Starting phenix.real_space_refine on Fri Sep 19 05:35:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ewx_50025/09_2025/9ewx_50025.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ewx_50025/09_2025/9ewx_50025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ewx_50025/09_2025/9ewx_50025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ewx_50025/09_2025/9ewx_50025.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ewx_50025/09_2025/9ewx_50025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ewx_50025/09_2025/9ewx_50025.map" } resolution = 3.17 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= 0.005 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 92 5.16 5 C 15111 2.51 5 N 3933 2.21 5 O 4853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23989 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W Time building chain proxies: 2.33, per 1000 atoms: 0.10 Number of scatterers: 23989 At special positions: 0 Unit cell: (71.688, 71.688, 319.712, 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 92 16.00 O 4853 8.00 N 3933 7.00 C 15111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 147 " distance=2.03 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 147 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 147 " distance=2.03 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 147 " distance=2.03 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 147 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 147 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 147 " distance=2.03 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 147 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 147 " distance=2.03 Simple disulfide: pdb=" SG CYS O 134 " - pdb=" SG CYS O 147 " distance=2.03 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 147 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 134 " - pdb=" SG CYS Q 147 " distance=2.03 Simple disulfide: pdb=" SG CYS R 134 " - pdb=" SG CYS R 147 " distance=2.03 Simple disulfide: pdb=" SG CYS S 134 " - pdb=" SG CYS S 147 " distance=2.03 Simple disulfide: pdb=" SG CYS T 134 " - pdb=" SG CYS T 147 " distance=2.03 Simple disulfide: pdb=" SG CYS U 134 " - pdb=" SG CYS U 147 " distance=2.03 Simple disulfide: pdb=" SG CYS V 134 " - pdb=" SG CYS V 147 " distance=2.03 Simple disulfide: pdb=" SG CYS W 134 " - pdb=" SG CYS W 147 " distance=2.03 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: 2.39 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6026 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 46 sheets defined 34.3% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 30 through 47 Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 30 through 47 Processing helix chain 'B' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 30 through 47 Processing helix chain 'C' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR C 52 " --> pdb=" O PRO C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 30 through 47 Processing helix chain 'D' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'E' and resid 8 through 23 Processing helix chain 'E' and resid 30 through 47 Processing helix chain 'E' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR E 52 " --> pdb=" O PRO E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'F' and resid 8 through 23 Processing helix chain 'F' and resid 30 through 47 Processing helix chain 'F' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR F 52 " --> pdb=" O PRO F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 47 Processing helix chain 'G' and resid 48 through 59 removed outlier: 3.596A pdb=" N THR G 52 " --> pdb=" O PRO G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'H' and resid 8 through 23 Processing helix chain 'H' and resid 30 through 47 Processing helix chain 'H' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR H 52 " --> pdb=" O PRO H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'I' and resid 8 through 23 Processing helix chain 'I' and resid 30 through 47 Processing helix chain 'I' and resid 48 through 59 removed outlier: 3.594A pdb=" N THR I 52 " --> pdb=" O PRO I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'J' and resid 8 through 23 Processing helix chain 'J' and resid 30 through 47 Processing helix chain 'J' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR J 52 " --> pdb=" O PRO J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'K' and resid 8 through 23 Processing helix chain 'K' and resid 30 through 47 Processing helix chain 'K' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR K 52 " --> pdb=" O PRO K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'L' and resid 8 through 23 Processing helix chain 'L' and resid 30 through 47 Processing helix chain 'L' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR L 52 " --> pdb=" O PRO L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'M' and resid 8 through 23 Processing helix chain 'M' and resid 30 through 47 Processing helix chain 'M' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR M 52 " --> pdb=" O PRO M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 64 No H-bonds generated for 'chain 'M' and resid 62 through 64' Processing helix chain 'N' and resid 8 through 23 Processing helix chain 'N' and resid 30 through 47 Processing helix chain 'N' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR N 52 " --> pdb=" O PRO N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'O' and resid 8 through 23 Processing helix chain 'O' and resid 30 through 47 Processing helix chain 'O' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR O 52 " --> pdb=" O PRO O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 64 No H-bonds generated for 'chain 'O' and resid 62 through 64' Processing helix chain 'P' and resid 8 through 23 Processing helix chain 'P' and resid 30 through 47 Processing helix chain 'P' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR P 52 " --> pdb=" O PRO P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 64 No H-bonds generated for 'chain 'P' and resid 62 through 64' Processing helix chain 'Q' and resid 8 through 23 Processing helix chain 'Q' and resid 30 through 47 Processing helix chain 'Q' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR Q 52 " --> pdb=" O PRO Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 64 No H-bonds generated for 'chain 'Q' and resid 62 through 64' Processing helix chain 'R' and resid 8 through 23 Processing helix chain 'R' and resid 30 through 47 Processing helix chain 'R' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR R 52 " --> pdb=" O PRO R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 64 No H-bonds generated for 'chain 'R' and resid 62 through 64' Processing helix chain 'S' and resid 8 through 23 Processing helix chain 'S' and resid 30 through 47 Processing helix chain 'S' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR S 52 " --> pdb=" O PRO S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'T' and resid 8 through 23 Processing helix chain 'T' and resid 30 through 47 Processing helix chain 'T' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR T 52 " --> pdb=" O PRO T 48 " (cutoff:3.500A) Processing helix chain 'T' and resid 62 through 64 No H-bonds generated for 'chain 'T' and resid 62 through 64' Processing helix chain 'U' and resid 8 through 23 Processing helix chain 'U' and resid 30 through 47 Processing helix chain 'U' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR U 52 " --> pdb=" O PRO U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 62 through 64 No H-bonds generated for 'chain 'U' and resid 62 through 64' Processing helix chain 'V' and resid 8 through 23 Processing helix chain 'V' and resid 30 through 47 Processing helix chain 'V' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR V 52 " --> pdb=" O PRO V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 62 through 64 No H-bonds generated for 'chain 'V' and resid 62 through 64' Processing helix chain 'W' and resid 8 through 23 Processing helix chain 'W' and resid 30 through 47 Processing helix chain 'W' and resid 48 through 59 removed outlier: 3.594A pdb=" N THR W 52 " --> pdb=" O PRO W 48 " (cutoff:3.500A) Processing helix chain 'W' and resid 62 through 64 No H-bonds generated for 'chain 'W' and resid 62 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 96 Processing sheet with id=AA3, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 96 Processing sheet with id=AA5, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 96 Processing sheet with id=AA7, first strand: chain 'D' and resid 66 through 67 Processing sheet with id=AA8, first strand: chain 'D' and resid 90 through 96 Processing sheet with id=AA9, first strand: chain 'E' and resid 66 through 67 Processing sheet with id=AB1, first strand: chain 'E' and resid 90 through 96 Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 67 Processing sheet with id=AB3, first strand: chain 'F' and resid 90 through 96 Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 67 Processing sheet with id=AB5, first strand: chain 'G' and resid 90 through 96 Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 67 Processing sheet with id=AB7, first strand: chain 'H' and resid 90 through 96 Processing sheet with id=AB8, first strand: chain 'I' and resid 66 through 67 Processing sheet with id=AB9, first strand: chain 'I' and resid 90 through 96 Processing sheet with id=AC1, first strand: chain 'J' and resid 66 through 67 Processing sheet with id=AC2, first strand: chain 'J' and resid 90 through 96 Processing sheet with id=AC3, first strand: chain 'K' and resid 66 through 67 Processing sheet with id=AC4, first strand: chain 'K' and resid 90 through 96 Processing sheet with id=AC5, first strand: chain 'L' and resid 66 through 67 Processing sheet with id=AC6, first strand: chain 'L' and resid 90 through 96 Processing sheet with id=AC7, first strand: chain 'M' and resid 66 through 67 Processing sheet with id=AC8, first strand: chain 'M' and resid 90 through 96 Processing sheet with id=AC9, first strand: chain 'N' and resid 66 through 67 Processing sheet with id=AD1, first strand: chain 'N' and resid 90 through 96 Processing sheet with id=AD2, first strand: chain 'O' and resid 66 through 67 Processing sheet with id=AD3, first strand: chain 'O' and resid 90 through 96 Processing sheet with id=AD4, first strand: chain 'P' and resid 66 through 67 Processing sheet with id=AD5, first strand: chain 'P' and resid 90 through 96 Processing sheet with id=AD6, first strand: chain 'Q' and resid 66 through 67 Processing sheet with id=AD7, first strand: chain 'Q' and resid 90 through 96 Processing sheet with id=AD8, first strand: chain 'R' and resid 66 through 67 Processing sheet with id=AD9, first strand: chain 'R' and resid 90 through 96 Processing sheet with id=AE1, first strand: chain 'S' and resid 66 through 67 Processing sheet with id=AE2, first strand: chain 'S' and resid 90 through 96 Processing sheet with id=AE3, first strand: chain 'T' and resid 66 through 67 Processing sheet with id=AE4, first strand: chain 'T' and resid 90 through 96 Processing sheet with id=AE5, first strand: chain 'U' and resid 66 through 67 Processing sheet with id=AE6, first strand: chain 'U' and resid 90 through 96 Processing sheet with id=AE7, first strand: chain 'V' and resid 66 through 67 Processing sheet with id=AE8, first strand: chain 'V' and resid 90 through 96 Processing sheet with id=AE9, first strand: chain 'W' and resid 66 through 67 Processing sheet with id=AF1, first strand: chain 'W' and resid 90 through 96 1150 hydrogen bonds defined for protein. 3381 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7843 1.35 - 1.46: 4991 1.46 - 1.58: 11339 1.58 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 24311 Sorted by residual: bond pdb=" CG GLN K 109 " pdb=" CD GLN K 109 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.54e-01 bond pdb=" CG GLN F 109 " pdb=" CD GLN F 109 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.47e-01 bond pdb=" CG GLN J 109 " pdb=" CD GLN J 109 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.36e-01 bond pdb=" CG GLN O 109 " pdb=" CD GLN O 109 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.35e-01 bond pdb=" CG GLN P 109 " pdb=" CD GLN P 109 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.30e-01 ... (remaining 24306 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 32130 0.91 - 1.81: 682 1.81 - 2.72: 216 2.72 - 3.63: 92 3.63 - 4.54: 23 Bond angle restraints: 33143 Sorted by residual: angle pdb=" CB GLN E 109 " pdb=" CG GLN E 109 " pdb=" CD GLN E 109 " ideal model delta sigma weight residual 112.60 115.48 -2.88 1.70e+00 3.46e-01 2.87e+00 angle pdb=" CB GLN R 109 " pdb=" CG GLN R 109 " pdb=" CD GLN R 109 " ideal model delta sigma weight residual 112.60 115.47 -2.87 1.70e+00 3.46e-01 2.86e+00 angle pdb=" CB GLN H 109 " pdb=" CG GLN H 109 " pdb=" CD GLN H 109 " ideal model delta sigma weight residual 112.60 115.46 -2.86 1.70e+00 3.46e-01 2.84e+00 angle pdb=" CB GLN P 109 " pdb=" CG GLN P 109 " pdb=" CD GLN P 109 " ideal model delta sigma weight residual 112.60 115.46 -2.86 1.70e+00 3.46e-01 2.83e+00 angle pdb=" CB GLN N 109 " pdb=" CG GLN N 109 " pdb=" CD GLN N 109 " ideal model delta sigma weight residual 112.60 115.45 -2.85 1.70e+00 3.46e-01 2.81e+00 ... (remaining 33138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 12765 16.52 - 33.04: 1426 33.04 - 49.56: 391 49.56 - 66.07: 46 66.07 - 82.59: 115 Dihedral angle restraints: 14743 sinusoidal: 5382 harmonic: 9361 Sorted by residual: dihedral pdb=" CA GLU B 77 " pdb=" CB GLU B 77 " pdb=" CG GLU B 77 " pdb=" CD GLU B 77 " ideal model delta sinusoidal sigma weight residual 60.00 115.07 -55.07 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" CA GLU R 77 " pdb=" CB GLU R 77 " pdb=" CG GLU R 77 " pdb=" CD GLU R 77 " ideal model delta sinusoidal sigma weight residual 60.00 115.07 -55.07 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" CA GLU L 77 " pdb=" CB GLU L 77 " pdb=" CG GLU L 77 " pdb=" CD GLU L 77 " ideal model delta sinusoidal sigma weight residual 60.00 115.07 -55.07 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 14740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2396 0.026 - 0.052: 967 0.052 - 0.078: 412 0.078 - 0.104: 238 0.104 - 0.131: 173 Chirality restraints: 4186 Sorted by residual: chirality pdb=" CA ILE B 104 " pdb=" N ILE B 104 " pdb=" C ILE B 104 " pdb=" CB ILE B 104 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE F 104 " pdb=" N ILE F 104 " pdb=" C ILE F 104 " pdb=" CB ILE F 104 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE V 104 " pdb=" N ILE V 104 " pdb=" C ILE V 104 " pdb=" CB ILE V 104 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 4183 not shown) Planarity restraints: 4209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE S 10 " 0.004 2.00e-02 2.50e+03 7.66e-03 5.87e-01 pdb=" C ILE S 10 " -0.013 2.00e-02 2.50e+03 pdb=" O ILE S 10 " 0.005 2.00e-02 2.50e+03 pdb=" N GLU S 11 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE P 10 " 0.004 2.00e-02 2.50e+03 7.46e-03 5.56e-01 pdb=" C ILE P 10 " -0.013 2.00e-02 2.50e+03 pdb=" O ILE P 10 " 0.005 2.00e-02 2.50e+03 pdb=" N GLU P 11 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE W 10 " 0.004 2.00e-02 2.50e+03 7.42e-03 5.50e-01 pdb=" C ILE W 10 " -0.013 2.00e-02 2.50e+03 pdb=" O ILE W 10 " 0.005 2.00e-02 2.50e+03 pdb=" N GLU W 11 " 0.004 2.00e-02 2.50e+03 ... (remaining 4206 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 7980 2.83 - 3.35: 22886 3.35 - 3.87: 40923 3.87 - 4.38: 47391 4.38 - 4.90: 83514 Nonbonded interactions: 202694 Sorted by model distance: nonbonded pdb=" OG1 THR H 143 " pdb=" OD1 ASN H 149 " model vdw 2.318 3.040 nonbonded pdb=" OG1 THR V 143 " pdb=" OD1 ASN V 149 " model vdw 2.318 3.040 nonbonded pdb=" OG1 THR I 143 " pdb=" OD1 ASN I 149 " model vdw 2.318 3.040 nonbonded pdb=" OG1 THR R 143 " pdb=" OD1 ASN R 149 " model vdw 2.318 3.040 nonbonded pdb=" OG1 THR M 143 " pdb=" OD1 ASN M 149 " model vdw 2.318 3.040 ... (remaining 202689 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 20.590 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 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 : 0.002 0.019 24334 Z= 0.097 Angle : 0.416 4.536 33189 Z= 0.226 Chirality : 0.044 0.131 4186 Planarity : 0.003 0.017 4209 Dihedral : 17.574 82.593 8648 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.88 % Allowed : 26.36 % Favored : 72.76 % 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: 2.80 (0.15), residues: 3243 helix: 2.22 (0.17), residues: 1081 sheet: 0.79 (0.20), residues: 713 loop : 2.47 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 59 TYR 0.006 0.001 TYR D 33 PHE 0.004 0.001 PHE Q 142 TRP 0.004 0.001 TRP T 132 Details of bonding type rmsd covalent geometry : bond 0.00211 (24311) covalent geometry : angle 0.41622 (33143) SS BOND : bond 0.00084 ( 23) SS BOND : angle 0.38254 ( 46) hydrogen bonds : bond 0.18216 ( 1150) hydrogen bonds : angle 6.92051 ( 3381) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 616 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 VAL cc_start: 0.8742 (m) cc_final: 0.8460 (m) REVERT: A 136 SER cc_start: 0.8544 (t) cc_final: 0.8274 (p) REVERT: B 65 LYS cc_start: 0.8414 (mmtt) cc_final: 0.7720 (mttt) REVERT: B 77 GLU cc_start: 0.8336 (mp0) cc_final: 0.7999 (mp0) REVERT: C 67 LYS cc_start: 0.8535 (mttm) cc_final: 0.8316 (mtmm) REVERT: C 124 LEU cc_start: 0.9135 (mt) cc_final: 0.8883 (mp) REVERT: D 65 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8327 (mmtp) REVERT: E 103 ASP cc_start: 0.8694 (p0) cc_final: 0.8433 (p0) REVERT: I 70 THR cc_start: 0.8556 (p) cc_final: 0.8238 (m) REVERT: I 97 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7731 (mm-30) REVERT: I 116 LYS cc_start: 0.8061 (mmtm) cc_final: 0.7784 (mmtt) REVERT: K 29 GLN cc_start: 0.7969 (tt0) cc_final: 0.7512 (tt0) REVERT: L 103 ASP cc_start: 0.8283 (p0) cc_final: 0.7895 (p0) REVERT: M 29 GLN cc_start: 0.7881 (tt0) cc_final: 0.7350 (mt0) REVERT: M 70 THR cc_start: 0.8636 (p) cc_final: 0.8315 (m) REVERT: N 129 ASP cc_start: 0.7671 (m-30) cc_final: 0.7330 (m-30) REVERT: O 29 GLN cc_start: 0.7816 (tt0) cc_final: 0.7514 (mt0) REVERT: O 43 LEU cc_start: 0.9028 (tp) cc_final: 0.8805 (tp) REVERT: O 61 ILE cc_start: 0.8400 (mt) cc_final: 0.8197 (mt) REVERT: P 29 GLN cc_start: 0.7492 (tt0) cc_final: 0.7146 (mt0) REVERT: P 85 ASP cc_start: 0.7915 (p0) cc_final: 0.7667 (p0) REVERT: Q 116 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8377 (mmtp) REVERT: Q 125 ASN cc_start: 0.8845 (t0) cc_final: 0.8610 (t0) REVERT: Q 135 LYS cc_start: 0.7812 (tptt) cc_final: 0.7470 (tttm) outliers start: 23 outliers final: 3 residues processed: 638 average time/residue: 0.1771 time to fit residues: 175.8673 Evaluate side-chains 454 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 451 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain U residue 52 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.0980 chunk 298 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN B 47 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 149 ASN D 125 ASN D 149 ASN E 149 ASN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN G 109 GLN G 149 ASN H 149 ASN I 149 ASN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 149 ASN K 149 ASN L 29 GLN L 87 ASN L 149 ASN M 109 GLN M 149 ASN N 149 ASN O 87 ASN P 149 ASN ** R 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 125 ASN R 149 ASN S 29 GLN ** S 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 149 ASN T 149 ASN ** U 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 149 ASN V 149 ASN W 149 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.096751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.087939 restraints weight = 32811.889| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.17 r_work: 0.2816 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24334 Z= 0.142 Angle : 0.480 4.593 33189 Z= 0.259 Chirality : 0.047 0.159 4186 Planarity : 0.004 0.029 4209 Dihedral : 3.848 17.698 3430 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.77 % Allowed : 21.01 % Favored : 75.22 % 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: 2.96 (0.15), residues: 3243 helix: 2.33 (0.17), residues: 1081 sheet: 1.22 (0.20), residues: 713 loop : 2.37 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 59 TYR 0.012 0.001 TYR U 33 PHE 0.009 0.001 PHE W 108 TRP 0.009 0.001 TRP Q 132 Details of bonding type rmsd covalent geometry : bond 0.00329 (24311) covalent geometry : angle 0.47923 (33143) SS BOND : bond 0.00312 ( 23) SS BOND : angle 0.79433 ( 46) hydrogen bonds : bond 0.04004 ( 1150) hydrogen bonds : angle 4.76670 ( 3381) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 484 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 VAL cc_start: 0.8606 (m) cc_final: 0.8366 (m) REVERT: B 65 LYS cc_start: 0.8335 (mmtt) cc_final: 0.7347 (mttt) REVERT: C 67 LYS cc_start: 0.8533 (mttm) cc_final: 0.8044 (mtmm) REVERT: C 135 LYS cc_start: 0.8186 (tptt) cc_final: 0.7965 (mptt) REVERT: D 65 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8137 (mmtp) REVERT: I 91 VAL cc_start: 0.9214 (m) cc_final: 0.8998 (t) REVERT: I 97 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7722 (mm-30) REVERT: I 116 LYS cc_start: 0.8183 (mmtm) cc_final: 0.7909 (mmtt) REVERT: J 103 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7686 (p0) REVERT: K 91 VAL cc_start: 0.8999 (m) cc_final: 0.8729 (t) REVERT: L 135 LYS cc_start: 0.8233 (tmtt) cc_final: 0.7861 (mtpt) REVERT: M 29 GLN cc_start: 0.8084 (tt0) cc_final: 0.7651 (mt0) REVERT: N 87 ASN cc_start: 0.9156 (t0) cc_final: 0.8882 (t0) REVERT: P 85 ASP cc_start: 0.8180 (p0) cc_final: 0.7974 (p0) REVERT: Q 91 VAL cc_start: 0.9030 (m) cc_final: 0.8788 (t) REVERT: Q 97 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8010 (mt-10) REVERT: Q 135 LYS cc_start: 0.8029 (tptt) cc_final: 0.7740 (tttm) REVERT: R 135 LYS cc_start: 0.8410 (tptt) cc_final: 0.7865 (ttpp) REVERT: R 141 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8218 (ptm) REVERT: S 91 VAL cc_start: 0.9199 (m) cc_final: 0.8925 (t) REVERT: U 129 ASP cc_start: 0.7403 (m-30) cc_final: 0.7140 (m-30) REVERT: V 135 LYS cc_start: 0.8486 (mptt) cc_final: 0.8114 (mttt) REVERT: W 8 THR cc_start: 0.6749 (OUTLIER) cc_final: 0.6357 (m) REVERT: W 135 LYS cc_start: 0.8430 (tptt) cc_final: 0.8166 (mtpp) outliers start: 98 outliers final: 66 residues processed: 550 average time/residue: 0.1638 time to fit residues: 144.3282 Evaluate side-chains 513 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 444 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 141 MET Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 112 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 141 MET Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain V residue 97 GLU Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 112 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 284 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 226 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 105 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 109 GLN B 138 GLN B 149 ASN ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 31 GLN G 109 GLN H 109 GLN I 109 GLN J 109 GLN M 109 GLN O 29 GLN Q 149 ASN R 109 GLN S 109 GLN T 109 GLN U 29 GLN U 109 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.100171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.091381 restraints weight = 32466.928| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.16 r_work: 0.2872 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 24334 Z= 0.084 Angle : 0.412 4.452 33189 Z= 0.219 Chirality : 0.045 0.141 4186 Planarity : 0.003 0.021 4209 Dihedral : 3.469 14.966 3427 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 2.54 % Allowed : 22.09 % Favored : 75.38 % 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: 3.23 (0.15), residues: 3243 helix: 2.60 (0.17), residues: 1081 sheet: 1.52 (0.20), residues: 713 loop : 2.38 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 59 TYR 0.007 0.001 TYR G 33 PHE 0.005 0.001 PHE T 108 TRP 0.004 0.001 TRP L 132 Details of bonding type rmsd covalent geometry : bond 0.00178 (24311) covalent geometry : angle 0.41188 (33143) SS BOND : bond 0.00158 ( 23) SS BOND : angle 0.55495 ( 46) hydrogen bonds : bond 0.03085 ( 1150) hydrogen bonds : angle 4.24901 ( 3381) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 472 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LEU cc_start: 0.9124 (tp) cc_final: 0.8827 (tp) REVERT: B 65 LYS cc_start: 0.8335 (mmtt) cc_final: 0.7433 (mttt) REVERT: B 77 GLU cc_start: 0.8234 (mp0) cc_final: 0.7801 (mp0) REVERT: B 109 GLN cc_start: 0.6630 (mm-40) cc_final: 0.6357 (mm-40) REVERT: C 67 LYS cc_start: 0.8460 (mttm) cc_final: 0.8049 (mtmm) REVERT: D 65 LYS cc_start: 0.8602 (mmtt) cc_final: 0.8119 (mmtp) REVERT: I 97 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7747 (mm-30) REVERT: I 116 LYS cc_start: 0.8190 (mmtm) cc_final: 0.7918 (mmtt) REVERT: K 91 VAL cc_start: 0.8972 (m) cc_final: 0.8727 (t) REVERT: L 103 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7559 (p0) REVERT: L 135 LYS cc_start: 0.8221 (tmtt) cc_final: 0.7871 (mtpt) REVERT: M 7 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6340 (t80) REVERT: M 11 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8476 (tm-30) REVERT: M 29 GLN cc_start: 0.7840 (tt0) cc_final: 0.7457 (mt0) REVERT: N 87 ASN cc_start: 0.9160 (t0) cc_final: 0.8952 (t0) REVERT: O 7 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.6919 (t80) REVERT: O 43 LEU cc_start: 0.9060 (tp) cc_final: 0.8809 (tp) REVERT: O 148 ASP cc_start: 0.8775 (m-30) cc_final: 0.8268 (m-30) REVERT: Q 22 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8307 (mt) REVERT: Q 77 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8073 (mt-10) REVERT: Q 135 LYS cc_start: 0.8046 (tptt) cc_final: 0.7766 (tttm) REVERT: R 91 VAL cc_start: 0.9152 (m) cc_final: 0.8897 (t) REVERT: R 135 LYS cc_start: 0.8356 (tptt) cc_final: 0.7694 (ttpp) REVERT: S 7 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.7016 (t80) REVERT: S 91 VAL cc_start: 0.9241 (m) cc_final: 0.8980 (t) REVERT: U 10 ILE cc_start: 0.8495 (tt) cc_final: 0.8261 (mm) REVERT: V 77 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8236 (mt-10) REVERT: W 10 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7895 (mm) REVERT: W 135 LYS cc_start: 0.8423 (tptt) cc_final: 0.8139 (mtpp) outliers start: 66 outliers final: 44 residues processed: 519 average time/residue: 0.1629 time to fit residues: 135.9028 Evaluate side-chains 494 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 444 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain S residue 7 PHE Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 127 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 285 optimal weight: 9.9990 chunk 151 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 299 optimal weight: 3.9990 chunk 219 optimal weight: 0.4980 chunk 211 optimal weight: 5.9990 chunk 318 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 138 GLN B 149 ASN D 31 GLN D 125 ASN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 GLN H 149 ASN I 109 GLN J 31 GLN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN P 149 ASN Q 149 ASN U 138 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.093845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.085143 restraints weight = 32928.756| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.14 r_work: 0.2780 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 24334 Z= 0.191 Angle : 0.511 4.743 33189 Z= 0.277 Chirality : 0.049 0.185 4186 Planarity : 0.004 0.032 4209 Dihedral : 4.239 22.991 3427 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.08 % Allowed : 19.93 % Favored : 74.99 % 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: 2.78 (0.15), residues: 3243 helix: 2.24 (0.17), residues: 1081 sheet: 1.29 (0.19), residues: 713 loop : 2.10 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG T 126 TYR 0.010 0.001 TYR G 33 PHE 0.011 0.001 PHE E 142 TRP 0.011 0.002 TRP F 132 Details of bonding type rmsd covalent geometry : bond 0.00461 (24311) covalent geometry : angle 0.50857 (33143) SS BOND : bond 0.00323 ( 23) SS BOND : angle 1.30221 ( 46) hydrogen bonds : bond 0.04296 ( 1150) hydrogen bonds : angle 4.47704 ( 3381) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 436 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8208 (pt0) REVERT: B 65 LYS cc_start: 0.8312 (mmtt) cc_final: 0.7427 (mttt) REVERT: B 77 GLU cc_start: 0.8179 (mp0) cc_final: 0.7769 (mp0) REVERT: B 129 ASP cc_start: 0.7696 (t0) cc_final: 0.7457 (t0) REVERT: C 22 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8122 (mp) REVERT: D 65 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8086 (mmtp) REVERT: E 141 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8151 (ptt) REVERT: F 22 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8134 (mp) REVERT: I 97 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7746 (mm-30) REVERT: J 13 MET cc_start: 0.8525 (mmm) cc_final: 0.8321 (mmm) REVERT: J 22 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8095 (mp) REVERT: K 31 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7829 (pt0) REVERT: L 22 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8322 (mp) REVERT: L 135 LYS cc_start: 0.8193 (tmtt) cc_final: 0.7850 (mtpt) REVERT: M 7 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.5970 (t80) REVERT: M 22 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8136 (mp) REVERT: M 29 GLN cc_start: 0.8171 (tt0) cc_final: 0.7672 (mt0) REVERT: P 7 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7707 (t80) REVERT: P 22 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8364 (mp) REVERT: P 109 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7939 (mm110) REVERT: Q 22 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8339 (mp) REVERT: Q 55 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: Q 77 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8064 (mt-10) REVERT: Q 135 LYS cc_start: 0.8191 (tptt) cc_final: 0.7759 (tttm) REVERT: R 91 VAL cc_start: 0.9140 (m) cc_final: 0.8918 (t) REVERT: R 135 LYS cc_start: 0.8377 (tptt) cc_final: 0.7775 (ttpp) REVERT: S 22 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8373 (mp) REVERT: S 91 VAL cc_start: 0.9197 (m) cc_final: 0.8973 (t) REVERT: U 10 ILE cc_start: 0.8487 (tt) cc_final: 0.8258 (mm) REVERT: V 135 LYS cc_start: 0.8500 (mptt) cc_final: 0.8177 (mttt) REVERT: W 10 ILE cc_start: 0.8451 (mt) cc_final: 0.8225 (mm) REVERT: W 135 LYS cc_start: 0.8455 (tptt) cc_final: 0.8238 (mtpp) outliers start: 132 outliers final: 93 residues processed: 534 average time/residue: 0.1612 time to fit residues: 138.8771 Evaluate side-chains 527 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 420 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 135 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 31 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 31 GLN Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 141 MET Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 55 GLU Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 103 ASP Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 125 ASN Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 139 ASP Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 112 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 311 optimal weight: 0.9980 chunk 203 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 282 optimal weight: 0.9980 chunk 226 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 315 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 138 GLN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 GLN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN T 87 ASN U 138 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.094664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.085524 restraints weight = 32713.482| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.24 r_work: 0.2786 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24334 Z= 0.143 Angle : 0.468 4.655 33189 Z= 0.252 Chirality : 0.047 0.160 4186 Planarity : 0.003 0.029 4209 Dihedral : 4.092 26.285 3427 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.85 % Allowed : 19.85 % Favored : 75.30 % 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: 2.74 (0.15), residues: 3243 helix: 2.28 (0.17), residues: 1081 sheet: 1.15 (0.19), residues: 713 loop : 2.09 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 59 TYR 0.012 0.001 TYR G 33 PHE 0.007 0.001 PHE W 108 TRP 0.008 0.001 TRP F 132 Details of bonding type rmsd covalent geometry : bond 0.00337 (24311) covalent geometry : angle 0.46708 (33143) SS BOND : bond 0.00207 ( 23) SS BOND : angle 0.98037 ( 46) hydrogen bonds : bond 0.03770 ( 1150) hydrogen bonds : angle 4.31118 ( 3381) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 445 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8130 (pt0) REVERT: B 65 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7370 (mttt) REVERT: B 77 GLU cc_start: 0.8124 (mp0) cc_final: 0.7742 (mp0) REVERT: C 22 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8199 (mp) REVERT: D 65 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8024 (mmtp) REVERT: E 141 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8198 (ptt) REVERT: F 22 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8093 (mp) REVERT: I 97 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7708 (mm-30) REVERT: J 22 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8038 (mp) REVERT: K 22 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8002 (mp) REVERT: K 31 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7818 (pt0) REVERT: L 22 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8266 (mp) REVERT: L 135 LYS cc_start: 0.8212 (tmtt) cc_final: 0.7823 (mtpt) REVERT: M 7 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.5976 (t80) REVERT: M 22 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8061 (mp) REVERT: M 29 GLN cc_start: 0.8157 (tt0) cc_final: 0.7695 (mt0) REVERT: O 7 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7442 (t80) REVERT: P 7 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7735 (t80) REVERT: P 22 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8338 (mp) REVERT: Q 55 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: Q 77 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8022 (mt-10) REVERT: Q 135 LYS cc_start: 0.8229 (tptt) cc_final: 0.7683 (tttm) REVERT: R 135 LYS cc_start: 0.8419 (tptt) cc_final: 0.7755 (ttpp) REVERT: S 7 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.7223 (t80) REVERT: S 22 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8379 (mp) REVERT: S 91 VAL cc_start: 0.9195 (m) cc_final: 0.8989 (t) REVERT: U 10 ILE cc_start: 0.8497 (tt) cc_final: 0.8210 (mm) REVERT: V 135 LYS cc_start: 0.8491 (mptt) cc_final: 0.8099 (mttt) REVERT: W 10 ILE cc_start: 0.8454 (mt) cc_final: 0.8247 (mm) REVERT: W 135 LYS cc_start: 0.8451 (tptt) cc_final: 0.8193 (mtpp) outliers start: 126 outliers final: 94 residues processed: 538 average time/residue: 0.1584 time to fit residues: 138.1073 Evaluate side-chains 533 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 423 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 31 GLN Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 148 ASP Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 141 MET Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 55 GLU Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain S residue 7 PHE Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 87 ASN Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 125 ASN Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 112 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 191 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 chunk 182 optimal weight: 1.9990 chunk 75 optimal weight: 0.0030 chunk 155 optimal weight: 0.5980 chunk 121 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 260 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 309 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN G 109 GLN H 149 ASN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN P 149 ASN Q 87 ASN Q 149 ASN R 109 GLN T 87 ASN V 31 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.097866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.088760 restraints weight = 32626.666| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.24 r_work: 0.2835 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 24334 Z= 0.094 Angle : 0.424 4.695 33189 Z= 0.226 Chirality : 0.045 0.141 4186 Planarity : 0.003 0.025 4209 Dihedral : 3.702 23.169 3427 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 4.31 % Allowed : 20.74 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.95 (0.15), residues: 3243 helix: 2.52 (0.17), residues: 1081 sheet: 1.19 (0.19), residues: 713 loop : 2.20 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 59 TYR 0.007 0.001 TYR G 33 PHE 0.006 0.001 PHE T 108 TRP 0.005 0.001 TRP L 132 Details of bonding type rmsd covalent geometry : bond 0.00204 (24311) covalent geometry : angle 0.42400 (33143) SS BOND : bond 0.00305 ( 23) SS BOND : angle 0.60617 ( 46) hydrogen bonds : bond 0.03029 ( 1150) hydrogen bonds : angle 4.00646 ( 3381) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 445 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8129 (p0) cc_final: 0.7848 (p0) REVERT: A 109 GLN cc_start: 0.7739 (mm110) cc_final: 0.7507 (mm110) REVERT: A 125 ASN cc_start: 0.8168 (t0) cc_final: 0.7748 (t0) REVERT: B 65 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7388 (mttt) REVERT: B 77 GLU cc_start: 0.8162 (mp0) cc_final: 0.7631 (mp0) REVERT: C 22 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8185 (mp) REVERT: C 124 LEU cc_start: 0.8949 (mt) cc_final: 0.8734 (mp) REVERT: D 65 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8040 (mmtp) REVERT: H 31 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7172 (pt0) REVERT: I 97 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7745 (mm-30) REVERT: J 22 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8142 (mp) REVERT: J 67 LYS cc_start: 0.8746 (mmtt) cc_final: 0.8436 (mmtt) REVERT: K 31 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7678 (pt0) REVERT: K 91 VAL cc_start: 0.8992 (m) cc_final: 0.8749 (t) REVERT: L 22 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8267 (mp) REVERT: L 88 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8469 (mmmt) REVERT: L 103 ASP cc_start: 0.7964 (p0) cc_final: 0.7587 (p0) REVERT: L 129 ASP cc_start: 0.7543 (t0) cc_final: 0.7134 (t0) REVERT: L 135 LYS cc_start: 0.8180 (tmtt) cc_final: 0.7805 (mtpt) REVERT: M 7 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.6026 (t80) REVERT: M 22 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8025 (mp) REVERT: M 29 GLN cc_start: 0.7927 (tt0) cc_final: 0.7514 (mt0) REVERT: M 77 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7915 (mm-30) REVERT: N 87 ASN cc_start: 0.9112 (t0) cc_final: 0.8894 (t0) REVERT: O 7 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7401 (t80) REVERT: P 7 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7773 (t80) REVERT: Q 7 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7184 (t80) REVERT: Q 55 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: Q 77 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8090 (mt-10) REVERT: Q 135 LYS cc_start: 0.8196 (tptt) cc_final: 0.7629 (tttm) REVERT: R 7 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7167 (t80) REVERT: R 135 LYS cc_start: 0.8386 (tptt) cc_final: 0.7727 (ttpp) REVERT: S 7 PHE cc_start: 0.7460 (OUTLIER) cc_final: 0.7227 (t80) REVERT: S 22 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8402 (mp) REVERT: T 7 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7591 (t80) REVERT: T 135 LYS cc_start: 0.8591 (tppt) cc_final: 0.8325 (mptt) REVERT: U 10 ILE cc_start: 0.8477 (tt) cc_final: 0.8128 (mm) REVERT: V 7 PHE cc_start: 0.6365 (OUTLIER) cc_final: 0.5357 (m-80) REVERT: V 135 LYS cc_start: 0.8459 (mptt) cc_final: 0.8103 (mttt) REVERT: W 77 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7687 (mt-10) REVERT: W 135 LYS cc_start: 0.8465 (tptt) cc_final: 0.8188 (mtpp) outliers start: 112 outliers final: 78 residues processed: 532 average time/residue: 0.1542 time to fit residues: 131.7393 Evaluate side-chains 520 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 426 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 141 MET Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 148 ASP Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 7 PHE Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain Q residue 7 PHE Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 55 GLU Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 7 PHE Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain S residue 7 PHE Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 87 ASN Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 125 ASN Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 148 optimal weight: 2.9990 chunk 173 optimal weight: 0.3980 chunk 183 optimal weight: 0.0470 chunk 261 optimal weight: 9.9990 chunk 290 optimal weight: 0.8980 chunk 131 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 114 optimal weight: 0.6980 chunk 280 optimal weight: 0.0050 chunk 1 optimal weight: 2.9990 overall best weight: 0.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 47 ASN B 149 ASN D 31 GLN D 125 ASN G 109 GLN S 109 GLN V 31 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.101578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.092986 restraints weight = 32295.681| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.14 r_work: 0.2901 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 24334 Z= 0.078 Angle : 0.413 7.901 33189 Z= 0.218 Chirality : 0.045 0.138 4186 Planarity : 0.003 0.023 4209 Dihedral : 3.430 15.998 3427 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 3.42 % Allowed : 21.39 % Favored : 75.18 % 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: 3.13 (0.15), residues: 3243 helix: 2.71 (0.17), residues: 1081 sheet: 1.27 (0.19), residues: 713 loop : 2.27 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 59 TYR 0.004 0.000 TYR I 33 PHE 0.004 0.001 PHE G 142 TRP 0.005 0.001 TRP L 132 Details of bonding type rmsd covalent geometry : bond 0.00159 (24311) covalent geometry : angle 0.41127 (33143) SS BOND : bond 0.00065 ( 23) SS BOND : angle 1.02537 ( 46) hydrogen bonds : bond 0.02609 ( 1150) hydrogen bonds : angle 3.71240 ( 3381) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 472 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8142 (p0) cc_final: 0.7848 (p0) REVERT: A 125 ASN cc_start: 0.8139 (t0) cc_final: 0.7822 (t0) REVERT: B 31 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7954 (pt0) REVERT: B 65 LYS cc_start: 0.8332 (mmtt) cc_final: 0.7414 (mttt) REVERT: B 77 GLU cc_start: 0.8138 (mp0) cc_final: 0.7621 (mp0) REVERT: C 22 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8135 (mp) REVERT: D 65 LYS cc_start: 0.8646 (mmtt) cc_final: 0.8156 (mmtp) REVERT: H 31 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.7091 (pt0) REVERT: I 97 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7894 (mm-30) REVERT: J 67 LYS cc_start: 0.8722 (mmtt) cc_final: 0.8445 (mmtt) REVERT: K 31 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7635 (pt0) REVERT: K 91 VAL cc_start: 0.8970 (m) cc_final: 0.8738 (t) REVERT: L 88 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8452 (mmmt) REVERT: L 135 LYS cc_start: 0.8170 (tmtt) cc_final: 0.7848 (mtpt) REVERT: M 7 PHE cc_start: 0.6903 (OUTLIER) cc_final: 0.6152 (t80) REVERT: M 22 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7978 (mp) REVERT: M 29 GLN cc_start: 0.7734 (tt0) cc_final: 0.7359 (mt0) REVERT: N 7 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.6142 (m-80) REVERT: O 7 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7184 (t80) REVERT: O 129 ASP cc_start: 0.8301 (t70) cc_final: 0.7638 (t0) REVERT: P 7 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7683 (t80) REVERT: Q 7 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7320 (t80) REVERT: Q 77 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8124 (mt-10) REVERT: Q 91 VAL cc_start: 0.9064 (m) cc_final: 0.8703 (t) REVERT: Q 135 LYS cc_start: 0.8188 (tptt) cc_final: 0.7648 (tttm) REVERT: R 135 LYS cc_start: 0.8353 (tptt) cc_final: 0.7667 (ttpp) REVERT: S 7 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.7229 (t80) REVERT: T 7 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7538 (t80) REVERT: U 10 ILE cc_start: 0.8458 (tt) cc_final: 0.8052 (mm) REVERT: V 7 PHE cc_start: 0.6349 (OUTLIER) cc_final: 0.5366 (m-80) REVERT: V 97 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: V 109 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7609 (mm-40) REVERT: V 135 LYS cc_start: 0.8452 (mptt) cc_final: 0.8123 (mttt) REVERT: W 67 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8495 (mmmt) REVERT: W 77 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7660 (mt-10) REVERT: W 135 LYS cc_start: 0.8450 (tptt) cc_final: 0.8173 (mtpp) outliers start: 89 outliers final: 61 residues processed: 543 average time/residue: 0.1653 time to fit residues: 143.6747 Evaluate side-chains 520 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 445 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 7 PHE Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain Q residue 7 PHE Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain S residue 7 PHE Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 125 ASN Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 97 GLU Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 36 optimal weight: 10.0000 chunk 292 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 311 optimal weight: 0.9980 chunk 307 optimal weight: 0.0870 chunk 93 optimal weight: 6.9990 chunk 302 optimal weight: 10.0000 chunk 122 optimal weight: 0.2980 chunk 282 optimal weight: 1.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 149 ASN G 29 GLN G 109 GLN I 109 GLN M 109 GLN S 109 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.099671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.091045 restraints weight = 32355.493| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.13 r_work: 0.2868 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 24334 Z= 0.091 Angle : 0.426 6.892 33189 Z= 0.225 Chirality : 0.045 0.144 4186 Planarity : 0.003 0.026 4209 Dihedral : 3.514 15.816 3427 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 4.12 % Allowed : 20.43 % Favored : 75.45 % 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: 3.14 (0.15), residues: 3243 helix: 2.71 (0.17), residues: 1081 sheet: 1.29 (0.19), residues: 713 loop : 2.28 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 59 TYR 0.009 0.001 TYR I 33 PHE 0.005 0.001 PHE I 108 TRP 0.006 0.001 TRP F 132 Details of bonding type rmsd covalent geometry : bond 0.00198 (24311) covalent geometry : angle 0.42496 (33143) SS BOND : bond 0.00121 ( 23) SS BOND : angle 1.03791 ( 46) hydrogen bonds : bond 0.02930 ( 1150) hydrogen bonds : angle 3.71941 ( 3381) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 442 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8117 (p0) cc_final: 0.7809 (p0) REVERT: A 125 ASN cc_start: 0.8114 (t0) cc_final: 0.7792 (t0) REVERT: B 31 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7946 (pt0) REVERT: B 65 LYS cc_start: 0.8329 (mmtt) cc_final: 0.7403 (mttt) REVERT: B 77 GLU cc_start: 0.8116 (mp0) cc_final: 0.7604 (mp0) REVERT: C 22 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8110 (mp) REVERT: D 65 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8147 (mmtp) REVERT: E 98 ASP cc_start: 0.8425 (m-30) cc_final: 0.7762 (m-30) REVERT: H 31 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.7072 (pt0) REVERT: I 97 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7904 (mm-30) REVERT: J 67 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8515 (mmtt) REVERT: J 129 ASP cc_start: 0.7546 (m-30) cc_final: 0.6831 (t70) REVERT: K 31 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7700 (pt0) REVERT: K 91 VAL cc_start: 0.8942 (m) cc_final: 0.8683 (t) REVERT: L 22 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8223 (mp) REVERT: L 129 ASP cc_start: 0.7599 (t0) cc_final: 0.7188 (t0) REVERT: L 135 LYS cc_start: 0.8166 (tmtt) cc_final: 0.7855 (mtpt) REVERT: M 7 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.6121 (t80) REVERT: M 22 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7989 (mp) REVERT: M 29 GLN cc_start: 0.7854 (tt0) cc_final: 0.7442 (mt0) REVERT: N 7 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.6156 (m-80) REVERT: O 7 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7218 (t80) REVERT: P 7 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7731 (t80) REVERT: P 22 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8248 (mp) REVERT: Q 7 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7323 (t80) REVERT: Q 77 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8095 (mt-10) REVERT: Q 135 LYS cc_start: 0.8210 (tptt) cc_final: 0.7656 (tttm) REVERT: R 7 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.7137 (t80) REVERT: R 135 LYS cc_start: 0.8379 (tptt) cc_final: 0.7747 (ttpp) REVERT: S 7 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.7218 (t80) REVERT: T 7 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7653 (t80) REVERT: T 135 LYS cc_start: 0.8593 (tppt) cc_final: 0.8326 (mptt) REVERT: V 7 PHE cc_start: 0.6354 (OUTLIER) cc_final: 0.5396 (m-80) REVERT: V 97 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: V 109 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7629 (mm-40) REVERT: V 135 LYS cc_start: 0.8450 (mptt) cc_final: 0.8112 (mttt) REVERT: W 67 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8496 (mmmt) REVERT: W 77 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7691 (mt-10) REVERT: W 135 LYS cc_start: 0.8441 (tptt) cc_final: 0.8153 (mtpp) outliers start: 107 outliers final: 77 residues processed: 530 average time/residue: 0.1658 time to fit residues: 140.7695 Evaluate side-chains 532 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 438 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 141 MET Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 7 PHE Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 PHE Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 7 PHE Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain S residue 7 PHE Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 7 PHE Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 125 ASN Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 97 GLU Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 50 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 257 optimal weight: 8.9990 chunk 239 optimal weight: 0.4980 chunk 153 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 167 optimal weight: 0.5980 chunk 123 optimal weight: 10.0000 chunk 243 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 87 ASN F 31 GLN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 GLN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 GLN M 109 GLN ** S 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.094934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.086360 restraints weight = 32955.302| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.14 r_work: 0.2792 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24334 Z= 0.163 Angle : 0.494 7.215 33189 Z= 0.265 Chirality : 0.048 0.166 4186 Planarity : 0.003 0.035 4209 Dihedral : 4.064 25.389 3427 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.19 % Allowed : 20.35 % Favored : 75.45 % 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: 2.85 (0.15), residues: 3243 helix: 2.40 (0.17), residues: 1081 sheet: 1.17 (0.19), residues: 713 loop : 2.14 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 59 TYR 0.012 0.001 TYR G 33 PHE 0.008 0.001 PHE E 142 TRP 0.008 0.001 TRP F 132 Details of bonding type rmsd covalent geometry : bond 0.00389 (24311) covalent geometry : angle 0.49186 (33143) SS BOND : bond 0.00278 ( 23) SS BOND : angle 1.43497 ( 46) hydrogen bonds : bond 0.03865 ( 1150) hydrogen bonds : angle 4.09278 ( 3381) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 433 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.8384 (m) cc_final: 0.8106 (m) REVERT: A 85 ASP cc_start: 0.8085 (p0) cc_final: 0.7830 (p0) REVERT: A 125 ASN cc_start: 0.8172 (t0) cc_final: 0.7762 (t0) REVERT: B 31 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8122 (pt0) REVERT: B 65 LYS cc_start: 0.8313 (mmtt) cc_final: 0.7418 (mttt) REVERT: B 77 GLU cc_start: 0.8139 (mp0) cc_final: 0.7627 (mp0) REVERT: C 22 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8163 (mp) REVERT: D 65 LYS cc_start: 0.8608 (mmtt) cc_final: 0.8139 (mmtp) REVERT: E 98 ASP cc_start: 0.8448 (m-30) cc_final: 0.7798 (m-30) REVERT: I 97 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7794 (mm-30) REVERT: J 67 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8547 (mmtt) REVERT: J 129 ASP cc_start: 0.7556 (m-30) cc_final: 0.6940 (t70) REVERT: K 31 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7804 (pt0) REVERT: L 22 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8261 (mp) REVERT: L 135 LYS cc_start: 0.8188 (tmtt) cc_final: 0.7841 (mtpt) REVERT: M 7 PHE cc_start: 0.7037 (OUTLIER) cc_final: 0.6363 (t80) REVERT: M 22 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8090 (mp) REVERT: M 29 GLN cc_start: 0.8105 (tt0) cc_final: 0.7645 (mt0) REVERT: M 109 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6480 (mm110) REVERT: N 7 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.6229 (m-80) REVERT: O 7 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7584 (t80) REVERT: P 7 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7789 (t80) REVERT: P 22 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8310 (mp) REVERT: Q 77 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8072 (mt-10) REVERT: Q 135 LYS cc_start: 0.8222 (tptt) cc_final: 0.7682 (tttm) REVERT: R 7 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7439 (t80) REVERT: R 135 LYS cc_start: 0.8389 (tptt) cc_final: 0.7779 (ttpp) REVERT: S 7 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.7276 (t80) REVERT: S 22 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8420 (mp) REVERT: V 97 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: V 135 LYS cc_start: 0.8520 (mptt) cc_final: 0.8181 (mttt) REVERT: W 77 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7714 (mt-10) REVERT: W 135 LYS cc_start: 0.8466 (tptt) cc_final: 0.8225 (mtpp) outliers start: 109 outliers final: 87 residues processed: 519 average time/residue: 0.1543 time to fit residues: 128.8391 Evaluate side-chains 521 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 419 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 141 MET Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 148 ASP Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 109 GLN Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 7 PHE Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 7 PHE Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain S residue 7 PHE Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 125 ASN Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 97 GLU Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 129 optimal weight: 0.9980 chunk 302 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 chunk 301 optimal weight: 0.9990 chunk 318 optimal weight: 0.6980 chunk 107 optimal weight: 0.0980 chunk 297 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN G 29 GLN G 109 GLN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN ** S 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.098516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.089537 restraints weight = 32415.729| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.23 r_work: 0.2844 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24334 Z= 0.091 Angle : 0.433 5.647 33189 Z= 0.230 Chirality : 0.045 0.143 4186 Planarity : 0.003 0.023 4209 Dihedral : 3.698 22.619 3427 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 3.62 % Allowed : 21.09 % Favored : 75.30 % 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: 3.01 (0.15), residues: 3243 helix: 2.59 (0.17), residues: 1081 sheet: 1.24 (0.19), residues: 713 loop : 2.21 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 59 TYR 0.007 0.001 TYR I 33 PHE 0.012 0.001 PHE M 108 TRP 0.004 0.001 TRP O 132 Details of bonding type rmsd covalent geometry : bond 0.00196 (24311) covalent geometry : angle 0.43233 (33143) SS BOND : bond 0.00090 ( 23) SS BOND : angle 0.91911 ( 46) hydrogen bonds : bond 0.02967 ( 1150) hydrogen bonds : angle 3.83763 ( 3381) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 435 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8039 (p0) cc_final: 0.7699 (p0) REVERT: A 109 GLN cc_start: 0.7874 (mm110) cc_final: 0.7476 (mm110) REVERT: A 125 ASN cc_start: 0.8107 (t0) cc_final: 0.7729 (t0) REVERT: B 31 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7996 (pt0) REVERT: B 65 LYS cc_start: 0.8284 (mmtt) cc_final: 0.7354 (mttt) REVERT: B 77 GLU cc_start: 0.8087 (mp0) cc_final: 0.7592 (mp0) REVERT: C 22 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8187 (mp) REVERT: D 65 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8105 (mmtp) REVERT: I 97 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7790 (mm-30) REVERT: J 129 ASP cc_start: 0.7592 (m-30) cc_final: 0.6859 (t70) REVERT: K 31 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7675 (pt0) REVERT: K 91 VAL cc_start: 0.8925 (m) cc_final: 0.8645 (t) REVERT: L 88 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8484 (mmmt) REVERT: L 103 ASP cc_start: 0.8064 (m-30) cc_final: 0.7834 (m-30) REVERT: L 135 LYS cc_start: 0.8154 (tmtt) cc_final: 0.7777 (mtpt) REVERT: L 148 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7389 (p0) REVERT: M 7 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6198 (t80) REVERT: M 22 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8009 (mp) REVERT: M 29 GLN cc_start: 0.7836 (tt0) cc_final: 0.7427 (mt0) REVERT: N 7 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.6221 (m-80) REVERT: O 7 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7408 (t80) REVERT: O 129 ASP cc_start: 0.8297 (t70) cc_final: 0.7866 (t70) REVERT: P 7 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7764 (t80) REVERT: P 22 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8263 (mp) REVERT: Q 77 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8092 (mt-10) REVERT: Q 135 LYS cc_start: 0.8178 (tptt) cc_final: 0.7597 (tttm) REVERT: R 7 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7224 (t80) REVERT: R 135 LYS cc_start: 0.8354 (tptt) cc_final: 0.7646 (ttpp) REVERT: S 22 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8403 (mp) REVERT: T 135 LYS cc_start: 0.8567 (tppt) cc_final: 0.8291 (mptt) REVERT: V 7 PHE cc_start: 0.6367 (OUTLIER) cc_final: 0.5437 (m-80) REVERT: V 135 LYS cc_start: 0.8485 (mptt) cc_final: 0.8118 (mttt) REVERT: W 77 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7648 (mt-10) REVERT: W 135 LYS cc_start: 0.8472 (tptt) cc_final: 0.8177 (mtpp) outliers start: 94 outliers final: 76 residues processed: 508 average time/residue: 0.1598 time to fit residues: 130.0350 Evaluate side-chains 516 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 427 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 109 GLN Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 148 ASP Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 7 PHE Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 7 PHE Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 125 ASN Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 10 ILE Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 78 THR Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 221 optimal weight: 5.9990 chunk 287 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 210 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 313 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 239 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 138 GLN E 31 GLN E 149 ASN G 29 GLN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 149 ASN Q 149 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.093324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.084793 restraints weight = 33044.683| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.14 r_work: 0.2774 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24334 Z= 0.204 Angle : 0.539 7.083 33189 Z= 0.290 Chirality : 0.050 0.168 4186 Planarity : 0.004 0.041 4209 Dihedral : 4.292 29.848 3427 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.12 % Allowed : 20.93 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.15), residues: 3243 helix: 2.25 (0.17), residues: 1081 sheet: 1.03 (0.19), residues: 713 loop : 1.98 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 59 TYR 0.012 0.001 TYR G 33 PHE 0.011 0.001 PHE E 142 TRP 0.011 0.001 TRP F 132 Details of bonding type rmsd covalent geometry : bond 0.00496 (24311) covalent geometry : angle 0.53549 (33143) SS BOND : bond 0.00341 ( 23) SS BOND : angle 1.62889 ( 46) hydrogen bonds : bond 0.04248 ( 1150) hydrogen bonds : angle 4.21679 ( 3381) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5232.92 seconds wall clock time: 91 minutes 6.10 seconds (5466.10 seconds total)