Starting phenix.real_space_refine on Tue Aug 26 01:19:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zlg_11265/08_2025/6zlg_11265.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zlg_11265/08_2025/6zlg_11265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6zlg_11265/08_2025/6zlg_11265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zlg_11265/08_2025/6zlg_11265.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6zlg_11265/08_2025/6zlg_11265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zlg_11265/08_2025/6zlg_11265.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 112 5.16 5 C 20720 2.51 5 N 5968 2.21 5 O 6208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 264 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33008 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1370 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "B" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "C" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "D" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "E" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1370 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "I" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1370 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "J" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "K" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "L" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "M" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "N" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1370 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "O" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1370 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "P" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "Q" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "R" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "S" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "T" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1370 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "U" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1370 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Chain: "V" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "W" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "X" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "Y" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1378 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 1 Chain: "Z" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1370 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N ARG A 40 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG A 40 " occ=0.50 residue: pdb=" N ARG B 76 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG B 76 " occ=0.50 residue: pdb=" N ARG C 40 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG C 40 " occ=0.50 residue: pdb=" N ARG D 19 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG D 19 " occ=0.50 residue: pdb=" N ARG D 76 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG D 76 " occ=0.50 residue: pdb=" N GLU E 57 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU E 57 " occ=0.50 residue: pdb=" N ARG I 40 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG I 40 " occ=0.50 residue: pdb=" N ARG J 76 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG J 76 " occ=0.50 residue: pdb=" N ARG K 40 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG K 40 " occ=0.50 residue: pdb=" N ARG L 19 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG L 19 " occ=0.50 residue: pdb=" N ARG L 76 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG L 76 " occ=0.50 residue: pdb=" N GLU M 57 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU M 57 " occ=0.50 ... (remaining 12 not shown) Time building chain proxies: 6.68, per 1000 atoms: 0.20 Number of scatterers: 33008 At special positions: 0 Unit cell: (128.7, 128.7, 128.7, 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 112 16.00 O 6208 8.00 N 5968 7.00 C 20720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7664 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 10 through 38 Processing helix chain 'A' and resid 45 through 73 Processing helix chain 'A' and resid 92 through 121 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 134 through 156 Processing helix chain 'A' and resid 170 through 179 Processing helix chain 'B' and resid 10 through 38 Processing helix chain 'B' and resid 45 through 74 Processing helix chain 'B' and resid 92 through 121 Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'C' and resid 10 through 38 Processing helix chain 'C' and resid 45 through 73 Processing helix chain 'C' and resid 92 through 121 Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 134 through 156 Processing helix chain 'C' and resid 170 through 179 Processing helix chain 'D' and resid 10 through 38 Processing helix chain 'D' and resid 45 through 73 Processing helix chain 'D' and resid 92 through 121 Processing helix chain 'D' and resid 123 through 134 Processing helix chain 'D' and resid 134 through 156 Processing helix chain 'D' and resid 170 through 179 Processing helix chain 'E' and resid 10 through 38 Processing helix chain 'E' and resid 45 through 74 Processing helix chain 'E' and resid 92 through 121 Processing helix chain 'E' and resid 123 through 134 Processing helix chain 'E' and resid 134 through 156 Processing helix chain 'E' and resid 170 through 179 Processing helix chain 'F' and resid 10 through 38 Processing helix chain 'F' and resid 45 through 73 Processing helix chain 'F' and resid 92 through 121 Processing helix chain 'F' and resid 123 through 134 Processing helix chain 'F' and resid 134 through 156 Processing helix chain 'F' and resid 170 through 179 Processing helix chain 'I' and resid 10 through 38 Processing helix chain 'I' and resid 45 through 73 Processing helix chain 'I' and resid 92 through 121 Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 134 through 156 Processing helix chain 'I' and resid 170 through 179 Processing helix chain 'J' and resid 10 through 38 Processing helix chain 'J' and resid 45 through 74 Processing helix chain 'J' and resid 92 through 121 Processing helix chain 'J' and resid 123 through 134 Processing helix chain 'J' and resid 134 through 156 Processing helix chain 'J' and resid 170 through 179 Processing helix chain 'K' and resid 10 through 38 Processing helix chain 'K' and resid 45 through 73 removed outlier: 3.506A pdb=" N GLY K 62 " --> pdb=" O GLU K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 121 Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 134 through 156 Processing helix chain 'K' and resid 170 through 179 Processing helix chain 'L' and resid 10 through 38 Processing helix chain 'L' and resid 45 through 73 Processing helix chain 'L' and resid 92 through 121 Processing helix chain 'L' and resid 123 through 134 Processing helix chain 'L' and resid 134 through 156 Processing helix chain 'L' and resid 170 through 179 Processing helix chain 'M' and resid 10 through 38 Processing helix chain 'M' and resid 45 through 74 Processing helix chain 'M' and resid 92 through 121 Processing helix chain 'M' and resid 123 through 134 Processing helix chain 'M' and resid 134 through 156 Processing helix chain 'M' and resid 170 through 179 Processing helix chain 'N' and resid 10 through 38 Processing helix chain 'N' and resid 45 through 73 Processing helix chain 'N' and resid 92 through 121 Processing helix chain 'N' and resid 123 through 134 Processing helix chain 'N' and resid 134 through 156 Processing helix chain 'N' and resid 170 through 179 Processing helix chain 'O' and resid 10 through 38 Processing helix chain 'O' and resid 45 through 73 Processing helix chain 'O' and resid 92 through 121 Processing helix chain 'O' and resid 123 through 134 Processing helix chain 'O' and resid 134 through 156 Processing helix chain 'O' and resid 170 through 179 Processing helix chain 'P' and resid 10 through 38 Processing helix chain 'P' and resid 45 through 74 Processing helix chain 'P' and resid 92 through 121 Processing helix chain 'P' and resid 123 through 134 Processing helix chain 'P' and resid 134 through 156 Processing helix chain 'P' and resid 170 through 179 Processing helix chain 'Q' and resid 10 through 38 Processing helix chain 'Q' and resid 45 through 73 Processing helix chain 'Q' and resid 92 through 121 Processing helix chain 'Q' and resid 123 through 134 Processing helix chain 'Q' and resid 134 through 156 Processing helix chain 'Q' and resid 170 through 179 Processing helix chain 'R' and resid 10 through 38 Processing helix chain 'R' and resid 45 through 73 Processing helix chain 'R' and resid 92 through 121 Processing helix chain 'R' and resid 123 through 134 Processing helix chain 'R' and resid 134 through 156 Processing helix chain 'R' and resid 170 through 179 Processing helix chain 'S' and resid 10 through 38 Processing helix chain 'S' and resid 45 through 74 Processing helix chain 'S' and resid 92 through 121 Processing helix chain 'S' and resid 123 through 134 Processing helix chain 'S' and resid 134 through 156 Processing helix chain 'S' and resid 170 through 179 Processing helix chain 'T' and resid 10 through 38 Processing helix chain 'T' and resid 45 through 73 Processing helix chain 'T' and resid 92 through 121 Processing helix chain 'T' and resid 123 through 134 Processing helix chain 'T' and resid 134 through 156 Processing helix chain 'T' and resid 170 through 179 Processing helix chain 'U' and resid 10 through 38 Processing helix chain 'U' and resid 45 through 73 Processing helix chain 'U' and resid 92 through 121 Processing helix chain 'U' and resid 123 through 134 Processing helix chain 'U' and resid 134 through 156 Processing helix chain 'U' and resid 170 through 179 Processing helix chain 'V' and resid 10 through 38 Processing helix chain 'V' and resid 45 through 74 Processing helix chain 'V' and resid 92 through 121 Processing helix chain 'V' and resid 123 through 134 Processing helix chain 'V' and resid 134 through 156 Processing helix chain 'V' and resid 170 through 179 Processing helix chain 'W' and resid 10 through 38 Processing helix chain 'W' and resid 45 through 73 Processing helix chain 'W' and resid 92 through 121 Processing helix chain 'W' and resid 123 through 134 Processing helix chain 'W' and resid 134 through 156 Processing helix chain 'W' and resid 170 through 179 Processing helix chain 'X' and resid 10 through 38 Processing helix chain 'X' and resid 45 through 73 Processing helix chain 'X' and resid 92 through 121 Processing helix chain 'X' and resid 123 through 134 Processing helix chain 'X' and resid 134 through 156 Processing helix chain 'X' and resid 170 through 179 Processing helix chain 'Y' and resid 10 through 38 Processing helix chain 'Y' and resid 45 through 73 Processing helix chain 'Y' and resid 92 through 121 Processing helix chain 'Y' and resid 123 through 134 Processing helix chain 'Y' and resid 134 through 156 Processing helix chain 'Y' and resid 170 through 179 Processing helix chain 'Z' and resid 10 through 38 Processing helix chain 'Z' and resid 45 through 73 Processing helix chain 'Z' and resid 92 through 121 Processing helix chain 'Z' and resid 123 through 134 Processing helix chain 'Z' and resid 134 through 156 Processing helix chain 'Z' and resid 170 through 179 2622 hydrogen bonds defined for protein. 7866 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: 6.02 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11432 1.34 - 1.46: 6464 1.46 - 1.58: 15464 1.58 - 1.69: 0 1.69 - 1.81: 200 Bond restraints: 33560 Sorted by residual: bond pdb=" CB GLU F 104 " pdb=" CG GLU F 104 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.10e+00 bond pdb=" CB GLU E 104 " pdb=" CG GLU E 104 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.04e+00 bond pdb=" CB GLU N 104 " pdb=" CG GLU N 104 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.00e+00 bond pdb=" CB GLU C 104 " pdb=" CG GLU C 104 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.94e-01 bond pdb=" CB GLU I 104 " pdb=" CG GLU I 104 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.77e-01 ... (remaining 33555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.81: 42111 0.81 - 1.63: 2550 1.63 - 2.44: 292 2.44 - 3.26: 77 3.26 - 4.07: 34 Bond angle restraints: 45064 Sorted by residual: angle pdb=" N VAL E 43 " pdb=" CA VAL E 43 " pdb=" C VAL E 43 " ideal model delta sigma weight residual 111.48 107.97 3.51 9.40e-01 1.13e+00 1.39e+01 angle pdb=" N VAL C 43 " pdb=" CA VAL C 43 " pdb=" C VAL C 43 " ideal model delta sigma weight residual 111.48 108.04 3.44 9.40e-01 1.13e+00 1.34e+01 angle pdb=" N VAL M 43 " pdb=" CA VAL M 43 " pdb=" C VAL M 43 " ideal model delta sigma weight residual 111.48 108.07 3.41 9.40e-01 1.13e+00 1.32e+01 angle pdb=" N VAL F 43 " pdb=" CA VAL F 43 " pdb=" C VAL F 43 " ideal model delta sigma weight residual 111.48 108.12 3.36 9.40e-01 1.13e+00 1.28e+01 angle pdb=" N VAL J 43 " pdb=" CA VAL J 43 " pdb=" C VAL J 43 " ideal model delta sigma weight residual 111.48 108.15 3.33 9.40e-01 1.13e+00 1.25e+01 ... (remaining 45059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17708 17.93 - 35.86: 1938 35.86 - 53.79: 451 53.79 - 71.72: 107 71.72 - 89.65: 52 Dihedral angle restraints: 20256 sinusoidal: 8448 harmonic: 11808 Sorted by residual: dihedral pdb=" CB GLU S 138 " pdb=" CG GLU S 138 " pdb=" CD GLU S 138 " pdb=" OE1 GLU S 138 " ideal model delta sinusoidal sigma weight residual 0.00 89.65 -89.65 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU V 61 " pdb=" CG GLU V 61 " pdb=" CD GLU V 61 " pdb=" OE1 GLU V 61 " ideal model delta sinusoidal sigma weight residual 0.00 89.58 -89.58 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU S 61 " pdb=" CG GLU S 61 " pdb=" CD GLU S 61 " pdb=" OE1 GLU S 61 " ideal model delta sinusoidal sigma weight residual 0.00 89.55 -89.55 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 20253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 3142 0.024 - 0.049: 1157 0.049 - 0.073: 357 0.073 - 0.097: 123 0.097 - 0.122: 61 Chirality restraints: 4840 Sorted by residual: chirality pdb=" CB VAL U 21 " pdb=" CA VAL U 21 " pdb=" CG1 VAL U 21 " pdb=" CG2 VAL U 21 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CB VAL N 21 " pdb=" CA VAL N 21 " pdb=" CG1 VAL N 21 " pdb=" CG2 VAL N 21 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CB VAL Z 21 " pdb=" CA VAL Z 21 " pdb=" CG1 VAL Z 21 " pdb=" CG2 VAL Z 21 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.58e-01 ... (remaining 4837 not shown) Planarity restraints: 5944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP Q 39 " -0.005 2.00e-02 2.50e+03 1.00e-02 1.01e+00 pdb=" CG ASP Q 39 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP Q 39 " -0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP Q 39 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP Y 39 " 0.005 2.00e-02 2.50e+03 9.92e-03 9.83e-01 pdb=" CG ASP Y 39 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP Y 39 " 0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP Y 39 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP W 39 " -0.005 2.00e-02 2.50e+03 9.69e-03 9.40e-01 pdb=" CG ASP W 39 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASP W 39 " -0.006 2.00e-02 2.50e+03 pdb=" OD2 ASP W 39 " -0.006 2.00e-02 2.50e+03 ... (remaining 5941 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1388 2.72 - 3.27: 32885 3.27 - 3.81: 60566 3.81 - 4.36: 71961 4.36 - 4.90: 124485 Nonbonded interactions: 291285 Sorted by model distance: nonbonded pdb=" O GLY O 62 " pdb=" OH TYR O 134 " model vdw 2.180 3.040 nonbonded pdb=" O GLY U 62 " pdb=" OH TYR U 134 " model vdw 2.185 3.040 nonbonded pdb=" O GLY B 62 " pdb=" OH TYR B 134 " model vdw 2.186 3.040 nonbonded pdb=" O GLY J 62 " pdb=" OH TYR J 134 " model vdw 2.188 3.040 nonbonded pdb=" O GLY N 62 " pdb=" OH TYR N 134 " model vdw 2.188 3.040 ... (remaining 291280 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 'B' and resid 2 through 182) selection = (chain 'C' and resid 2 through 182) selection = (chain 'D' and resid 2 through 182) selection = (chain 'E' and resid 2 through 182) selection = chain 'F' selection = chain 'I' selection = (chain 'J' and resid 2 through 182) selection = (chain 'K' and resid 2 through 182) selection = (chain 'L' and resid 2 through 182) selection = (chain 'M' and resid 2 through 182) selection = chain 'N' selection = chain 'O' selection = (chain 'P' and resid 2 through 182) selection = (chain 'Q' and resid 2 through 182) selection = (chain 'R' and resid 2 through 182) selection = (chain 'S' and resid 2 through 182) selection = chain 'T' selection = chain 'U' selection = (chain 'V' and resid 2 through 182) selection = (chain 'W' and resid 2 through 182) selection = (chain 'X' and resid 2 through 182) selection = (chain 'Y' and resid 2 through 182) selection = chain 'Z' } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 27.240 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 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 : 0.003 0.031 33560 Z= 0.145 Angle : 0.437 4.072 45064 Z= 0.292 Chirality : 0.031 0.122 4840 Planarity : 0.002 0.024 5944 Dihedral : 16.497 89.647 12592 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 4.15 % Allowed : 18.91 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.12), residues: 3976 helix: 1.53 (0.08), residues: 3144 sheet: None (None), residues: 0 loop : -1.83 (0.17), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 26 TYR 0.009 0.001 TYR T 9 PHE 0.013 0.001 PHE L 129 TRP 0.003 0.000 TRP M 90 HIS 0.008 0.001 HIS V 182 Details of bonding type rmsd covalent geometry : bond 0.00320 (33560) covalent geometry : angle 0.43655 (45064) hydrogen bonds : bond 0.09149 ( 2622) hydrogen bonds : angle 4.05557 ( 7866) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 781 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7350 (mt-10) REVERT: A 72 ASP cc_start: 0.8436 (m-30) cc_final: 0.8077 (m-30) REVERT: A 87 GLN cc_start: 0.9039 (mt0) cc_final: 0.8833 (mt0) REVERT: A 123 ASP cc_start: 0.8887 (t0) cc_final: 0.8610 (t0) REVERT: B 68 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7351 (mt-10) REVERT: B 72 ASP cc_start: 0.8219 (m-30) cc_final: 0.7984 (m-30) REVERT: B 97 MET cc_start: 0.7480 (tpp) cc_final: 0.7134 (tpp) REVERT: C 68 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7330 (mt-10) REVERT: C 72 ASP cc_start: 0.8396 (m-30) cc_final: 0.8019 (m-30) REVERT: C 123 ASP cc_start: 0.8897 (t0) cc_final: 0.8608 (t0) REVERT: C 138 GLU cc_start: 0.8368 (tp30) cc_final: 0.8140 (tp30) REVERT: D 68 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7353 (mt-10) REVERT: D 72 ASP cc_start: 0.8400 (m-30) cc_final: 0.8014 (m-30) REVERT: D 87 GLN cc_start: 0.9071 (mt0) cc_final: 0.8807 (mt0) REVERT: D 97 MET cc_start: 0.7555 (tpp) cc_final: 0.7281 (tpp) REVERT: E 68 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7398 (mt-10) REVERT: E 72 ASP cc_start: 0.8375 (m-30) cc_final: 0.8043 (m-30) REVERT: E 87 GLN cc_start: 0.9057 (mt0) cc_final: 0.8821 (mt0) REVERT: E 123 ASP cc_start: 0.8975 (t0) cc_final: 0.8704 (t0) REVERT: F 68 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7402 (mt-10) REVERT: F 72 ASP cc_start: 0.8401 (m-30) cc_final: 0.8090 (m-30) REVERT: F 97 MET cc_start: 0.7520 (tpp) cc_final: 0.7317 (tpp) REVERT: F 123 ASP cc_start: 0.8890 (t0) cc_final: 0.8654 (t0) REVERT: I 68 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7214 (mt-10) REVERT: I 72 ASP cc_start: 0.8436 (m-30) cc_final: 0.8074 (m-30) REVERT: I 87 GLN cc_start: 0.9070 (mt0) cc_final: 0.8814 (mt0) REVERT: I 123 ASP cc_start: 0.8837 (t0) cc_final: 0.8618 (t0) REVERT: J 68 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7304 (mt-10) REVERT: J 72 ASP cc_start: 0.8396 (m-30) cc_final: 0.8065 (m-30) REVERT: J 87 GLN cc_start: 0.9150 (mt0) cc_final: 0.8918 (mt0) REVERT: J 97 MET cc_start: 0.7528 (tpp) cc_final: 0.7232 (tpp) REVERT: K 68 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7382 (mt-10) REVERT: K 72 ASP cc_start: 0.8417 (m-30) cc_final: 0.8046 (m-30) REVERT: K 97 MET cc_start: 0.8760 (tpp) cc_final: 0.8024 (tpp) REVERT: K 123 ASP cc_start: 0.8893 (t0) cc_final: 0.8614 (t0) REVERT: L 68 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7195 (mt-10) REVERT: L 72 ASP cc_start: 0.8388 (m-30) cc_final: 0.7963 (m-30) REVERT: L 97 MET cc_start: 0.7488 (tpp) cc_final: 0.7260 (tpp) REVERT: M 68 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7334 (mt-10) REVERT: M 72 ASP cc_start: 0.8366 (m-30) cc_final: 0.8037 (m-30) REVERT: M 87 GLN cc_start: 0.9070 (mt0) cc_final: 0.8863 (mt0) REVERT: M 123 ASP cc_start: 0.8964 (t0) cc_final: 0.8742 (t0) REVERT: N 68 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7353 (mt-10) REVERT: N 72 ASP cc_start: 0.8398 (m-30) cc_final: 0.8038 (m-30) REVERT: N 87 GLN cc_start: 0.9138 (mt0) cc_final: 0.8925 (mt0) REVERT: N 97 MET cc_start: 0.7456 (tpp) cc_final: 0.7159 (tpp) REVERT: N 123 ASP cc_start: 0.8889 (t0) cc_final: 0.8651 (t0) REVERT: O 61 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7539 (mm-30) REVERT: O 72 ASP cc_start: 0.8430 (m-30) cc_final: 0.8106 (m-30) REVERT: O 97 MET cc_start: 0.7585 (tpp) cc_final: 0.7233 (tpp) REVERT: O 169 SER cc_start: 0.8584 (p) cc_final: 0.8023 (p) REVERT: P 72 ASP cc_start: 0.8390 (m-30) cc_final: 0.8027 (m-30) REVERT: P 97 MET cc_start: 0.7501 (tpp) cc_final: 0.7163 (tpp) REVERT: Q 68 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7343 (mt-10) REVERT: Q 72 ASP cc_start: 0.8392 (m-30) cc_final: 0.7998 (m-30) REVERT: Q 97 MET cc_start: 0.8678 (tpp) cc_final: 0.8070 (tpp) REVERT: Q 123 ASP cc_start: 0.8879 (t0) cc_final: 0.8593 (t0) REVERT: R 72 ASP cc_start: 0.8394 (m-30) cc_final: 0.7996 (m-30) REVERT: R 87 GLN cc_start: 0.9128 (mt0) cc_final: 0.8878 (mt0) REVERT: R 97 MET cc_start: 0.7496 (tpp) cc_final: 0.7175 (tpp) REVERT: S 31 TYR cc_start: 0.9095 (m-80) cc_final: 0.8822 (m-10) REVERT: S 72 ASP cc_start: 0.8389 (m-30) cc_final: 0.8060 (m-30) REVERT: T 68 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7349 (mt-10) REVERT: T 72 ASP cc_start: 0.8362 (m-30) cc_final: 0.8100 (m-30) REVERT: T 97 MET cc_start: 0.7509 (tpp) cc_final: 0.7186 (tpp) REVERT: T 123 ASP cc_start: 0.8966 (t0) cc_final: 0.8691 (t0) REVERT: T 181 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7155 (mmmt) REVERT: U 72 ASP cc_start: 0.8417 (m-30) cc_final: 0.8087 (m-30) REVERT: U 87 GLN cc_start: 0.9153 (mt0) cc_final: 0.8899 (mt0) REVERT: U 123 ASP cc_start: 0.8929 (t0) cc_final: 0.8690 (t0) REVERT: V 68 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7254 (mt-10) REVERT: V 72 ASP cc_start: 0.8412 (m-30) cc_final: 0.8065 (m-30) REVERT: V 123 ASP cc_start: 0.8967 (t0) cc_final: 0.8716 (t0) REVERT: W 72 ASP cc_start: 0.8378 (m-30) cc_final: 0.7997 (m-30) REVERT: W 87 GLN cc_start: 0.9119 (mt0) cc_final: 0.8901 (mt0) REVERT: W 97 MET cc_start: 0.8748 (tpp) cc_final: 0.8016 (tpp) REVERT: W 123 ASP cc_start: 0.8938 (t0) cc_final: 0.8691 (t0) REVERT: X 68 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7170 (mt-10) REVERT: X 72 ASP cc_start: 0.8403 (m-30) cc_final: 0.8000 (m-30) REVERT: X 123 ASP cc_start: 0.8934 (t0) cc_final: 0.8676 (t0) REVERT: X 181 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.7109 (mmmt) REVERT: Y 72 ASP cc_start: 0.8365 (m-30) cc_final: 0.8038 (m-30) REVERT: Y 123 ASP cc_start: 0.8920 (t0) cc_final: 0.8654 (t0) REVERT: Y 138 GLU cc_start: 0.8117 (tp30) cc_final: 0.7677 (tp30) REVERT: Y 140 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8267 (mmtp) REVERT: Z 72 ASP cc_start: 0.8383 (m-30) cc_final: 0.7966 (m-30) REVERT: Z 87 GLN cc_start: 0.9159 (mt0) cc_final: 0.8938 (mt0) REVERT: Z 97 MET cc_start: 0.7523 (tpp) cc_final: 0.7174 (tpp) REVERT: Z 123 ASP cc_start: 0.8910 (t0) cc_final: 0.8630 (t0) outliers start: 143 outliers final: 51 residues processed: 893 average time/residue: 0.6834 time to fit residues: 724.9490 Evaluate side-chains 742 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 689 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 33 SER Chi-restraints excluded: chain J residue 42 ASP Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 181 LYS Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 42 ASP Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain O residue 42 ASP Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain P residue 42 ASP Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 181 LYS Chi-restraints excluded: chain T residue 33 SER Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 126 LEU Chi-restraints excluded: chain T residue 181 LYS Chi-restraints excluded: chain U residue 42 ASP Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain U residue 182 HIS Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain W residue 10 SER Chi-restraints excluded: chain W residue 33 SER Chi-restraints excluded: chain W residue 42 ASP Chi-restraints excluded: chain X residue 10 SER Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 78 LEU Chi-restraints excluded: chain X residue 181 LYS Chi-restraints excluded: chain Y residue 33 SER Chi-restraints excluded: chain Y residue 46 GLU Chi-restraints excluded: chain Y residue 181 LYS Chi-restraints excluded: chain Z residue 10 SER Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 86 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 197 optimal weight: 0.0970 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.0980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 83 GLN A 87 GLN A 133 HIS A 147 ASN B 7 GLN B 133 HIS C 22 ASN C 83 GLN C 133 HIS D 87 GLN D 133 HIS D 147 ASN E 83 GLN E 87 GLN E 133 HIS F 133 HIS I 87 GLN I 133 HIS J 87 GLN J 133 HIS K 22 ASN K 83 GLN K 133 HIS L 133 HIS M 83 GLN M 87 GLN M 133 HIS N 87 GLN N 133 HIS N 182 HIS O 133 HIS P 133 HIS Q 133 HIS R 83 GLN R 87 GLN R 133 HIS S 22 ASN S 83 GLN S 133 HIS T 133 HIS U 22 ASN U 87 GLN U 133 HIS V 133 HIS W 87 GLN W 133 HIS W 182 HIS X 108 ASN X 133 HIS Y 22 ASN Y 83 GLN Y 133 HIS Z 87 GLN Z 133 HIS Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.103830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.092994 restraints weight = 40897.882| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.85 r_work: 0.2879 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 33560 Z= 0.105 Angle : 0.382 4.835 45064 Z= 0.206 Chirality : 0.031 0.115 4840 Planarity : 0.003 0.029 5944 Dihedral : 5.390 55.995 4558 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.89 % Allowed : 20.56 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.80 (0.13), residues: 3976 helix: 3.27 (0.09), residues: 3208 sheet: None (None), residues: 0 loop : -1.07 (0.19), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 76 TYR 0.006 0.001 TYR A 31 PHE 0.014 0.001 PHE L 129 TRP 0.004 0.001 TRP P 90 HIS 0.007 0.000 HIS V 182 Details of bonding type rmsd covalent geometry : bond 0.00243 (33560) covalent geometry : angle 0.38222 (45064) hydrogen bonds : bond 0.03161 ( 2622) hydrogen bonds : angle 3.02843 ( 7866) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 659 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8618 (m-30) cc_final: 0.8346 (m-30) REVERT: A 140 LYS cc_start: 0.8902 (mmtt) cc_final: 0.8564 (mmtp) REVERT: B 72 ASP cc_start: 0.8636 (m-30) cc_final: 0.8379 (m-30) REVERT: B 104 GLU cc_start: 0.8571 (mm-30) cc_final: 0.7974 (mm-30) REVERT: C 72 ASP cc_start: 0.8718 (m-30) cc_final: 0.8411 (m-30) REVERT: C 121 ARG cc_start: 0.8548 (mmm160) cc_final: 0.8254 (mmp80) REVERT: C 128 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7826 (t70) REVERT: D 72 ASP cc_start: 0.8673 (m-30) cc_final: 0.8367 (m-30) REVERT: D 87 GLN cc_start: 0.9056 (mt0) cc_final: 0.8810 (mt0) REVERT: E 68 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7989 (mt-10) REVERT: E 72 ASP cc_start: 0.8734 (m-30) cc_final: 0.8436 (m-30) REVERT: E 128 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7900 (t70) REVERT: E 140 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8487 (mmtp) REVERT: F 72 ASP cc_start: 0.8708 (m-30) cc_final: 0.8324 (m-30) REVERT: F 128 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7895 (t70) REVERT: F 140 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8558 (mmtp) REVERT: I 72 ASP cc_start: 0.8605 (m-30) cc_final: 0.8337 (m-30) REVERT: I 87 GLN cc_start: 0.9085 (mt0) cc_final: 0.8868 (mt0) REVERT: I 140 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8533 (mmtp) REVERT: I 181 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7328 (tptp) REVERT: J 72 ASP cc_start: 0.8691 (m-30) cc_final: 0.8450 (m-30) REVERT: J 128 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7886 (t70) REVERT: K 72 ASP cc_start: 0.8695 (m-30) cc_final: 0.8386 (m-30) REVERT: K 138 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8443 (mm-30) REVERT: L 72 ASP cc_start: 0.8638 (m-30) cc_final: 0.8340 (m-30) REVERT: M 72 ASP cc_start: 0.8740 (m-30) cc_final: 0.8462 (m-30) REVERT: M 138 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8381 (mm-30) REVERT: N 72 ASP cc_start: 0.8648 (m-30) cc_final: 0.8348 (m-30) REVERT: N 87 GLN cc_start: 0.9086 (mt0) cc_final: 0.8886 (mt0) REVERT: N 140 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8487 (mmtp) REVERT: O 61 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8431 (mt-10) REVERT: O 68 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7979 (mt-10) REVERT: O 72 ASP cc_start: 0.8635 (m-30) cc_final: 0.8378 (m-30) REVERT: O 140 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8507 (mmtp) REVERT: O 169 SER cc_start: 0.8675 (p) cc_final: 0.8127 (p) REVERT: P 9 TYR cc_start: 0.9223 (OUTLIER) cc_final: 0.8462 (t80) REVERT: P 40 ARG cc_start: 0.7928 (mtp85) cc_final: 0.7478 (mtp85) REVERT: P 42 ASP cc_start: 0.8767 (p0) cc_final: 0.7919 (p0) REVERT: P 72 ASP cc_start: 0.8706 (m-30) cc_final: 0.8486 (m-30) REVERT: Q 61 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8339 (mt-10) REVERT: Q 72 ASP cc_start: 0.8703 (m-30) cc_final: 0.8389 (m-30) REVERT: Q 97 MET cc_start: 0.9027 (tpp) cc_final: 0.8730 (tpp) REVERT: Q 181 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7625 (tptp) REVERT: R 68 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7972 (mt-10) REVERT: R 72 ASP cc_start: 0.8717 (m-30) cc_final: 0.8413 (m-30) REVERT: R 87 GLN cc_start: 0.9096 (mt0) cc_final: 0.8865 (mt0) REVERT: S 72 ASP cc_start: 0.8687 (m-30) cc_final: 0.8454 (m-30) REVERT: T 72 ASP cc_start: 0.8668 (m-30) cc_final: 0.8336 (m-30) REVERT: T 140 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8498 (mmtp) REVERT: T 181 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7331 (mmmt) REVERT: U 72 ASP cc_start: 0.8610 (m-30) cc_final: 0.8351 (m-30) REVERT: U 87 GLN cc_start: 0.9056 (mt0) cc_final: 0.8781 (mt0) REVERT: U 181 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7431 (tptp) REVERT: V 9 TYR cc_start: 0.9223 (OUTLIER) cc_final: 0.8413 (t80) REVERT: V 72 ASP cc_start: 0.8725 (m-30) cc_final: 0.8491 (m-30) REVERT: V 181 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7607 (tptp) REVERT: W 72 ASP cc_start: 0.8695 (m-30) cc_final: 0.8383 (m-30) REVERT: W 128 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7845 (t70) REVERT: X 68 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8024 (mt-10) REVERT: X 72 ASP cc_start: 0.8690 (m-30) cc_final: 0.8361 (m-30) REVERT: X 104 GLU cc_start: 0.8492 (mm-30) cc_final: 0.7967 (mm-30) REVERT: X 181 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7325 (mmmt) REVERT: Y 9 TYR cc_start: 0.9208 (OUTLIER) cc_final: 0.8472 (t80) REVERT: Y 72 ASP cc_start: 0.8634 (m-30) cc_final: 0.8404 (m-30) REVERT: Z 9 TYR cc_start: 0.9225 (OUTLIER) cc_final: 0.8306 (t80) REVERT: Z 72 ASP cc_start: 0.8672 (m-30) cc_final: 0.8334 (m-30) REVERT: Z 140 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8530 (mmtp) outliers start: 134 outliers final: 37 residues processed: 768 average time/residue: 0.7391 time to fit residues: 667.8625 Evaluate side-chains 665 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 611 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain J residue 128 ASP Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain M residue 138 GLU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 181 LYS Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 182 HIS Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 181 LYS Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 181 LYS Chi-restraints excluded: chain T residue 181 LYS Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain V residue 9 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 126 LEU Chi-restraints excluded: chain V residue 181 LYS Chi-restraints excluded: chain W residue 3 SER Chi-restraints excluded: chain W residue 128 ASP Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 181 LYS Chi-restraints excluded: chain Y residue 9 TYR Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 46 GLU Chi-restraints excluded: chain Y residue 181 LYS Chi-restraints excluded: chain Z residue 9 TYR Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 126 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 44 optimal weight: 5.9990 chunk 321 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.096973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.086510 restraints weight = 41447.363| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.79 r_work: 0.2768 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2522 r_free = 0.2522 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 33560 Z= 0.172 Angle : 0.409 4.538 45064 Z= 0.217 Chirality : 0.033 0.129 4840 Planarity : 0.003 0.027 5944 Dihedral : 4.677 55.436 4488 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 4.81 % Allowed : 18.42 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.39 (0.13), residues: 3976 helix: 3.63 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.69 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 40 TYR 0.010 0.001 TYR V 31 PHE 0.013 0.002 PHE P 38 TRP 0.004 0.001 TRP V 90 HIS 0.006 0.001 HIS V 182 Details of bonding type rmsd covalent geometry : bond 0.00420 (33560) covalent geometry : angle 0.40850 (45064) hydrogen bonds : bond 0.03488 ( 2622) hydrogen bonds : angle 3.01805 ( 7866) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 660 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8620 (m-30) cc_final: 0.8371 (m-30) REVERT: B 72 ASP cc_start: 0.8683 (m-30) cc_final: 0.8465 (m-30) REVERT: C 72 ASP cc_start: 0.8662 (m-30) cc_final: 0.8322 (m-30) REVERT: C 138 GLU cc_start: 0.8882 (tp30) cc_final: 0.8578 (tp30) REVERT: D 61 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8503 (mm-30) REVERT: D 72 ASP cc_start: 0.8688 (m-30) cc_final: 0.8360 (m-30) REVERT: D 123 ASP cc_start: 0.8958 (t0) cc_final: 0.8723 (t70) REVERT: D 182 HIS cc_start: 0.6840 (OUTLIER) cc_final: 0.6257 (m90) REVERT: E 72 ASP cc_start: 0.8724 (m-30) cc_final: 0.8441 (m-30) REVERT: E 169 SER cc_start: 0.8671 (p) cc_final: 0.8166 (p) REVERT: F 72 ASP cc_start: 0.8681 (m-30) cc_final: 0.8339 (m-30) REVERT: I 68 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7974 (mt-10) REVERT: I 72 ASP cc_start: 0.8617 (m-30) cc_final: 0.8330 (m-30) REVERT: I 181 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7398 (tptp) REVERT: J 9 TYR cc_start: 0.9237 (OUTLIER) cc_final: 0.8386 (t80) REVERT: J 61 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8506 (mm-30) REVERT: J 72 ASP cc_start: 0.8733 (m-30) cc_final: 0.8434 (m-30) REVERT: J 109 GLN cc_start: 0.9076 (tp40) cc_final: 0.8707 (mm-40) REVERT: J 138 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8210 (tp30) REVERT: J 169 SER cc_start: 0.8806 (p) cc_final: 0.8299 (p) REVERT: K 68 GLU cc_start: 0.8235 (mt-10) cc_final: 0.8021 (mt-10) REVERT: K 72 ASP cc_start: 0.8672 (m-30) cc_final: 0.8365 (m-30) REVERT: K 138 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8540 (mm-30) REVERT: L 68 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8012 (mt-10) REVERT: L 72 ASP cc_start: 0.8646 (m-30) cc_final: 0.8326 (m-30) REVERT: L 109 GLN cc_start: 0.9066 (tp40) cc_final: 0.8675 (mm-40) REVERT: L 123 ASP cc_start: 0.8904 (t0) cc_final: 0.8687 (t70) REVERT: M 9 TYR cc_start: 0.9224 (OUTLIER) cc_final: 0.8479 (t80) REVERT: M 72 ASP cc_start: 0.8722 (m-30) cc_final: 0.8427 (m-30) REVERT: M 123 ASP cc_start: 0.9017 (t0) cc_final: 0.8774 (t70) REVERT: N 72 ASP cc_start: 0.8684 (m-30) cc_final: 0.8349 (m-30) REVERT: N 87 GLN cc_start: 0.9122 (mt0) cc_final: 0.8903 (mt0) REVERT: O 72 ASP cc_start: 0.8628 (m-30) cc_final: 0.8331 (m-30) REVERT: O 169 SER cc_start: 0.8702 (p) cc_final: 0.8146 (p) REVERT: P 9 TYR cc_start: 0.9249 (OUTLIER) cc_final: 0.8398 (t80) REVERT: P 72 ASP cc_start: 0.8735 (m-30) cc_final: 0.8468 (m-30) REVERT: P 109 GLN cc_start: 0.9044 (tp40) cc_final: 0.8674 (mm-40) REVERT: Q 61 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8405 (mt-10) REVERT: Q 72 ASP cc_start: 0.8679 (m-30) cc_final: 0.8337 (m-30) REVERT: R 72 ASP cc_start: 0.8697 (m-30) cc_final: 0.8349 (m-30) REVERT: S 72 ASP cc_start: 0.8693 (m-30) cc_final: 0.8414 (m-30) REVERT: T 72 ASP cc_start: 0.8683 (m-30) cc_final: 0.8374 (m-30) REVERT: T 140 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8637 (mmtp) REVERT: T 169 SER cc_start: 0.8734 (p) cc_final: 0.8247 (p) REVERT: U 61 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8551 (mm-30) REVERT: U 72 ASP cc_start: 0.8628 (m-30) cc_final: 0.8342 (m-30) REVERT: U 109 GLN cc_start: 0.9083 (tp40) cc_final: 0.8732 (mm-40) REVERT: U 181 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7512 (tptp) REVERT: V 9 TYR cc_start: 0.9214 (OUTLIER) cc_final: 0.8301 (t80) REVERT: V 72 ASP cc_start: 0.8736 (m-30) cc_final: 0.8456 (m-30) REVERT: V 103 MET cc_start: 0.9128 (ttm) cc_final: 0.8914 (ttm) REVERT: V 169 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8268 (p) REVERT: V 181 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7570 (tptp) REVERT: W 68 GLU cc_start: 0.8228 (mt-10) cc_final: 0.8001 (mt-10) REVERT: W 72 ASP cc_start: 0.8665 (m-30) cc_final: 0.8322 (m-30) REVERT: X 68 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8042 (mt-10) REVERT: X 72 ASP cc_start: 0.8662 (m-30) cc_final: 0.8328 (m-30) REVERT: Y 9 TYR cc_start: 0.9216 (OUTLIER) cc_final: 0.8369 (t80) REVERT: Y 72 ASP cc_start: 0.8663 (m-30) cc_final: 0.8371 (m-30) REVERT: Y 169 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8249 (p) REVERT: Z 9 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.8310 (t80) REVERT: Z 72 ASP cc_start: 0.8672 (m-30) cc_final: 0.8339 (m-30) outliers start: 166 outliers final: 71 residues processed: 780 average time/residue: 0.7627 time to fit residues: 697.8127 Evaluate side-chains 702 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 617 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain J residue 9 TYR Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 182 HIS Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 138 GLU Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain M residue 9 TYR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 138 GLU Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 181 LYS Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 181 LYS Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 119 SER Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 138 GLU Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain V residue 9 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 126 LEU Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain V residue 181 LYS Chi-restraints excluded: chain W residue 3 SER Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 138 GLU Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 78 LEU Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain Y residue 9 TYR Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 46 GLU Chi-restraints excluded: chain Y residue 169 SER Chi-restraints excluded: chain Y residue 181 LYS Chi-restraints excluded: chain Z residue 9 TYR Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 126 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 274 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 277 optimal weight: 0.6980 chunk 218 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 311 optimal weight: 0.8980 chunk 376 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 251 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 87 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.098310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.087854 restraints weight = 41096.278| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.79 r_work: 0.2808 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33560 Z= 0.115 Angle : 0.370 4.709 45064 Z= 0.199 Chirality : 0.031 0.117 4840 Planarity : 0.003 0.033 5944 Dihedral : 4.130 58.993 4474 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.71 % Allowed : 19.61 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.85 (0.13), residues: 3976 helix: 3.98 (0.09), residues: 3208 sheet: None (None), residues: 0 loop : -0.64 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 121 TYR 0.008 0.001 TYR T 173 PHE 0.011 0.001 PHE L 129 TRP 0.005 0.001 TRP V 90 HIS 0.005 0.000 HIS V 182 Details of bonding type rmsd covalent geometry : bond 0.00275 (33560) covalent geometry : angle 0.36988 (45064) hydrogen bonds : bond 0.03053 ( 2622) hydrogen bonds : angle 2.85736 ( 7866) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 638 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8589 (m-30) cc_final: 0.8387 (m-30) REVERT: A 83 GLN cc_start: 0.8794 (mt0) cc_final: 0.8556 (mm-40) REVERT: A 140 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8599 (mmtp) REVERT: B 72 ASP cc_start: 0.8653 (m-30) cc_final: 0.8357 (m-30) REVERT: C 72 ASP cc_start: 0.8628 (m-30) cc_final: 0.8325 (m-30) REVERT: C 138 GLU cc_start: 0.8875 (tp30) cc_final: 0.8612 (tp30) REVERT: D 68 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7976 (mt-10) REVERT: D 72 ASP cc_start: 0.8620 (m-30) cc_final: 0.8309 (m-30) REVERT: E 9 TYR cc_start: 0.9213 (OUTLIER) cc_final: 0.8489 (t80) REVERT: E 68 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7985 (mt-10) REVERT: E 72 ASP cc_start: 0.8687 (m-30) cc_final: 0.8399 (m-30) REVERT: E 169 SER cc_start: 0.8587 (p) cc_final: 0.8106 (p) REVERT: F 72 ASP cc_start: 0.8645 (m-30) cc_final: 0.8305 (m-30) REVERT: I 9 TYR cc_start: 0.9230 (OUTLIER) cc_final: 0.8372 (t80) REVERT: I 72 ASP cc_start: 0.8546 (m-30) cc_final: 0.8335 (m-30) REVERT: I 138 GLU cc_start: 0.8862 (tp30) cc_final: 0.8645 (tp30) REVERT: I 140 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8547 (mmtp) REVERT: I 181 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7416 (tptp) REVERT: J 9 TYR cc_start: 0.9220 (OUTLIER) cc_final: 0.8484 (t80) REVERT: J 40 ARG cc_start: 0.7867 (mtp85) cc_final: 0.7487 (mtp85) REVERT: J 42 ASP cc_start: 0.8796 (p0) cc_final: 0.7859 (p0) REVERT: J 61 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8568 (mm-30) REVERT: J 72 ASP cc_start: 0.8697 (m-30) cc_final: 0.8427 (m-30) REVERT: J 169 SER cc_start: 0.8719 (p) cc_final: 0.8223 (p) REVERT: K 68 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7959 (mt-10) REVERT: K 72 ASP cc_start: 0.8616 (m-30) cc_final: 0.8318 (m-30) REVERT: L 9 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.8418 (t80) REVERT: L 68 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8007 (mt-10) REVERT: L 72 ASP cc_start: 0.8600 (m-30) cc_final: 0.8284 (m-30) REVERT: M 9 TYR cc_start: 0.9207 (OUTLIER) cc_final: 0.8370 (t80) REVERT: M 72 ASP cc_start: 0.8683 (m-30) cc_final: 0.8399 (m-30) REVERT: M 138 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8209 (tp30) REVERT: M 169 SER cc_start: 0.8712 (p) cc_final: 0.8225 (p) REVERT: N 72 ASP cc_start: 0.8643 (m-30) cc_final: 0.8357 (m-30) REVERT: N 87 GLN cc_start: 0.9102 (mt0) cc_final: 0.8901 (mt0) REVERT: N 140 LYS cc_start: 0.8876 (mmtt) cc_final: 0.8565 (mmtp) REVERT: N 181 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7245 (mmmt) REVERT: O 9 TYR cc_start: 0.9198 (OUTLIER) cc_final: 0.8272 (t80) REVERT: O 61 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8486 (mt-10) REVERT: O 72 ASP cc_start: 0.8568 (m-30) cc_final: 0.8322 (m-30) REVERT: O 169 SER cc_start: 0.8673 (OUTLIER) cc_final: 0.8137 (p) REVERT: P 9 TYR cc_start: 0.9228 (OUTLIER) cc_final: 0.8367 (t80) REVERT: P 72 ASP cc_start: 0.8712 (m-30) cc_final: 0.8456 (m-30) REVERT: Q 61 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8375 (mt-10) REVERT: Q 72 ASP cc_start: 0.8622 (m-30) cc_final: 0.8336 (m-30) REVERT: R 72 ASP cc_start: 0.8672 (m-30) cc_final: 0.8358 (m-30) REVERT: S 72 ASP cc_start: 0.8676 (m-30) cc_final: 0.8394 (m-30) REVERT: T 72 ASP cc_start: 0.8641 (m-30) cc_final: 0.8318 (m-30) REVERT: T 140 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8646 (mmtp) REVERT: T 169 SER cc_start: 0.8668 (p) cc_final: 0.8213 (p) REVERT: U 9 TYR cc_start: 0.9197 (OUTLIER) cc_final: 0.8435 (t80) REVERT: U 72 ASP cc_start: 0.8588 (m-30) cc_final: 0.8359 (m-30) REVERT: U 109 GLN cc_start: 0.9081 (tp40) cc_final: 0.8708 (mm-40) REVERT: V 9 TYR cc_start: 0.9220 (OUTLIER) cc_final: 0.8417 (t80) REVERT: V 72 ASP cc_start: 0.8691 (m-30) cc_final: 0.8418 (m-30) REVERT: V 169 SER cc_start: 0.8729 (p) cc_final: 0.8182 (p) REVERT: W 68 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7864 (mt-10) REVERT: W 72 ASP cc_start: 0.8643 (m-30) cc_final: 0.8352 (m-30) REVERT: X 72 ASP cc_start: 0.8609 (m-30) cc_final: 0.8267 (m-30) REVERT: Y 9 TYR cc_start: 0.9212 (OUTLIER) cc_final: 0.8384 (t80) REVERT: Y 72 ASP cc_start: 0.8610 (m-30) cc_final: 0.8339 (m-30) REVERT: Y 169 SER cc_start: 0.8693 (p) cc_final: 0.8155 (p) REVERT: Y 181 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7204 (mmmt) REVERT: Z 9 TYR cc_start: 0.9210 (OUTLIER) cc_final: 0.8424 (t80) REVERT: Z 72 ASP cc_start: 0.8683 (m-30) cc_final: 0.8355 (m-30) REVERT: Z 140 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8506 (mmtp) outliers start: 128 outliers final: 64 residues processed: 735 average time/residue: 0.7201 time to fit residues: 620.9952 Evaluate side-chains 680 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 600 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain E residue 3 SER Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain I residue 9 TYR Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain J residue 9 TYR Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 182 HIS Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain L residue 9 TYR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain M residue 9 TYR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 138 GLU Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 181 LYS Chi-restraints excluded: chain O residue 9 TYR Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 78 LEU Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 119 SER Chi-restraints excluded: chain T residue 181 LYS Chi-restraints excluded: chain U residue 9 TYR Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain V residue 9 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 126 LEU Chi-restraints excluded: chain W residue 3 SER Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 138 GLU Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 126 LEU Chi-restraints excluded: chain Y residue 9 TYR Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 181 LYS Chi-restraints excluded: chain Z residue 9 TYR Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 126 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 203 optimal weight: 4.9990 chunk 384 optimal weight: 5.9990 chunk 268 optimal weight: 6.9990 chunk 319 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 397 optimal weight: 6.9990 chunk 320 optimal weight: 0.9980 chunk 352 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 309 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.084098 restraints weight = 41659.597| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.87 r_work: 0.2686 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2477 r_free = 0.2477 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 33560 Z= 0.186 Angle : 0.410 4.813 45064 Z= 0.219 Chirality : 0.033 0.134 4840 Planarity : 0.003 0.031 5944 Dihedral : 3.711 52.329 4460 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 4.38 % Allowed : 20.01 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.82 (0.13), residues: 3976 helix: 3.93 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : -0.53 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 40 TYR 0.010 0.001 TYR K 31 PHE 0.013 0.002 PHE Y 38 TRP 0.005 0.001 TRP P 90 HIS 0.005 0.001 HIS V 182 Details of bonding type rmsd covalent geometry : bond 0.00453 (33560) covalent geometry : angle 0.41037 (45064) hydrogen bonds : bond 0.03482 ( 2622) hydrogen bonds : angle 2.98002 ( 7866) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 643 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8631 (m-30) cc_final: 0.8365 (m-30) REVERT: B 109 GLN cc_start: 0.9021 (tp40) cc_final: 0.8674 (mm-40) REVERT: C 72 ASP cc_start: 0.8667 (m-30) cc_final: 0.8384 (m-30) REVERT: C 138 GLU cc_start: 0.8915 (tp30) cc_final: 0.8618 (tp30) REVERT: D 72 ASP cc_start: 0.8654 (m-30) cc_final: 0.8327 (m-30) REVERT: D 109 GLN cc_start: 0.9016 (tp40) cc_final: 0.8644 (mm-40) REVERT: D 182 HIS cc_start: 0.6690 (OUTLIER) cc_final: 0.6002 (m90) REVERT: E 9 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.8389 (t80) REVERT: E 72 ASP cc_start: 0.8732 (m-30) cc_final: 0.8454 (m-30) REVERT: E 109 GLN cc_start: 0.9017 (tp40) cc_final: 0.8642 (mm-40) REVERT: E 140 LYS cc_start: 0.8974 (mmtp) cc_final: 0.8717 (mmtt) REVERT: E 169 SER cc_start: 0.8636 (p) cc_final: 0.8104 (p) REVERT: F 72 ASP cc_start: 0.8659 (m-30) cc_final: 0.8328 (m-30) REVERT: I 9 TYR cc_start: 0.9236 (OUTLIER) cc_final: 0.8263 (t80) REVERT: I 68 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7954 (mt-10) REVERT: I 72 ASP cc_start: 0.8618 (m-30) cc_final: 0.8340 (m-30) REVERT: I 138 GLU cc_start: 0.8931 (tp30) cc_final: 0.8665 (tp30) REVERT: J 9 TYR cc_start: 0.9212 (OUTLIER) cc_final: 0.8346 (t80) REVERT: J 72 ASP cc_start: 0.8756 (m-30) cc_final: 0.8491 (m-30) REVERT: J 109 GLN cc_start: 0.9050 (tp40) cc_final: 0.8682 (mm-40) REVERT: J 169 SER cc_start: 0.8689 (p) cc_final: 0.8142 (p) REVERT: K 72 ASP cc_start: 0.8666 (m-30) cc_final: 0.8321 (m-30) REVERT: K 109 GLN cc_start: 0.9030 (tp40) cc_final: 0.8656 (mm-40) REVERT: L 68 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7993 (mt-10) REVERT: L 72 ASP cc_start: 0.8619 (m-30) cc_final: 0.8304 (m-30) REVERT: L 109 GLN cc_start: 0.9028 (tp40) cc_final: 0.8661 (mm-40) REVERT: M 9 TYR cc_start: 0.9242 (OUTLIER) cc_final: 0.8377 (t80) REVERT: M 72 ASP cc_start: 0.8725 (m-30) cc_final: 0.8455 (m-30) REVERT: M 169 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.8171 (p) REVERT: N 72 ASP cc_start: 0.8651 (m-30) cc_final: 0.8315 (m-30) REVERT: N 97 MET cc_start: 0.8840 (tpp) cc_final: 0.8551 (tpp) REVERT: N 109 GLN cc_start: 0.9058 (tp40) cc_final: 0.8707 (mm-40) REVERT: N 140 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8646 (mmtp) REVERT: O 9 TYR cc_start: 0.9202 (OUTLIER) cc_final: 0.8138 (t80) REVERT: O 61 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8417 (mt-10) REVERT: O 72 ASP cc_start: 0.8629 (m-30) cc_final: 0.8347 (m-30) REVERT: O 138 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8286 (tp30) REVERT: O 169 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.8149 (p) REVERT: P 9 TYR cc_start: 0.9214 (OUTLIER) cc_final: 0.8373 (t80) REVERT: P 72 ASP cc_start: 0.8762 (m-30) cc_final: 0.8471 (m-30) REVERT: P 109 GLN cc_start: 0.9014 (tp40) cc_final: 0.8654 (mm-40) REVERT: Q 61 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8415 (mt-10) REVERT: Q 72 ASP cc_start: 0.8668 (m-30) cc_final: 0.8328 (m-30) REVERT: Q 109 GLN cc_start: 0.9052 (tp40) cc_final: 0.8671 (mm-40) REVERT: R 72 ASP cc_start: 0.8663 (m-30) cc_final: 0.8332 (m-30) REVERT: R 181 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7301 (mmmt) REVERT: S 9 TYR cc_start: 0.9248 (OUTLIER) cc_final: 0.8411 (t80) REVERT: S 72 ASP cc_start: 0.8727 (m-30) cc_final: 0.8476 (m-30) REVERT: S 169 SER cc_start: 0.8425 (p) cc_final: 0.8150 (t) REVERT: T 68 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7954 (mt-10) REVERT: T 72 ASP cc_start: 0.8692 (m-30) cc_final: 0.8410 (m-30) REVERT: T 169 SER cc_start: 0.8666 (p) cc_final: 0.8141 (p) REVERT: U 9 TYR cc_start: 0.9201 (OUTLIER) cc_final: 0.8263 (t80) REVERT: U 72 ASP cc_start: 0.8646 (m-30) cc_final: 0.8363 (m-30) REVERT: U 109 GLN cc_start: 0.9060 (tp40) cc_final: 0.8721 (mm-40) REVERT: U 138 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8534 (mm-30) REVERT: V 9 TYR cc_start: 0.9202 (OUTLIER) cc_final: 0.8170 (t80) REVERT: V 72 ASP cc_start: 0.8744 (m-30) cc_final: 0.8475 (m-30) REVERT: V 109 GLN cc_start: 0.9024 (tp40) cc_final: 0.8682 (mm-40) REVERT: V 169 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8162 (p) REVERT: W 68 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7985 (mt-10) REVERT: W 72 ASP cc_start: 0.8653 (m-30) cc_final: 0.8323 (m-30) REVERT: W 97 MET cc_start: 0.8886 (tpp) cc_final: 0.8484 (tpp) REVERT: W 109 GLN cc_start: 0.9070 (tp40) cc_final: 0.8716 (mm-40) REVERT: X 72 ASP cc_start: 0.8635 (m-30) cc_final: 0.8309 (m-30) REVERT: Y 9 TYR cc_start: 0.9231 (OUTLIER) cc_final: 0.8374 (t80) REVERT: Y 72 ASP cc_start: 0.8670 (m-30) cc_final: 0.8365 (m-30) REVERT: Y 109 GLN cc_start: 0.8972 (tp-100) cc_final: 0.8619 (mm-40) REVERT: Y 169 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8112 (p) REVERT: Z 72 ASP cc_start: 0.8658 (m-30) cc_final: 0.8350 (m-30) outliers start: 151 outliers final: 92 residues processed: 752 average time/residue: 0.7634 time to fit residues: 673.0907 Evaluate side-chains 738 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 628 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 3 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain I residue 9 TYR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 119 SER Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain J residue 9 TYR Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 182 HIS Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 57 GLU Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 181 LYS Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain M residue 9 TYR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 138 GLU Chi-restraints excluded: chain M residue 169 SER Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain O residue 9 TYR Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain P residue 3 SER Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 181 LYS Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 119 SER Chi-restraints excluded: chain T residue 181 LYS Chi-restraints excluded: chain U residue 9 TYR Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 138 GLU Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain V residue 9 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 33 SER Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 126 LEU Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain W residue 3 SER Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 138 GLU Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 78 LEU Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 126 LEU Chi-restraints excluded: chain Y residue 3 SER Chi-restraints excluded: chain Y residue 9 TYR Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 169 SER Chi-restraints excluded: chain Y residue 181 LYS Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 126 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 227 optimal weight: 0.6980 chunk 309 optimal weight: 1.9990 chunk 327 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 359 optimal weight: 2.9990 chunk 376 optimal weight: 0.7980 chunk 196 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 379 optimal weight: 0.1980 chunk 242 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 87 GLN R 182 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.097695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.086774 restraints weight = 41325.590| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.90 r_work: 0.2759 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 33560 Z= 0.093 Angle : 0.354 4.958 45064 Z= 0.192 Chirality : 0.030 0.117 4840 Planarity : 0.002 0.027 5944 Dihedral : 3.535 57.736 4460 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.57 % Allowed : 21.08 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.15 (0.13), residues: 3976 helix: 4.18 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.53 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 121 TYR 0.009 0.001 TYR S 173 PHE 0.011 0.001 PHE L 129 TRP 0.004 0.001 TRP V 90 HIS 0.010 0.000 HIS R 182 Details of bonding type rmsd covalent geometry : bond 0.00218 (33560) covalent geometry : angle 0.35351 (45064) hydrogen bonds : bond 0.02833 ( 2622) hydrogen bonds : angle 2.76773 ( 7866) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 637 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8572 (m-30) cc_final: 0.8292 (m-30) REVERT: A 83 GLN cc_start: 0.8757 (mt0) cc_final: 0.8448 (mp-120) REVERT: A 140 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8556 (mmtp) REVERT: B 40 ARG cc_start: 0.7804 (mtp85) cc_final: 0.7373 (mtp85) REVERT: B 42 ASP cc_start: 0.8733 (p0) cc_final: 0.7806 (p0) REVERT: B 70 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.7859 (tp40) REVERT: C 72 ASP cc_start: 0.8648 (m-30) cc_final: 0.8330 (m-30) REVERT: C 104 GLU cc_start: 0.8852 (tp30) cc_final: 0.8595 (mm-30) REVERT: C 138 GLU cc_start: 0.8845 (tp30) cc_final: 0.8085 (mm-30) REVERT: D 72 ASP cc_start: 0.8606 (m-30) cc_final: 0.8308 (m-30) REVERT: E 9 TYR cc_start: 0.9197 (OUTLIER) cc_final: 0.8381 (t80) REVERT: E 72 ASP cc_start: 0.8686 (m-30) cc_final: 0.8378 (m-30) REVERT: E 119 SER cc_start: 0.9056 (OUTLIER) cc_final: 0.8850 (m) REVERT: E 169 SER cc_start: 0.8498 (p) cc_final: 0.7961 (p) REVERT: F 72 ASP cc_start: 0.8638 (m-30) cc_final: 0.8316 (m-30) REVERT: F 104 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8150 (mm-30) REVERT: I 9 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.8466 (t80) REVERT: I 72 ASP cc_start: 0.8598 (m-30) cc_final: 0.8336 (m-30) REVERT: I 138 GLU cc_start: 0.8859 (tp30) cc_final: 0.8631 (tp30) REVERT: J 9 TYR cc_start: 0.9212 (OUTLIER) cc_final: 0.8229 (t80) REVERT: J 70 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.7744 (tp40) REVERT: J 72 ASP cc_start: 0.8701 (m-30) cc_final: 0.8427 (m-30) REVERT: J 138 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8213 (mm-30) REVERT: J 169 SER cc_start: 0.8569 (p) cc_final: 0.8045 (p) REVERT: K 72 ASP cc_start: 0.8609 (m-30) cc_final: 0.8302 (m-30) REVERT: K 83 GLN cc_start: 0.8903 (mt0) cc_final: 0.8577 (mm110) REVERT: L 68 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7926 (mt-10) REVERT: L 72 ASP cc_start: 0.8597 (m-30) cc_final: 0.8261 (m-30) REVERT: L 119 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8890 (m) REVERT: M 72 ASP cc_start: 0.8690 (m-30) cc_final: 0.8396 (m-30) REVERT: M 138 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8371 (mm-30) REVERT: M 169 SER cc_start: 0.8596 (p) cc_final: 0.8024 (p) REVERT: N 72 ASP cc_start: 0.8541 (m-30) cc_final: 0.8334 (m-30) REVERT: N 97 MET cc_start: 0.8796 (tpp) cc_final: 0.8477 (tpp) REVERT: N 140 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8451 (mmtp) REVERT: N 181 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7172 (mmmt) REVERT: O 9 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.8383 (t80) REVERT: O 61 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8415 (mt-10) REVERT: O 72 ASP cc_start: 0.8600 (m-30) cc_final: 0.8332 (m-30) REVERT: O 138 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8228 (tp30) REVERT: O 169 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8030 (p) REVERT: P 9 TYR cc_start: 0.9209 (OUTLIER) cc_final: 0.8477 (t80) REVERT: P 40 ARG cc_start: 0.7852 (mtp85) cc_final: 0.7537 (mtp85) REVERT: P 72 ASP cc_start: 0.8736 (m-30) cc_final: 0.8463 (m-30) REVERT: Q 61 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8390 (mt-10) REVERT: Q 72 ASP cc_start: 0.8645 (m-30) cc_final: 0.8340 (m-30) REVERT: R 72 ASP cc_start: 0.8651 (m-30) cc_final: 0.8319 (m-30) REVERT: R 181 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7249 (mmmt) REVERT: S 72 ASP cc_start: 0.8672 (m-30) cc_final: 0.8379 (m-30) REVERT: S 140 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8569 (mmtp) REVERT: S 169 SER cc_start: 0.8330 (p) cc_final: 0.7993 (t) REVERT: T 72 ASP cc_start: 0.8598 (m-30) cc_final: 0.8340 (m-30) REVERT: T 169 SER cc_start: 0.8542 (p) cc_final: 0.8035 (p) REVERT: T 181 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7317 (mmmt) REVERT: U 72 ASP cc_start: 0.8589 (m-30) cc_final: 0.8362 (m-30) REVERT: U 138 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8489 (mm-30) REVERT: V 9 TYR cc_start: 0.9209 (OUTLIER) cc_final: 0.8380 (t80) REVERT: V 72 ASP cc_start: 0.8709 (m-30) cc_final: 0.8413 (m-30) REVERT: V 169 SER cc_start: 0.8607 (p) cc_final: 0.8041 (p) REVERT: W 68 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7931 (mt-10) REVERT: W 72 ASP cc_start: 0.8636 (m-30) cc_final: 0.8309 (m-30) REVERT: X 72 ASP cc_start: 0.8627 (m-30) cc_final: 0.8269 (m-30) REVERT: Y 9 TYR cc_start: 0.9221 (OUTLIER) cc_final: 0.8466 (t80) REVERT: Y 72 ASP cc_start: 0.8638 (m-30) cc_final: 0.8347 (m-30) REVERT: Y 89 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: Y 169 SER cc_start: 0.8554 (p) cc_final: 0.7998 (p) REVERT: Z 9 TYR cc_start: 0.9189 (OUTLIER) cc_final: 0.8465 (t80) REVERT: Z 72 ASP cc_start: 0.8661 (m-30) cc_final: 0.8378 (m-30) REVERT: Z 140 LYS cc_start: 0.8802 (mmtt) cc_final: 0.8470 (mmtp) outliers start: 123 outliers final: 68 residues processed: 739 average time/residue: 0.7584 time to fit residues: 661.3369 Evaluate side-chains 688 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 599 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain I residue 9 TYR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain J residue 9 TYR Chi-restraints excluded: chain J residue 70 GLN Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 182 HIS Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 181 LYS Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 138 GLU Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain N residue 181 LYS Chi-restraints excluded: chain O residue 9 TYR Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 57 GLU Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 181 LYS Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 57 GLU Chi-restraints excluded: chain T residue 119 SER Chi-restraints excluded: chain T residue 181 LYS Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 138 GLU Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain V residue 9 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 126 LEU Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 78 LEU Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 126 LEU Chi-restraints excluded: chain Y residue 9 TYR Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 41 ASP Chi-restraints excluded: chain Y residue 89 GLU Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Z residue 9 TYR Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 126 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 153 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 237 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 376 optimal weight: 0.7980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.097151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.086707 restraints weight = 41477.141| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 1.79 r_work: 0.2717 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 33560 Z= 0.150 Angle : 0.391 4.295 45064 Z= 0.211 Chirality : 0.032 0.126 4840 Planarity : 0.003 0.042 5944 Dihedral : 3.402 12.870 4456 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.74 % Allowed : 22.30 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.08 (0.13), residues: 3976 helix: 4.13 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.54 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 121 TYR 0.009 0.001 TYR N 173 PHE 0.012 0.002 PHE S 38 TRP 0.004 0.001 TRP Q 90 HIS 0.011 0.001 HIS R 182 Details of bonding type rmsd covalent geometry : bond 0.00365 (33560) covalent geometry : angle 0.39106 (45064) hydrogen bonds : bond 0.03234 ( 2622) hydrogen bonds : angle 2.88876 ( 7866) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 620 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8623 (m-30) cc_final: 0.8401 (m-30) REVERT: A 109 GLN cc_start: 0.9131 (tp40) cc_final: 0.8812 (mm-40) REVERT: A 140 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8597 (mmtp) REVERT: B 70 GLN cc_start: 0.9320 (OUTLIER) cc_final: 0.7954 (tp40) REVERT: C 68 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8009 (mt-10) REVERT: C 72 ASP cc_start: 0.8667 (m-30) cc_final: 0.8375 (m-30) REVERT: D 72 ASP cc_start: 0.8622 (m-30) cc_final: 0.8354 (m-30) REVERT: D 182 HIS cc_start: 0.6819 (OUTLIER) cc_final: 0.6174 (m90) REVERT: E 9 TYR cc_start: 0.9233 (OUTLIER) cc_final: 0.8533 (t80) REVERT: E 72 ASP cc_start: 0.8716 (m-30) cc_final: 0.8435 (m-30) REVERT: E 109 GLN cc_start: 0.9081 (tp40) cc_final: 0.8710 (mm-40) REVERT: E 169 SER cc_start: 0.8644 (p) cc_final: 0.8139 (p) REVERT: F 72 ASP cc_start: 0.8631 (m-30) cc_final: 0.8329 (m-30) REVERT: I 9 TYR cc_start: 0.9224 (OUTLIER) cc_final: 0.8285 (t80) REVERT: I 72 ASP cc_start: 0.8587 (m-30) cc_final: 0.8345 (m-30) REVERT: I 104 GLU cc_start: 0.8755 (tp30) cc_final: 0.8483 (mm-30) REVERT: I 138 GLU cc_start: 0.8863 (tp30) cc_final: 0.8139 (mm-30) REVERT: J 9 TYR cc_start: 0.9233 (OUTLIER) cc_final: 0.8143 (t80) REVERT: J 70 GLN cc_start: 0.9333 (OUTLIER) cc_final: 0.7580 (tp-100) REVERT: J 72 ASP cc_start: 0.8753 (m-30) cc_final: 0.8485 (m-30) REVERT: J 138 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8272 (tp30) REVERT: J 169 SER cc_start: 0.8692 (p) cc_final: 0.8193 (p) REVERT: K 72 ASP cc_start: 0.8634 (m-30) cc_final: 0.8370 (m-30) REVERT: K 83 GLN cc_start: 0.8828 (mt0) cc_final: 0.8555 (mm110) REVERT: L 9 TYR cc_start: 0.9222 (OUTLIER) cc_final: 0.8443 (t80) REVERT: L 72 ASP cc_start: 0.8600 (m-30) cc_final: 0.8295 (m-30) REVERT: M 9 TYR cc_start: 0.9244 (OUTLIER) cc_final: 0.8390 (t80) REVERT: M 72 ASP cc_start: 0.8730 (m-30) cc_final: 0.8465 (m-30) REVERT: M 169 SER cc_start: 0.8729 (p) cc_final: 0.8204 (p) REVERT: M 181 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7306 (mmmt) REVERT: N 72 ASP cc_start: 0.8608 (m-30) cc_final: 0.8355 (m-30) REVERT: N 97 MET cc_start: 0.8938 (tpp) cc_final: 0.8654 (tpp) REVERT: N 140 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8544 (mmtp) REVERT: O 9 TYR cc_start: 0.9202 (OUTLIER) cc_final: 0.8259 (t80) REVERT: O 61 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8525 (mt-10) REVERT: O 72 ASP cc_start: 0.8601 (m-30) cc_final: 0.8366 (m-30) REVERT: O 104 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8400 (tp30) REVERT: O 138 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8285 (tp30) REVERT: O 169 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8173 (p) REVERT: P 9 TYR cc_start: 0.9234 (OUTLIER) cc_final: 0.8402 (t80) REVERT: P 72 ASP cc_start: 0.8756 (m-30) cc_final: 0.8473 (m-30) REVERT: P 109 GLN cc_start: 0.9082 (tp40) cc_final: 0.8764 (mm-40) REVERT: Q 61 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8525 (mt-10) REVERT: Q 72 ASP cc_start: 0.8643 (m-30) cc_final: 0.8350 (m-30) REVERT: R 72 ASP cc_start: 0.8682 (m-30) cc_final: 0.8347 (m-30) REVERT: R 182 HIS cc_start: 0.6728 (OUTLIER) cc_final: 0.6458 (p-80) REVERT: S 72 ASP cc_start: 0.8706 (m-30) cc_final: 0.8429 (m-30) REVERT: T 72 ASP cc_start: 0.8673 (m-30) cc_final: 0.8385 (m-30) REVERT: T 140 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8683 (mmtp) REVERT: T 169 SER cc_start: 0.8668 (p) cc_final: 0.8178 (p) REVERT: U 9 TYR cc_start: 0.9214 (OUTLIER) cc_final: 0.8302 (t80) REVERT: U 72 ASP cc_start: 0.8649 (m-30) cc_final: 0.8385 (m-30) REVERT: U 109 GLN cc_start: 0.9115 (tp40) cc_final: 0.8774 (mm-40) REVERT: U 138 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8529 (mm-30) REVERT: V 9 TYR cc_start: 0.9227 (OUTLIER) cc_final: 0.8377 (t80) REVERT: V 70 GLN cc_start: 0.9331 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: V 72 ASP cc_start: 0.8740 (m-30) cc_final: 0.8469 (m-30) REVERT: V 109 GLN cc_start: 0.9099 (tp40) cc_final: 0.8759 (mm-40) REVERT: V 169 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8214 (p) REVERT: W 72 ASP cc_start: 0.8656 (m-30) cc_final: 0.8358 (m-30) REVERT: X 72 ASP cc_start: 0.8598 (m-30) cc_final: 0.8290 (m-30) REVERT: Y 9 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.8408 (t80) REVERT: Y 72 ASP cc_start: 0.8652 (m-30) cc_final: 0.8397 (m-30) REVERT: Y 89 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: Y 109 GLN cc_start: 0.8983 (tp-100) cc_final: 0.8639 (mm-40) REVERT: Y 169 SER cc_start: 0.8669 (p) cc_final: 0.8140 (p) REVERT: Z 9 TYR cc_start: 0.9216 (OUTLIER) cc_final: 0.8319 (t80) REVERT: Z 72 ASP cc_start: 0.8634 (m-30) cc_final: 0.8328 (m-30) REVERT: Z 140 LYS cc_start: 0.8904 (mmtt) cc_final: 0.8608 (mmtp) outliers start: 129 outliers final: 88 residues processed: 724 average time/residue: 0.7050 time to fit residues: 601.2403 Evaluate side-chains 716 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 605 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain I residue 9 TYR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain J residue 9 TYR Chi-restraints excluded: chain J residue 70 GLN Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 181 LYS Chi-restraints excluded: chain J residue 182 HIS Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 181 LYS Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain L residue 9 TYR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain M residue 9 TYR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 138 GLU Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain O residue 9 TYR Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 57 GLU Chi-restraints excluded: chain T residue 119 SER Chi-restraints excluded: chain T residue 181 LYS Chi-restraints excluded: chain U residue 9 TYR Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 138 GLU Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain V residue 9 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 70 GLN Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 126 LEU Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 57 GLU Chi-restraints excluded: chain X residue 78 LEU Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 126 LEU Chi-restraints excluded: chain Y residue 9 TYR Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 89 GLU Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Z residue 9 TYR Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 126 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 362 optimal weight: 0.1980 chunk 221 optimal weight: 5.9990 chunk 214 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 381 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 158 optimal weight: 8.9990 chunk 255 optimal weight: 0.9980 chunk 250 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 GLN R 182 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.093963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.083496 restraints weight = 42125.275| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.75 r_work: 0.2879 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33560 Z= 0.111 Angle : 0.366 4.706 45064 Z= 0.199 Chirality : 0.031 0.117 4840 Planarity : 0.002 0.027 5944 Dihedral : 3.327 12.886 4456 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.48 % Allowed : 21.98 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.16 (0.13), residues: 3976 helix: 4.19 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.57 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 121 TYR 0.011 0.001 TYR T 173 PHE 0.011 0.001 PHE L 129 TRP 0.004 0.001 TRP A 90 HIS 0.009 0.001 HIS R 182 Details of bonding type rmsd covalent geometry : bond 0.00266 (33560) covalent geometry : angle 0.36599 (45064) hydrogen bonds : bond 0.02997 ( 2622) hydrogen bonds : angle 2.82238 ( 7866) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 733 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 613 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.9240 (OUTLIER) cc_final: 0.8525 (t80) REVERT: A 72 ASP cc_start: 0.8627 (m-30) cc_final: 0.8393 (m-30) REVERT: A 140 LYS cc_start: 0.8921 (mmtt) cc_final: 0.8538 (mmtp) REVERT: B 70 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.7902 (tp40) REVERT: C 72 ASP cc_start: 0.8644 (m-30) cc_final: 0.8348 (m-30) REVERT: C 138 GLU cc_start: 0.8866 (tp30) cc_final: 0.8319 (tp30) REVERT: D 72 ASP cc_start: 0.8626 (m-30) cc_final: 0.8347 (m-30) REVERT: E 9 TYR cc_start: 0.9240 (OUTLIER) cc_final: 0.8406 (t80) REVERT: E 72 ASP cc_start: 0.8662 (m-30) cc_final: 0.8417 (m-30) REVERT: E 169 SER cc_start: 0.8598 (p) cc_final: 0.8123 (p) REVERT: F 72 ASP cc_start: 0.8664 (m-30) cc_final: 0.8368 (m-30) REVERT: I 9 TYR cc_start: 0.9224 (OUTLIER) cc_final: 0.8418 (t80) REVERT: I 72 ASP cc_start: 0.8565 (m-30) cc_final: 0.8339 (m-30) REVERT: J 9 TYR cc_start: 0.9240 (OUTLIER) cc_final: 0.8287 (t80) REVERT: J 70 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.7763 (tp40) REVERT: J 72 ASP cc_start: 0.8643 (m-30) cc_final: 0.8381 (m-30) REVERT: J 138 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8194 (mm-30) REVERT: J 169 SER cc_start: 0.8661 (p) cc_final: 0.8179 (p) REVERT: K 72 ASP cc_start: 0.8620 (m-30) cc_final: 0.8370 (m-30) REVERT: K 83 GLN cc_start: 0.8837 (mt0) cc_final: 0.8597 (mm110) REVERT: L 9 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.8469 (t80) REVERT: L 72 ASP cc_start: 0.8638 (m-30) cc_final: 0.8324 (m-30) REVERT: M 9 TYR cc_start: 0.9243 (OUTLIER) cc_final: 0.8415 (t80) REVERT: M 72 ASP cc_start: 0.8652 (m-30) cc_final: 0.8376 (m-30) REVERT: M 140 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8662 (mmtp) REVERT: M 169 SER cc_start: 0.8689 (p) cc_final: 0.8169 (p) REVERT: M 181 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7308 (mmmt) REVERT: N 140 LYS cc_start: 0.8915 (mmtt) cc_final: 0.8541 (mmtp) REVERT: O 9 TYR cc_start: 0.9217 (OUTLIER) cc_final: 0.8332 (t80) REVERT: O 61 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8524 (mt-10) REVERT: O 68 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8013 (mt-10) REVERT: O 72 ASP cc_start: 0.8620 (m-30) cc_final: 0.8379 (m-30) REVERT: O 104 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8399 (mm-30) REVERT: O 169 SER cc_start: 0.8673 (OUTLIER) cc_final: 0.8148 (p) REVERT: P 9 TYR cc_start: 0.9228 (OUTLIER) cc_final: 0.8412 (t80) REVERT: P 72 ASP cc_start: 0.8665 (m-30) cc_final: 0.8378 (m-30) REVERT: Q 72 ASP cc_start: 0.8659 (m-30) cc_final: 0.8383 (m-30) REVERT: R 72 ASP cc_start: 0.8618 (m-30) cc_final: 0.8303 (m-30) REVERT: S 9 TYR cc_start: 0.9255 (OUTLIER) cc_final: 0.8425 (t80) REVERT: S 72 ASP cc_start: 0.8655 (m-30) cc_final: 0.8376 (m-30) REVERT: T 140 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8690 (mmtp) REVERT: T 169 SER cc_start: 0.8612 (p) cc_final: 0.8138 (p) REVERT: T 181 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7437 (mmmt) REVERT: U 9 TYR cc_start: 0.9221 (OUTLIER) cc_final: 0.8348 (t80) REVERT: U 72 ASP cc_start: 0.8576 (m-30) cc_final: 0.8364 (m-30) REVERT: U 109 GLN cc_start: 0.9147 (tp40) cc_final: 0.8807 (mm-40) REVERT: U 138 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8493 (mm-30) REVERT: U 181 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7460 (mmmt) REVERT: V 9 TYR cc_start: 0.9232 (OUTLIER) cc_final: 0.8439 (t80) REVERT: V 72 ASP cc_start: 0.8627 (m-30) cc_final: 0.8363 (m-30) REVERT: V 169 SER cc_start: 0.8718 (p) cc_final: 0.8197 (p) REVERT: W 72 ASP cc_start: 0.8636 (m-30) cc_final: 0.8351 (m-30) REVERT: X 72 ASP cc_start: 0.8635 (m-30) cc_final: 0.8315 (m-30) REVERT: Y 72 ASP cc_start: 0.8551 (m-30) cc_final: 0.8324 (m-30) REVERT: Y 89 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: Y 169 SER cc_start: 0.8640 (p) cc_final: 0.8139 (p) REVERT: Z 9 TYR cc_start: 0.9219 (OUTLIER) cc_final: 0.8348 (t80) REVERT: Z 72 ASP cc_start: 0.8666 (m-30) cc_final: 0.8362 (m-30) REVERT: Z 140 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8632 (mmtp) outliers start: 120 outliers final: 85 residues processed: 710 average time/residue: 0.7402 time to fit residues: 619.3565 Evaluate side-chains 690 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 584 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 TYR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain I residue 9 TYR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain J residue 9 TYR Chi-restraints excluded: chain J residue 70 GLN Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 181 LYS Chi-restraints excluded: chain J residue 182 HIS Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 181 LYS Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain L residue 9 TYR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain M residue 9 TYR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 138 GLU Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain O residue 9 TYR Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 57 GLU Chi-restraints excluded: chain T residue 119 SER Chi-restraints excluded: chain T residue 181 LYS Chi-restraints excluded: chain U residue 9 TYR Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 138 GLU Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain V residue 9 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 33 SER Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 126 LEU Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 57 GLU Chi-restraints excluded: chain X residue 78 LEU Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 126 LEU Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 89 GLU Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Z residue 9 TYR Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 126 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 389 optimal weight: 3.9990 chunk 241 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 320 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 182 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.094091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.083466 restraints weight = 41775.068| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.76 r_work: 0.2858 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 33560 Z= 0.117 Angle : 0.377 4.604 45064 Z= 0.205 Chirality : 0.031 0.117 4840 Planarity : 0.002 0.032 5944 Dihedral : 3.335 12.942 4456 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.68 % Allowed : 22.33 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.15 (0.13), residues: 3976 helix: 4.20 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.62 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 40 TYR 0.012 0.001 TYR I 173 PHE 0.011 0.001 PHE L 129 TRP 0.005 0.001 TRP B 90 HIS 0.011 0.001 HIS R 182 Details of bonding type rmsd covalent geometry : bond 0.00281 (33560) covalent geometry : angle 0.37710 (45064) hydrogen bonds : bond 0.03033 ( 2622) hydrogen bonds : angle 2.84109 ( 7866) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 602 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.9242 (OUTLIER) cc_final: 0.8545 (t80) REVERT: A 140 LYS cc_start: 0.8994 (mmtt) cc_final: 0.8647 (mmtp) REVERT: B 42 ASP cc_start: 0.8795 (p0) cc_final: 0.8080 (p0) REVERT: B 70 GLN cc_start: 0.9317 (OUTLIER) cc_final: 0.8001 (tp40) REVERT: C 72 ASP cc_start: 0.8653 (m-30) cc_final: 0.8373 (m-30) REVERT: D 72 ASP cc_start: 0.8637 (m-30) cc_final: 0.8362 (m-30) REVERT: E 9 TYR cc_start: 0.9245 (OUTLIER) cc_final: 0.8341 (t80) REVERT: E 70 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.7864 (tp40) REVERT: E 72 ASP cc_start: 0.8688 (m-30) cc_final: 0.8458 (m-30) REVERT: E 169 SER cc_start: 0.8647 (p) cc_final: 0.8192 (p) REVERT: F 72 ASP cc_start: 0.8689 (m-30) cc_final: 0.8411 (m-30) REVERT: I 9 TYR cc_start: 0.9228 (OUTLIER) cc_final: 0.8527 (t80) REVERT: J 9 TYR cc_start: 0.9247 (OUTLIER) cc_final: 0.8309 (t80) REVERT: J 70 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.7817 (tp40) REVERT: J 72 ASP cc_start: 0.8648 (m-30) cc_final: 0.8416 (m-30) REVERT: J 169 SER cc_start: 0.8718 (p) cc_final: 0.8254 (p) REVERT: K 72 ASP cc_start: 0.8636 (m-30) cc_final: 0.8378 (m-30) REVERT: L 9 TYR cc_start: 0.9213 (OUTLIER) cc_final: 0.8485 (t80) REVERT: L 72 ASP cc_start: 0.8618 (m-30) cc_final: 0.8335 (m-30) REVERT: M 9 TYR cc_start: 0.9236 (OUTLIER) cc_final: 0.8434 (t80) REVERT: M 72 ASP cc_start: 0.8662 (m-30) cc_final: 0.8413 (m-30) REVERT: M 140 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8748 (mmtp) REVERT: M 169 SER cc_start: 0.8750 (p) cc_final: 0.8258 (p) REVERT: M 181 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7406 (mmmt) REVERT: N 140 LYS cc_start: 0.8951 (mmtt) cc_final: 0.8611 (mmtp) REVERT: O 9 TYR cc_start: 0.9218 (OUTLIER) cc_final: 0.8341 (t80) REVERT: O 68 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8105 (mt-10) REVERT: O 104 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8472 (mm-30) REVERT: O 169 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.8235 (p) REVERT: P 9 TYR cc_start: 0.9220 (OUTLIER) cc_final: 0.8411 (t80) REVERT: P 72 ASP cc_start: 0.8668 (m-30) cc_final: 0.8435 (m-30) REVERT: Q 72 ASP cc_start: 0.8670 (m-30) cc_final: 0.8406 (m-30) REVERT: R 72 ASP cc_start: 0.8606 (m-30) cc_final: 0.8334 (m-30) REVERT: S 9 TYR cc_start: 0.9253 (OUTLIER) cc_final: 0.8437 (t80) REVERT: S 72 ASP cc_start: 0.8664 (m-30) cc_final: 0.8405 (m-30) REVERT: T 140 LYS cc_start: 0.8939 (mmtt) cc_final: 0.8721 (mmtp) REVERT: T 169 SER cc_start: 0.8678 (p) cc_final: 0.8222 (p) REVERT: U 9 TYR cc_start: 0.9222 (OUTLIER) cc_final: 0.8366 (t80) REVERT: U 109 GLN cc_start: 0.9198 (tp40) cc_final: 0.8870 (mm-40) REVERT: U 138 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8475 (mm-30) REVERT: U 181 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7552 (mmmt) REVERT: V 9 TYR cc_start: 0.9232 (OUTLIER) cc_final: 0.8531 (t80) REVERT: V 70 GLN cc_start: 0.9334 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: V 72 ASP cc_start: 0.8636 (m-30) cc_final: 0.8386 (m-30) REVERT: V 109 GLN cc_start: 0.9156 (tp40) cc_final: 0.8804 (mm-40) REVERT: V 169 SER cc_start: 0.8766 (p) cc_final: 0.8272 (p) REVERT: W 72 ASP cc_start: 0.8654 (m-30) cc_final: 0.8387 (m-30) REVERT: X 72 ASP cc_start: 0.8639 (m-30) cc_final: 0.8345 (m-30) REVERT: Y 9 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.8436 (t80) REVERT: Y 72 ASP cc_start: 0.8565 (m-30) cc_final: 0.8342 (m-30) REVERT: Y 89 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: Y 109 GLN cc_start: 0.9039 (tp-100) cc_final: 0.8740 (mm-40) REVERT: Y 169 SER cc_start: 0.8677 (OUTLIER) cc_final: 0.8192 (p) REVERT: Z 9 TYR cc_start: 0.9216 (OUTLIER) cc_final: 0.8354 (t80) REVERT: Z 72 ASP cc_start: 0.8665 (m-30) cc_final: 0.8389 (m-30) REVERT: Z 140 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8700 (mmtp) outliers start: 127 outliers final: 93 residues processed: 702 average time/residue: 0.6422 time to fit residues: 532.6774 Evaluate side-chains 702 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 586 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 TYR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain I residue 9 TYR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain J residue 9 TYR Chi-restraints excluded: chain J residue 70 GLN Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 181 LYS Chi-restraints excluded: chain J residue 182 HIS Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 119 SER Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 181 LYS Chi-restraints excluded: chain L residue 3 SER Chi-restraints excluded: chain L residue 9 TYR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 119 SER Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain M residue 9 TYR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain M residue 138 GLU Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain O residue 9 TYR Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 57 GLU Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 119 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 57 GLU Chi-restraints excluded: chain T residue 119 SER Chi-restraints excluded: chain T residue 181 LYS Chi-restraints excluded: chain U residue 9 TYR Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 76 ARG Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 138 GLU Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain V residue 9 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 70 GLN Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 126 LEU Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 78 LEU Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 126 LEU Chi-restraints excluded: chain Y residue 9 TYR Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 89 GLU Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 169 SER Chi-restraints excluded: chain Z residue 9 TYR Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 126 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 343 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 331 optimal weight: 3.9990 chunk 364 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 272 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 318 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 HIS F 50 HIS I 50 HIS J 50 HIS K 50 HIS K 83 GLN N 50 HIS O 50 HIS Q 50 HIS R 50 HIS R 182 HIS S 50 HIS U 50 HIS W 50 HIS X 50 HIS Z 50 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.095173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.084900 restraints weight = 42219.198| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.71 r_work: 0.2897 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 33560 Z= 0.104 Angle : 0.366 4.740 45064 Z= 0.201 Chirality : 0.031 0.117 4840 Planarity : 0.002 0.033 5944 Dihedral : 3.303 12.985 4456 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.51 % Allowed : 22.74 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.18 (0.13), residues: 3976 helix: 4.23 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.66 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 40 TYR 0.012 0.001 TYR I 173 PHE 0.011 0.001 PHE L 129 TRP 0.005 0.001 TRP J 90 HIS 0.010 0.001 HIS R 182 Details of bonding type rmsd covalent geometry : bond 0.00246 (33560) covalent geometry : angle 0.36641 (45064) hydrogen bonds : bond 0.02940 ( 2622) hydrogen bonds : angle 2.81155 ( 7866) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7952 Ramachandran restraints generated. 3976 Oldfield, 0 Emsley, 3976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 592 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 9 TYR cc_start: 0.9232 (OUTLIER) cc_final: 0.8527 (t80) REVERT: A 140 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8631 (mmtp) REVERT: B 70 GLN cc_start: 0.9302 (OUTLIER) cc_final: 0.7935 (tp40) REVERT: C 72 ASP cc_start: 0.8645 (m-30) cc_final: 0.8374 (m-30) REVERT: C 109 GLN cc_start: 0.9197 (tp40) cc_final: 0.8888 (mm-40) REVERT: C 119 SER cc_start: 0.9264 (OUTLIER) cc_final: 0.9041 (m) REVERT: D 72 ASP cc_start: 0.8622 (m-30) cc_final: 0.8351 (m-30) REVERT: E 9 TYR cc_start: 0.9236 (OUTLIER) cc_final: 0.8408 (t80) REVERT: E 70 GLN cc_start: 0.9326 (OUTLIER) cc_final: 0.7849 (tp40) REVERT: E 72 ASP cc_start: 0.8672 (m-30) cc_final: 0.8444 (m-30) REVERT: E 169 SER cc_start: 0.8630 (p) cc_final: 0.8121 (p) REVERT: F 72 ASP cc_start: 0.8628 (m-30) cc_final: 0.8337 (m-30) REVERT: I 9 TYR cc_start: 0.9219 (OUTLIER) cc_final: 0.8409 (t80) REVERT: J 9 TYR cc_start: 0.9238 (OUTLIER) cc_final: 0.8398 (t80) REVERT: J 70 GLN cc_start: 0.9328 (OUTLIER) cc_final: 0.7799 (tp40) REVERT: J 72 ASP cc_start: 0.8631 (m-30) cc_final: 0.8385 (m-30) REVERT: J 169 SER cc_start: 0.8694 (p) cc_final: 0.8181 (p) REVERT: K 72 ASP cc_start: 0.8620 (m-30) cc_final: 0.8404 (m-30) REVERT: L 9 TYR cc_start: 0.9207 (OUTLIER) cc_final: 0.8472 (t80) REVERT: L 72 ASP cc_start: 0.8592 (m-30) cc_final: 0.8318 (m-30) REVERT: M 9 TYR cc_start: 0.9226 (OUTLIER) cc_final: 0.8515 (t80) REVERT: M 72 ASP cc_start: 0.8605 (m-30) cc_final: 0.8346 (m-30) REVERT: M 138 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8320 (mm-30) REVERT: M 140 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8704 (mmtp) REVERT: M 169 SER cc_start: 0.8703 (p) cc_final: 0.8205 (p) REVERT: M 181 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7369 (mmmt) REVERT: N 140 LYS cc_start: 0.8938 (mmtt) cc_final: 0.8604 (mmtp) REVERT: O 9 TYR cc_start: 0.9216 (OUTLIER) cc_final: 0.8336 (t80) REVERT: O 104 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8473 (mm-30) REVERT: O 169 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8184 (p) REVERT: P 9 TYR cc_start: 0.9224 (OUTLIER) cc_final: 0.8517 (t80) REVERT: P 72 ASP cc_start: 0.8660 (m-30) cc_final: 0.8437 (m-30) REVERT: Q 72 ASP cc_start: 0.8638 (m-30) cc_final: 0.8390 (m-30) REVERT: R 72 ASP cc_start: 0.8578 (m-30) cc_final: 0.8320 (m-30) REVERT: S 9 TYR cc_start: 0.9247 (OUTLIER) cc_final: 0.8424 (t80) REVERT: S 72 ASP cc_start: 0.8635 (m-30) cc_final: 0.8388 (m-30) REVERT: S 169 SER cc_start: 0.8719 (p) cc_final: 0.8144 (t) REVERT: T 140 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8713 (mmtp) REVERT: T 169 SER cc_start: 0.8648 (p) cc_final: 0.8136 (p) REVERT: T 181 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7513 (mmmt) REVERT: U 9 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.8371 (t80) REVERT: U 109 GLN cc_start: 0.9187 (tp40) cc_final: 0.8858 (mm-40) REVERT: U 138 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8354 (mm-30) REVERT: U 181 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7524 (mmmt) REVERT: V 9 TYR cc_start: 0.9225 (OUTLIER) cc_final: 0.8610 (t80) REVERT: V 70 GLN cc_start: 0.9333 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: V 72 ASP cc_start: 0.8606 (m-30) cc_final: 0.8361 (m-30) REVERT: V 169 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.8237 (p) REVERT: W 72 ASP cc_start: 0.8612 (m-30) cc_final: 0.8359 (m-30) REVERT: X 72 ASP cc_start: 0.8597 (m-30) cc_final: 0.8316 (m-30) REVERT: X 119 SER cc_start: 0.9276 (OUTLIER) cc_final: 0.9049 (m) REVERT: Y 9 TYR cc_start: 0.9240 (OUTLIER) cc_final: 0.8418 (t80) REVERT: Y 72 ASP cc_start: 0.8573 (m-30) cc_final: 0.8327 (m-30) REVERT: Y 89 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: Y 169 SER cc_start: 0.8638 (OUTLIER) cc_final: 0.8155 (p) REVERT: Z 9 TYR cc_start: 0.9202 (OUTLIER) cc_final: 0.8457 (t80) REVERT: Z 72 ASP cc_start: 0.8613 (m-30) cc_final: 0.8344 (m-30) REVERT: Z 140 LYS cc_start: 0.8961 (mmtt) cc_final: 0.8702 (mmtp) outliers start: 121 outliers final: 88 residues processed: 683 average time/residue: 0.6708 time to fit residues: 542.5078 Evaluate side-chains 686 residues out of total 3448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 570 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 TYR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 70 GLN Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 70 GLN Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain I residue 9 TYR Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain J residue 9 TYR Chi-restraints excluded: chain J residue 70 GLN Chi-restraints excluded: chain J residue 86 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 181 LYS Chi-restraints excluded: chain J residue 182 HIS Chi-restraints excluded: chain K residue 10 SER Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain K residue 181 LYS Chi-restraints excluded: chain L residue 9 TYR Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain M residue 9 TYR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 126 LEU Chi-restraints excluded: chain M residue 138 GLU Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain N residue 126 LEU Chi-restraints excluded: chain O residue 9 TYR Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 33 SER Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 86 SER Chi-restraints excluded: chain O residue 126 LEU Chi-restraints excluded: chain O residue 169 SER Chi-restraints excluded: chain P residue 9 TYR Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 86 SER Chi-restraints excluded: chain P residue 126 LEU Chi-restraints excluded: chain P residue 181 LYS Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 119 SER Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 57 GLU Chi-restraints excluded: chain R residue 86 SER Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain S residue 9 TYR Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 33 SER Chi-restraints excluded: chain S residue 86 SER Chi-restraints excluded: chain S residue 119 SER Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 57 GLU Chi-restraints excluded: chain T residue 119 SER Chi-restraints excluded: chain T residue 181 LYS Chi-restraints excluded: chain U residue 9 TYR Chi-restraints excluded: chain U residue 10 SER Chi-restraints excluded: chain U residue 76 ARG Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 119 SER Chi-restraints excluded: chain U residue 126 LEU Chi-restraints excluded: chain U residue 138 GLU Chi-restraints excluded: chain U residue 181 LYS Chi-restraints excluded: chain V residue 9 TYR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 33 SER Chi-restraints excluded: chain V residue 70 GLN Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain V residue 126 LEU Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 86 SER Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 181 LYS Chi-restraints excluded: chain X residue 3 SER Chi-restraints excluded: chain X residue 57 GLU Chi-restraints excluded: chain X residue 78 LEU Chi-restraints excluded: chain X residue 119 SER Chi-restraints excluded: chain X residue 126 LEU Chi-restraints excluded: chain Y residue 9 TYR Chi-restraints excluded: chain Y residue 10 SER Chi-restraints excluded: chain Y residue 89 GLU Chi-restraints excluded: chain Y residue 119 SER Chi-restraints excluded: chain Y residue 169 SER Chi-restraints excluded: chain Z residue 9 TYR Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 126 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 13 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 309 optimal weight: 0.9980 chunk 358 optimal weight: 6.9990 chunk 349 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 332 optimal weight: 3.9990 chunk 375 optimal weight: 0.0670 chunk 40 optimal weight: 0.1980 chunk 251 optimal weight: 4.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS B 50 HIS E 50 HIS R 182 HIS Y 50 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.098517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.088281 restraints weight = 41736.742| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.71 r_work: 0.2877 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 33560 Z= 0.086 Angle : 0.359 4.970 45064 Z= 0.197 Chirality : 0.030 0.116 4840 Planarity : 0.003 0.055 5944 Dihedral : 3.248 13.014 4456 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.22 % Allowed : 23.49 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.25 (0.13), residues: 3976 helix: 4.29 (0.09), residues: 3216 sheet: None (None), residues: 0 loop : -0.70 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 76 TYR 0.013 0.001 TYR E 31 PHE 0.010 0.001 PHE L 129 TRP 0.010 0.001 TRP J 90 HIS 0.010 0.001 HIS R 182 Details of bonding type rmsd covalent geometry : bond 0.00194 (33560) covalent geometry : angle 0.35887 (45064) hydrogen bonds : bond 0.02737 ( 2622) hydrogen bonds : angle 2.75859 ( 7866) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11343.97 seconds wall clock time: 193 minutes 57.57 seconds (11637.57 seconds total)