 104 VAL cc_start: 0.9678 (m) cc_final: 0.9408 (p) REVERT: F 71 ASP cc_start: 0.9083 (m-30) cc_final: 0.8404 (t0) REVERT: F 116 ASP cc_start: 0.8481 (m-30) cc_final: 0.8023 (p0) REVERT: G 7 MET cc_start: 0.8926 (ppp) cc_final: 0.8640 (ppp) REVERT: G 61 TYR cc_start: 0.8161 (m-10) cc_final: 0.7812 (m-80) REVERT: H 63 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8611 (mm-30) REVERT: H 119 ARG cc_start: 0.9052 (tpm170) cc_final: 0.8834 (tpm170) REVERT: J 20 THR cc_start: 0.8356 (t) cc_final: 0.6827 (t) REVERT: J 22 ASP cc_start: 0.8917 (p0) cc_final: 0.8349 (t0) REVERT: J 48 LEU cc_start: 0.9353 (mm) cc_final: 0.8550 (tp) REVERT: J 95 HIS cc_start: 0.5670 (t-90) cc_final: 0.5347 (t-90) REVERT: K 39 GLU cc_start: 0.9459 (mp0) cc_final: 0.9170 (mp0) REVERT: L 39 LEU cc_start: 0.9710 (mm) cc_final: 0.9474 (pp) REVERT: L 63 GLU cc_start: 0.9126 (mp0) cc_final: 0.8866 (mp0) REVERT: L 73 TYR cc_start: 0.9012 (m-80) cc_final: 0.8550 (m-80) REVERT: L 77 PHE cc_start: 0.9446 (m-10) cc_final: 0.9222 (m-10) REVERT: M 7 MET cc_start: 0.9401 (mpp) cc_final: 0.9120 (mpp) REVERT: M 112 LEU cc_start: 0.9606 (mt) cc_final: 0.9391 (mt) REVERT: N 45 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8890 (mm-30) REVERT: Q 12 GLN cc_start: 0.9222 (pt0) cc_final: 0.8977 (pt0) REVERT: Q 95 PHE cc_start: 0.9193 (m-10) cc_final: 0.8765 (m-80) REVERT: R 25 LEU cc_start: 0.9578 (mm) cc_final: 0.9356 (mm) REVERT: R 26 LEU cc_start: 0.9631 (tp) cc_final: 0.9409 (tp) REVERT: R 33 GLU cc_start: 0.9162 (pm20) cc_final: 0.8951 (pp20) REVERT: R 45 GLU cc_start: 0.9188 (pp20) cc_final: 0.8715 (pp20) REVERT: R 64 ASN cc_start: 0.9517 (p0) cc_final: 0.9317 (p0) REVERT: R 66 LYS cc_start: 0.9563 (mmmt) cc_final: 0.9274 (mmmm) REVERT: T 26 LEU cc_start: 0.9474 (tp) cc_final: 0.9163 (tp) REVERT: T 35 GLU cc_start: 0.8925 (pm20) cc_final: 0.8648 (pm20) REVERT: V 22 ASP cc_start: 0.8286 (t70) cc_final: 0.6281 (t0) REVERT: V 52 VAL cc_start: 0.8136 (m) cc_final: 0.7904 (m) REVERT: V 104 VAL cc_start: 0.9629 (m) cc_final: 0.9405 (p) REVERT: W 14 GLU cc_start: 0.9457 (tp30) cc_final: 0.8917 (tp30) REVERT: W 76 TYR cc_start: 0.9400 (t80) cc_final: 0.9091 (t80) REVERT: X 24 ARG cc_start: 0.9067 (mpt180) cc_final: 0.8480 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 463 average time/residue: 0.2990 time to fit residues: 209.4765 Evaluate side-chains 353 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 20.0000 chunk 42 optimal weight: 0.0060 chunk 139 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 20 optimal weight: 0.2980 chunk 172 optimal weight: 3.9990 overall best weight: 1.2400 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN M 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.6654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 18933 Z= 0.198 Angle : 0.757 12.547 25761 Z= 0.376 Chirality : 0.043 0.192 3051 Planarity : 0.005 0.055 3249 Dihedral : 4.550 23.299 2601 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.17 (0.17), residues: 2322 helix: 0.92 (0.13), residues: 1440 sheet: -1.18 (0.25), residues: 300 loop : -1.00 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 90 HIS 0.004 0.001 HIS F 95 PHE 0.018 0.002 PHE K 95 TYR 0.040 0.002 TYR B 38 ARG 0.013 0.001 ARG D 61 *********************** 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 476 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 476 time to evaluate : 3.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASN cc_start: 0.9181 (t0) cc_final: 0.8958 (t0) REVERT: B 28 THR cc_start: 0.8292 (m) cc_final: 0.7926 (m) REVERT: B 59 ARG cc_start: 0.8440 (ttt90) cc_final: 0.8216 (ttt90) REVERT: B 78 LYS cc_start: 0.8909 (pttp) cc_final: 0.8509 (pttp) REVERT: C 14 GLU cc_start: 0.9493 (tp30) cc_final: 0.9107 (tp30) REVERT: C 65 LEU cc_start: 0.9560 (pp) cc_final: 0.9128 (mt) REVERT: D 22 ASP cc_start: 0.7951 (t0) cc_final: 0.7428 (t0) REVERT: D 28 THR cc_start: 0.8828 (m) cc_final: 0.8090 (p) REVERT: D 63 GLU cc_start: 0.9544 (tp30) cc_final: 0.8784 (pm20) REVERT: D 80 THR cc_start: 0.9402 (p) cc_final: 0.9156 (t) REVERT: D 104 VAL cc_start: 0.9659 (m) cc_final: 0.9385 (p) REVERT: F 38 TYR cc_start: 0.8560 (m-80) cc_final: 0.8358 (m-80) REVERT: F 71 ASP cc_start: 0.9169 (m-30) cc_final: 0.8472 (t0) REVERT: F 85 ASP cc_start: 0.9241 (m-30) cc_final: 0.8977 (t70) REVERT: F 116 ASP cc_start: 0.8405 (m-30) cc_final: 0.7945 (p0) REVERT: G 7 MET cc_start: 0.8878 (ppp) cc_final: 0.8576 (ppp) REVERT: G 61 TYR cc_start: 0.8101 (m-10) cc_final: 0.7863 (m-80) REVERT: H 71 ASP cc_start: 0.9215 (t0) cc_final: 0.9014 (t0) REVERT: H 119 ARG cc_start: 0.9072 (tpm170) cc_final: 0.8765 (tpm170) REVERT: J 20 THR cc_start: 0.8385 (t) cc_final: 0.6879 (t) REVERT: J 22 ASP cc_start: 0.8815 (p0) cc_final: 0.8398 (t0) REVERT: J 46 LYS cc_start: 0.8979 (ptpp) cc_final: 0.8688 (pttt) REVERT: J 48 LEU cc_start: 0.9385 (mm) cc_final: 0.8526 (tp) REVERT: J 95 HIS cc_start: 0.5767 (t-90) cc_final: 0.5439 (t-90) REVERT: K 39 GLU cc_start: 0.9471 (mp0) cc_final: 0.9195 (mp0) REVERT: K 68 ASP cc_start: 0.8369 (t0) cc_final: 0.8033 (t0) REVERT: L 45 GLU cc_start: 0.8944 (pp20) cc_final: 0.8731 (pp20) REVERT: L 63 GLU cc_start: 0.9160 (mp0) cc_final: 0.8955 (mp0) REVERT: L 73 TYR cc_start: 0.9030 (m-80) cc_final: 0.8534 (m-80) REVERT: L 77 PHE cc_start: 0.9433 (m-10) cc_final: 0.9226 (m-80) REVERT: M 112 LEU cc_start: 0.9585 (mt) cc_final: 0.9368 (mt) REVERT: N 45 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8810 (mm-30) REVERT: N 54 ILE cc_start: 0.8648 (tt) cc_final: 0.8349 (tp) REVERT: P 101 GLU cc_start: 0.7881 (tp30) cc_final: 0.7436 (mp0) REVERT: Q 12 GLN cc_start: 0.9162 (pt0) cc_final: 0.8909 (pt0) REVERT: Q 95 PHE cc_start: 0.9195 (m-10) cc_final: 0.8767 (m-80) REVERT: R 25 LEU cc_start: 0.9557 (mm) cc_final: 0.9346 (mm) REVERT: R 33 GLU cc_start: 0.9201 (pm20) cc_final: 0.8992 (pp20) REVERT: R 45 GLU cc_start: 0.9086 (pp20) cc_final: 0.8614 (pp20) REVERT: V 52 VAL cc_start: 0.8064 (m) cc_final: 0.7788 (m) REVERT: V 104 VAL cc_start: 0.9593 (m) cc_final: 0.9389 (p) REVERT: W 14 GLU cc_start: 0.9414 (tp30) cc_final: 0.8967 (tp30) REVERT: W 44 LEU cc_start: 0.9792 (tp) cc_final: 0.9276 (pp) REVERT: X 24 ARG cc_start: 0.8986 (mpt180) cc_final: 0.8415 (mmt-90) REVERT: X 66 LYS cc_start: 0.7081 (mmpt) cc_final: 0.6742 (mmmt) outliers start: 0 outliers final: 0 residues processed: 476 average time/residue: 0.3605 time to fit residues: 258.1453 Evaluate side-chains 373 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 0.0870 chunk 210 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 204 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 160 optimal weight: 0.0070 chunk 62 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 overall best weight: 2.2182 ------------------------------------------------------------------------------- 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 ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 43 ASN Q 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.6805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18933 Z= 0.205 Angle : 0.770 16.086 25761 Z= 0.384 Chirality : 0.044 0.296 3051 Planarity : 0.005 0.050 3249 Dihedral : 4.487 21.608 2601 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.17), residues: 2322 helix: 0.87 (0.13), residues: 1440 sheet: -1.17 (0.26), residues: 300 loop : -1.05 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 90 HIS 0.002 0.001 HIS F 95 PHE 0.018 0.002 PHE K 95 TYR 0.051 0.002 TYR B 38 ARG 0.010 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 455 time to evaluate : 1.997 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: 0.9194 (t0) cc_final: 0.8980 (t0) REVERT: B 59 ARG cc_start: 0.8488 (ttt90) cc_final: 0.8202 (ttt90) REVERT: B 78 LYS cc_start: 0.8914 (pttp) cc_final: 0.8474 (pttp) REVERT: C 14 GLU cc_start: 0.9494 (tp30) cc_final: 0.9109 (tp30) REVERT: C 65 LEU cc_start: 0.9558 (pp) cc_final: 0.9145 (mt) REVERT: D 26 LEU cc_start: 0.9607 (tp) cc_final: 0.9340 (tp) REVERT: D 28 THR cc_start: 0.8853 (m) cc_final: 0.8175 (m) REVERT: D 63 GLU cc_start: 0.9541 (tp30) cc_final: 0.8785 (pm20) REVERT: D 80 THR cc_start: 0.9385 (p) cc_final: 0.9135 (p) REVERT: D 101 GLU cc_start: 0.8993 (tp30) cc_final: 0.8388 (tp30) REVERT: D 103 LEU cc_start: 0.9652 (mt) cc_final: 0.9232 (mt) REVERT: D 104 VAL cc_start: 0.9653 (m) cc_final: 0.9400 (p) REVERT: D 115 ARG cc_start: 0.9342 (tpt170) cc_final: 0.9023 (tpt90) REVERT: F 38 TYR cc_start: 0.8528 (m-80) cc_final: 0.8321 (m-80) REVERT: F 71 ASP cc_start: 0.9112 (m-30) cc_final: 0.8445 (t0) REVERT: F 116 ASP cc_start: 0.8409 (m-30) cc_final: 0.7938 (p0) REVERT: G 7 MET cc_start: 0.8870 (ppp) cc_final: 0.8542 (ppp) REVERT: G 61 TYR cc_start: 0.8197 (m-10) cc_final: 0.7876 (m-80) REVERT: H 119 ARG cc_start: 0.9104 (tpm170) cc_final: 0.8812 (tpm170) REVERT: J 20 THR cc_start: 0.8458 (t) cc_final: 0.6944 (t) REVERT: J 22 ASP cc_start: 0.8831 (p0) cc_final: 0.8388 (t0) REVERT: J 48 LEU cc_start: 0.9409 (mm) cc_final: 0.8582 (tp) REVERT: K 19 ASN cc_start: 0.8627 (m-40) cc_final: 0.8122 (m-40) REVERT: K 39 GLU cc_start: 0.9481 (mp0) cc_final: 0.9172 (mp0) REVERT: K 68 ASP cc_start: 0.8359 (t0) cc_final: 0.8016 (t0) REVERT: L 45 GLU cc_start: 0.8991 (pp20) cc_final: 0.8756 (pp20) REVERT: L 63 GLU cc_start: 0.9205 (mp0) cc_final: 0.8975 (mp0) REVERT: L 73 TYR cc_start: 0.9094 (m-80) cc_final: 0.8605 (m-80) REVERT: L 77 PHE cc_start: 0.9419 (m-10) cc_final: 0.9150 (m-80) REVERT: L 84 LEU cc_start: 0.9163 (tp) cc_final: 0.8875 (pp) REVERT: M 112 LEU cc_start: 0.9585 (mt) cc_final: 0.9352 (mt) REVERT: N 54 ILE cc_start: 0.8596 (tt) cc_final: 0.8286 (tp) REVERT: P 101 GLU cc_start: 0.7966 (tp30) cc_final: 0.7489 (mp0) REVERT: Q 95 PHE cc_start: 0.9219 (m-10) cc_final: 0.8747 (m-80) REVERT: R 25 LEU cc_start: 0.9583 (mm) cc_final: 0.9371 (mm) REVERT: R 33 GLU cc_start: 0.9287 (pm20) cc_final: 0.9068 (pp20) REVERT: R 45 GLU cc_start: 0.9106 (pp20) cc_final: 0.8631 (pp20) REVERT: R 46 LYS cc_start: 0.8833 (pttp) cc_final: 0.8628 (pttm) REVERT: R 66 LYS cc_start: 0.9503 (mmmt) cc_final: 0.9290 (mtmm) REVERT: T 26 LEU cc_start: 0.9446 (tp) cc_final: 0.9170 (tp) REVERT: T 75 LEU cc_start: 0.8753 (mp) cc_final: 0.8501 (tp) REVERT: T 78 LYS cc_start: 0.9480 (ptpp) cc_final: 0.9260 (ptpp) REVERT: T 85 ASP cc_start: 0.8546 (m-30) cc_final: 0.8329 (m-30) REVERT: U 61 TYR cc_start: 0.9308 (m-80) cc_final: 0.8669 (m-80) REVERT: V 52 VAL cc_start: 0.7907 (m) cc_final: 0.7626 (m) REVERT: V 104 VAL cc_start: 0.9585 (m) cc_final: 0.9373 (p) REVERT: W 14 GLU cc_start: 0.9418 (tp30) cc_final: 0.8977 (tp30) REVERT: W 27 TYR cc_start: 0.9378 (m-80) cc_final: 0.9099 (m-80) REVERT: W 61 TYR cc_start: 0.9080 (m-80) cc_final: 0.8754 (m-80) REVERT: X 24 ARG cc_start: 0.8913 (mpt180) cc_final: 0.8379 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.3093 time to fit residues: 212.1670 Evaluate side-chains 365 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 150 optimal weight: 8.9990 chunk 227 optimal weight: 9.9990 chunk 209 optimal weight: 7.9990 chunk 180 optimal weight: 8.9990 chunk 18 optimal weight: 0.3980 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 30.0000 chunk 143 optimal weight: 6.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- 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 ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.7014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18933 Z= 0.230 Angle : 0.777 14.971 25761 Z= 0.392 Chirality : 0.044 0.317 3051 Planarity : 0.005 0.085 3249 Dihedral : 4.578 25.148 2601 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 21.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -0.01 (0.17), residues: 2322 helix: 0.80 (0.13), residues: 1440 sheet: -1.26 (0.26), residues: 300 loop : -1.11 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 90 HIS 0.008 0.001 HIS J 95 PHE 0.018 0.002 PHE K 95 TYR 0.046 0.003 TYR B 38 ARG 0.010 0.001 ARG L 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 2.249 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: A 53 ASN cc_start: 0.9263 (t0) cc_final: 0.9045 (t0) REVERT: B 59 ARG cc_start: 0.8477 (ttt90) cc_final: 0.8217 (ttt90) REVERT: B 103 LEU cc_start: 0.9311 (tp) cc_final: 0.9083 (mt) REVERT: C 14 GLU cc_start: 0.9457 (tp30) cc_final: 0.9074 (tp30) REVERT: C 65 LEU cc_start: 0.9596 (pp) cc_final: 0.9180 (mt) REVERT: D 22 ASP cc_start: 0.8133 (t0) cc_final: 0.7857 (t0) REVERT: D 26 LEU cc_start: 0.9610 (tp) cc_final: 0.9404 (tp) REVERT: D 28 THR cc_start: 0.8929 (m) cc_final: 0.8266 (p) REVERT: D 63 GLU cc_start: 0.9598 (tp30) cc_final: 0.9260 (tp30) REVERT: D 104 VAL cc_start: 0.9644 (m) cc_final: 0.9384 (p) REVERT: F 38 TYR cc_start: 0.8502 (m-80) cc_final: 0.8265 (m-80) REVERT: F 71 ASP cc_start: 0.8985 (m-30) cc_final: 0.8365 (t0) REVERT: F 85 ASP cc_start: 0.9247 (m-30) cc_final: 0.9014 (t70) REVERT: F 116 ASP cc_start: 0.8366 (m-30) cc_final: 0.7892 (p0) REVERT: G 7 MET cc_start: 0.8880 (ppp) cc_final: 0.8617 (ppp) REVERT: G 61 TYR cc_start: 0.8299 (m-10) cc_final: 0.7915 (m-80) REVERT: H 119 ARG cc_start: 0.9132 (tpm170) cc_final: 0.8836 (tpm170) REVERT: J 20 THR cc_start: 0.8495 (t) cc_final: 0.7010 (t) REVERT: J 22 ASP cc_start: 0.8851 (p0) cc_final: 0.8370 (t0) REVERT: K 19 ASN cc_start: 0.8679 (m-40) cc_final: 0.8149 (m-40) REVERT: K 39 GLU cc_start: 0.9472 (mp0) cc_final: 0.9180 (mp0) REVERT: K 68 ASP cc_start: 0.8406 (t0) cc_final: 0.8070 (t0) REVERT: L 45 GLU cc_start: 0.9029 (pp20) cc_final: 0.8749 (pp20) REVERT: L 63 GLU cc_start: 0.9207 (mp0) cc_final: 0.9003 (mp0) REVERT: L 73 TYR cc_start: 0.9067 (m-80) cc_final: 0.8622 (m-80) REVERT: L 77 PHE cc_start: 0.9425 (m-10) cc_final: 0.9154 (m-80) REVERT: N 45 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8857 (mm-30) REVERT: N 54 ILE cc_start: 0.8565 (tt) cc_final: 0.8231 (tp) REVERT: P 101 GLU cc_start: 0.8236 (tp30) cc_final: 0.7641 (mp0) REVERT: Q 12 GLN cc_start: 0.9177 (pt0) cc_final: 0.8959 (pt0) REVERT: Q 95 PHE cc_start: 0.9262 (m-10) cc_final: 0.8904 (m-80) REVERT: R 25 LEU cc_start: 0.9551 (mm) cc_final: 0.9329 (mm) REVERT: R 33 GLU cc_start: 0.9288 (pm20) cc_final: 0.9081 (pp20) REVERT: R 45 GLU cc_start: 0.9123 (pp20) cc_final: 0.8636 (pp20) REVERT: R 66 LYS cc_start: 0.9511 (mmmt) cc_final: 0.9298 (mtmm) REVERT: T 26 LEU cc_start: 0.9455 (tp) cc_final: 0.9202 (tp) REVERT: T 78 LYS cc_start: 0.9494 (ptpp) cc_final: 0.9266 (ptpp) REVERT: T 85 ASP cc_start: 0.8679 (m-30) cc_final: 0.8455 (m-30) REVERT: U 61 TYR cc_start: 0.9328 (m-80) cc_final: 0.8732 (m-80) REVERT: V 20 THR cc_start: 0.7812 (t) cc_final: 0.7378 (t) REVERT: V 52 VAL cc_start: 0.7763 (m) cc_final: 0.6809 (m) REVERT: V 78 LYS cc_start: 0.9224 (ptpp) cc_final: 0.9020 (ptpp) REVERT: W 14 GLU cc_start: 0.9415 (tp30) cc_final: 0.9005 (tp30) REVERT: W 61 TYR cc_start: 0.9089 (m-80) cc_final: 0.8825 (m-80) REVERT: X 24 ARG cc_start: 0.8836 (mpt180) cc_final: 0.8224 (mmt-90) REVERT: X 66 LYS cc_start: 0.7072 (mmpt) cc_final: 0.6735 (mmmt) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.2978 time to fit residues: 201.3626 Evaluate side-chains 352 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 ASN Q 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.051232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.037851 restraints weight = 119287.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.039168 restraints weight = 82500.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.040105 restraints weight = 62182.118| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.7322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18933 Z= 0.279 Angle : 0.798 14.050 25761 Z= 0.410 Chirality : 0.045 0.311 3051 Planarity : 0.006 0.070 3249 Dihedral : 4.777 24.453 2601 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 25.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: -0.12 (0.16), residues: 2322 helix: 0.66 (0.13), residues: 1440 sheet: -1.04 (0.25), residues: 324 loop : -1.14 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 90 HIS 0.004 0.001 HIS X 95 PHE 0.019 0.002 PHE K 95 TYR 0.047 0.003 TYR B 38 ARG 0.010 0.001 ARG V 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4334.21 seconds wall clock time: 106 minutes 51.53 seconds (6411.53 seconds total)