Starting phenix.real_space_refine on Fri May 23 00:17:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ewx_50025/05_2025/9ewx_50025.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ewx_50025/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ewx_50025/05_2025/9ewx_50025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ewx_50025/05_2025/9ewx_50025.map" model { file = "/net/cci-nas-00/data/ceres_data/9ewx_50025/05_2025/9ewx_50025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ewx_50025/05_2025/9ewx_50025.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V Time building chain proxies: 6.44, per 1000 atoms: 0.27 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 C 134 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 147 " distance=2.03 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 147 " distance=2.03 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 147 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 147 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 147 " distance=2.03 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 147 " distance=2.03 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 147 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 147 " distance=2.03 Simple disulfide: pdb=" SG CYS O 134 " - pdb=" SG CYS O 147 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 147 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 134 " - pdb=" SG CYS Q 147 " distance=2.03 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 147 " distance=2.03 Simple disulfide: pdb=" SG CYS S 134 " - pdb=" SG CYS S 147 " distance=2.03 Simple disulfide: pdb=" SG CYS R 134 " - pdb=" SG CYS R 147 " distance=2.03 Simple disulfide: pdb=" SG CYS U 134 " - pdb=" SG CYS U 147 " distance=2.03 Simple disulfide: pdb=" SG CYS T 134 " - pdb=" SG CYS T 147 " distance=2.03 Simple disulfide: pdb=" SG CYS W 134 " - pdb=" SG CYS W 147 " distance=2.03 Simple disulfide: pdb=" SG CYS V 134 " - pdb=" SG CYS V 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: 5.54 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 2.90 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: 7.32 Time building geometry restraints manager: 6.59 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: 0.22 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' } 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: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 43.230 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.260 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.004 0.001 TRP T 132 PHE 0.004 0.001 PHE Q 142 TYR 0.006 0.001 TYR D 33 ARG 0.001 0.000 ARG L 59 Details of bonding type rmsd hydrogen bonds : bond 0.18216 ( 1150) hydrogen bonds : angle 6.92051 ( 3381) SS BOND : bond 0.00084 ( 23) SS BOND : angle 0.38254 ( 46) covalent geometry : bond 0.00211 (24311) covalent geometry : angle 0.41622 (33143) *********************** 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 : 2.433 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: 0.8461 (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 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: 0.3503 time to fit residues: 345.1418 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 : 2.602 ------------------------------------------------------------------------------- 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 271 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 252 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 153 optimal weight: 0.0970 chunk 187 optimal weight: 0.5980 chunk 292 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN B 29 GLN B 47 ASN B 149 ASN ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 149 ASN D 125 ASN D 149 ASN E 31 GLN 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 J 149 ASN K 29 GLN K 149 ASN L 29 GLN L 87 ASN L 149 ASN M 29 GLN M 149 ASN N 149 ASN O 87 ASN O 149 ASN P 149 ASN Q 29 GLN Q 149 ASN ** R 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN S 29 GLN ** S 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 149 ASN T 149 ASN U 29 GLN U 149 ASN V 149 ASN W 149 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.100801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.092089 restraints weight = 32285.897| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.16 r_work: 0.2882 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 24334 Z= 0.096 Angle : 0.439 4.568 33189 Z= 0.234 Chirality : 0.045 0.141 4186 Planarity : 0.003 0.021 4209 Dihedral : 3.527 14.784 3430 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.54 % Allowed : 21.55 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.15), residues: 3243 helix: 2.46 (0.17), residues: 1081 sheet: 1.33 (0.20), residues: 713 loop : 2.50 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 132 PHE 0.008 0.001 PHE R 108 TYR 0.009 0.001 TYR U 33 ARG 0.002 0.000 ARG D 59 Details of bonding type rmsd hydrogen bonds : bond 0.03317 ( 1150) hydrogen bonds : angle 4.59808 ( 3381) SS BOND : bond 0.00240 ( 23) SS BOND : angle 0.49201 ( 46) covalent geometry : bond 0.00210 (24311) covalent geometry : angle 0.43881 (33143) *********************** 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 587 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 495 time to evaluate : 2.691 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: A 82 VAL cc_start: 0.8575 (m) cc_final: 0.8308 (m) REVERT: B 65 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7363 (mttt) REVERT: D 65 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8126 (mmtp) REVERT: I 65 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8262 (mmtm) REVERT: I 70 THR cc_start: 0.8666 (p) cc_final: 0.8458 (m) REVERT: I 97 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7714 (mm-30) REVERT: I 116 LYS cc_start: 0.8158 (mmtm) cc_final: 0.7901 (mmtt) REVERT: I 148 ASP cc_start: 0.7979 (m-30) cc_final: 0.7718 (m-30) REVERT: L 135 LYS cc_start: 0.8206 (tmtt) cc_final: 0.7856 (mtpt) REVERT: M 29 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7434 (mt0) REVERT: N 87 ASN cc_start: 0.9131 (t0) cc_final: 0.8915 (t0) REVERT: N 129 ASP cc_start: 0.7696 (m-30) cc_final: 0.7418 (m-30) REVERT: O 43 LEU cc_start: 0.9074 (tp) cc_final: 0.8798 (tp) REVERT: O 129 ASP cc_start: 0.8216 (t70) cc_final: 0.8002 (t70) REVERT: P 135 LYS cc_start: 0.8375 (mmtt) cc_final: 0.7809 (mptt) REVERT: Q 135 LYS cc_start: 0.8096 (tptt) cc_final: 0.7798 (tttm) REVERT: R 135 LYS cc_start: 0.8346 (tptt) cc_final: 0.7821 (ttpp) REVERT: R 141 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8244 (ptm) REVERT: S 91 VAL cc_start: 0.9216 (m) cc_final: 0.8916 (t) REVERT: W 8 THR cc_start: 0.6828 (OUTLIER) cc_final: 0.6447 (m) REVERT: W 91 VAL cc_start: 0.9073 (m) cc_final: 0.8759 (t) REVERT: W 135 LYS cc_start: 0.8365 (tptt) cc_final: 0.8091 (mtpp) outliers start: 92 outliers final: 56 residues processed: 551 average time/residue: 0.3268 time to fit residues: 285.1988 Evaluate side-chains 503 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 444 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 110 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 19 ILE 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 85 ASP Chi-restraints excluded: chain I residue 112 THR 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 8 THR 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 85 ASP Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 112 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 82 VAL Chi-restraints excluded: chain R residue 141 MET 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 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 193 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 318 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 305 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 138 GLN B 149 ASN ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 149 ASN F 87 ASN F 149 ASN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN H 31 GLN H 109 GLN H 149 ASN I 149 ASN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 GLN K 149 ASN L 149 ASN ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 149 ASN O 29 GLN O 149 ASN P 29 GLN P 149 ASN Q 149 ASN R 109 GLN R 125 ASN R 149 ASN S 109 GLN T 109 GLN T 149 ASN U 109 GLN U 138 GLN U 149 ASN W 149 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.090382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.081806 restraints weight = 33334.910| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.13 r_work: 0.2720 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 24334 Z= 0.361 Angle : 0.665 5.481 33189 Z= 0.364 Chirality : 0.056 0.233 4186 Planarity : 0.005 0.048 4209 Dihedral : 4.979 30.090 3427 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.58 % Allowed : 18.81 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.15), residues: 3243 helix: 1.69 (0.16), residues: 1081 sheet: 1.18 (0.19), residues: 713 loop : 1.81 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 132 PHE 0.019 0.002 PHE E 142 TYR 0.014 0.002 TYR Q 33 ARG 0.006 0.001 ARG Q 59 Details of bonding type rmsd hydrogen bonds : bond 0.05557 ( 1150) hydrogen bonds : angle 4.94148 ( 3381) SS BOND : bond 0.00674 ( 23) SS BOND : angle 2.24724 ( 46) covalent geometry : bond 0.00890 (24311) covalent geometry : angle 0.66012 (33143) *********************** 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 572 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 427 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.8398 (m) cc_final: 0.8124 (m) REVERT: B 22 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8598 (mp) REVERT: B 31 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8227 (pt0) REVERT: B 47 ASN cc_start: 0.9017 (m-40) cc_final: 0.8779 (m-40) REVERT: B 65 LYS cc_start: 0.8333 (mmtt) cc_final: 0.7417 (mttt) REVERT: B 77 GLU cc_start: 0.8231 (mp0) cc_final: 0.7991 (mp0) REVERT: C 22 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8091 (mp) REVERT: D 65 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8158 (mmtp) REVERT: E 141 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8190 (ptt) REVERT: F 22 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8177 (mp) REVERT: G 103 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7318 (p0) REVERT: H 22 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8479 (mp) REVERT: I 97 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7686 (mm-30) REVERT: J 22 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8111 (mp) REVERT: J 129 ASP cc_start: 0.7340 (m-30) cc_final: 0.6771 (t70) REVERT: K 31 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7891 (pt0) REVERT: L 22 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8318 (mp) REVERT: L 135 LYS cc_start: 0.8211 (tmtt) cc_final: 0.7820 (mtpt) REVERT: M 7 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.7204 (t80) REVERT: M 22 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8163 (mp) REVERT: M 135 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8518 (tttp) REVERT: N 22 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8538 (mp) REVERT: N 129 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7481 (m-30) REVERT: O 7 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7610 (t80) REVERT: P 22 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8361 (mp) REVERT: P 135 LYS cc_start: 0.8380 (mmtt) cc_final: 0.8060 (ttmt) REVERT: Q 22 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8344 (mp) REVERT: Q 87 ASN cc_start: 0.8753 (t0) cc_final: 0.8485 (t0) REVERT: Q 135 LYS cc_start: 0.8278 (tptt) cc_final: 0.7754 (tttm) REVERT: R 135 LYS cc_start: 0.8478 (tptt) cc_final: 0.7858 (ttpp) REVERT: R 141 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8266 (ptm) REVERT: S 22 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8409 (mp) REVERT: V 109 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8255 (mm-40) REVERT: V 135 LYS cc_start: 0.8509 (mptt) cc_final: 0.8164 (mttt) REVERT: W 135 LYS cc_start: 0.8479 (tptt) cc_final: 0.8214 (ttpp) outliers start: 145 outliers final: 97 residues processed: 531 average time/residue: 0.3296 time to fit residues: 278.9236 Evaluate side-chains 521 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 405 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR 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 B residue 22 LEU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 80 VAL 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 80 VAL 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 70 THR 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 76 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 76 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 22 LEU Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain K residue 29 GLN 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 78 THR Chi-restraints excluded: chain L residue 112 THR 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 8 THR Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 129 ASP 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 P residue 8 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 82 VAL 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 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 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 T residue 141 MET 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 201 optimal weight: 0.9990 chunk 232 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 chunk 282 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 236 optimal weight: 5.9990 chunk 225 optimal weight: 0.9990 chunk 319 optimal weight: 0.9980 chunk 173 optimal weight: 0.3980 chunk 318 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN D 109 GLN D 125 ASN G 109 GLN G 149 ASN H 109 GLN I 149 ASN J 109 GLN L 29 GLN M 29 GLN M 109 GLN M 149 ASN Q 149 ASN U 138 GLN V 31 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.095802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.087902 restraints weight = 32621.794| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 0.96 r_work: 0.2839 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2567 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= 0.093 Angle : 0.431 4.524 33189 Z= 0.232 Chirality : 0.046 0.142 4186 Planarity : 0.003 0.028 4209 Dihedral : 3.947 24.085 3427 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 3.23 % Allowed : 21.28 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.15), residues: 3243 helix: 2.36 (0.17), residues: 1081 sheet: 1.28 (0.19), residues: 713 loop : 2.09 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 132 PHE 0.006 0.001 PHE K 108 TYR 0.008 0.001 TYR K 30 ARG 0.003 0.000 ARG P 59 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 1150) hydrogen bonds : angle 4.28671 ( 3381) SS BOND : bond 0.00254 ( 23) SS BOND : angle 0.56101 ( 46) covalent geometry : bond 0.00196 (24311) covalent geometry : angle 0.43045 (33143) *********************** 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 550 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 466 time to evaluate : 2.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8150 (p0) cc_final: 0.7840 (p0) REVERT: B 65 LYS cc_start: 0.8349 (mmtt) cc_final: 0.7441 (mttt) REVERT: B 77 GLU cc_start: 0.8158 (mp0) cc_final: 0.7643 (mp0) REVERT: C 77 GLU cc_start: 0.8277 (mp0) cc_final: 0.7850 (mp0) REVERT: D 65 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8157 (mmtp) REVERT: E 141 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8180 (ptt) REVERT: G 85 ASP cc_start: 0.8250 (p0) cc_final: 0.7961 (p0) REVERT: I 97 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7762 (mm-30) REVERT: J 129 ASP cc_start: 0.7173 (m-30) cc_final: 0.6719 (t70) REVERT: K 31 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7702 (pt0) REVERT: L 103 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7512 (p0) REVERT: L 135 LYS cc_start: 0.8172 (tmtt) cc_final: 0.7853 (mtpt) REVERT: M 7 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.7046 (t80) REVERT: M 135 LYS cc_start: 0.8838 (mmtt) cc_final: 0.8502 (tttp) REVERT: N 129 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7396 (m-30) REVERT: O 22 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8298 (mp) REVERT: O 129 ASP cc_start: 0.8415 (t70) cc_final: 0.8073 (t0) REVERT: P 135 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8135 (tttp) REVERT: Q 77 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7945 (mt-10) REVERT: Q 135 LYS cc_start: 0.8193 (tptt) cc_final: 0.7744 (tttm) REVERT: R 135 LYS cc_start: 0.8380 (tptt) cc_final: 0.7793 (ttpp) REVERT: S 7 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.7216 (t80) REVERT: V 103 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7786 (p0) REVERT: V 135 LYS cc_start: 0.8530 (mptt) cc_final: 0.8223 (mttt) REVERT: W 10 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8207 (mm) REVERT: W 91 VAL cc_start: 0.8981 (m) cc_final: 0.8660 (t) REVERT: W 135 LYS cc_start: 0.8440 (tptt) cc_final: 0.8239 (mtpp) outliers start: 84 outliers final: 56 residues processed: 528 average time/residue: 0.3295 time to fit residues: 277.0327 Evaluate side-chains 507 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 442 time to evaluate : 2.440 ------------------------------------------------------------------------------- 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 C residue 73 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 73 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 29 GLN Chi-restraints excluded: chain F 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 78 THR Chi-restraints excluded: chain I residue 85 ASP 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 29 GLN Chi-restraints excluded: chain L residue 103 ASP 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 112 THR Chi-restraints excluded: chain M residue 141 MET Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 129 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 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 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 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 8 THR Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 141 MET Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain V residue 31 GLN Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 103 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 175 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 233 optimal weight: 0.5980 chunk 313 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 252 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 193 optimal weight: 8.9990 chunk 267 optimal weight: 4.9990 chunk 234 optimal weight: 0.0980 chunk 265 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN B 47 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 149 ASN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 GLN I 109 GLN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN R 109 GLN S 109 GLN V 31 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.095912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.087335 restraints weight = 32798.490| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.14 r_work: 0.2812 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 24334 Z= 0.112 Angle : 0.441 4.584 33189 Z= 0.237 Chirality : 0.046 0.149 4186 Planarity : 0.003 0.027 4209 Dihedral : 3.899 24.262 3427 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.04 % Allowed : 20.47 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.15), residues: 3243 helix: 2.43 (0.17), residues: 1081 sheet: 1.16 (0.19), residues: 713 loop : 2.09 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 132 PHE 0.006 0.001 PHE B 108 TYR 0.007 0.001 TYR G 33 ARG 0.003 0.000 ARG S 126 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 1150) hydrogen bonds : angle 4.15755 ( 3381) SS BOND : bond 0.00147 ( 23) SS BOND : angle 0.83800 ( 46) covalent geometry : bond 0.00255 (24311) covalent geometry : angle 0.44047 (33143) *********************** 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 551 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 446 time to evaluate : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8120 (p0) cc_final: 0.7823 (p0) REVERT: A 125 ASN cc_start: 0.8264 (t0) cc_final: 0.7844 (t0) REVERT: B 65 LYS cc_start: 0.8349 (mmtt) cc_final: 0.7461 (mttt) REVERT: B 77 GLU cc_start: 0.8204 (mp0) cc_final: 0.7708 (mp0) REVERT: C 22 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8208 (mp) REVERT: D 65 LYS cc_start: 0.8630 (mmtt) cc_final: 0.8127 (mmtp) REVERT: E 141 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8188 (ptt) REVERT: I 97 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7748 (mm-30) REVERT: J 22 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8044 (mp) REVERT: J 129 ASP cc_start: 0.7172 (m-30) cc_final: 0.6736 (t70) REVERT: K 31 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7726 (pt0) REVERT: L 103 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7490 (p0) REVERT: L 135 LYS cc_start: 0.8194 (tmtt) cc_final: 0.7842 (mtpt) REVERT: M 7 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.7082 (t80) REVERT: M 22 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8097 (mp) REVERT: N 87 ASN cc_start: 0.9106 (t0) cc_final: 0.8859 (t0) REVERT: N 129 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7397 (m-30) REVERT: O 7 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7439 (t80) REVERT: O 129 ASP cc_start: 0.8457 (t70) cc_final: 0.8027 (t0) REVERT: P 7 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7780 (t80) REVERT: P 135 LYS cc_start: 0.8389 (mmtt) cc_final: 0.8154 (tttp) REVERT: Q 77 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8071 (mt-10) REVERT: Q 135 LYS cc_start: 0.8224 (tptt) cc_final: 0.7735 (tttm) REVERT: R 135 LYS cc_start: 0.8395 (tptt) cc_final: 0.7718 (ttpp) REVERT: S 7 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.7249 (t80) REVERT: V 103 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7877 (p0) REVERT: V 135 LYS cc_start: 0.8544 (mptt) cc_final: 0.8172 (mttt) REVERT: W 10 ILE cc_start: 0.8494 (mt) cc_final: 0.8257 (mm) outliers start: 105 outliers final: 73 residues processed: 524 average time/residue: 0.3225 time to fit residues: 271.3192 Evaluate side-chains 519 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 434 time to evaluate : 2.478 ------------------------------------------------------------------------------- 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 29 GLN Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 73 SER 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 29 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G 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 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 K residue 8 THR Chi-restraints excluded: chain K residue 29 GLN 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 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 92 ILE Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 129 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 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 8 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 76 THR 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 129 ASP 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 8 THR 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 112 THR Chi-restraints excluded: chain T residue 125 ASN Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 103 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 139 optimal weight: 8.9990 chunk 298 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 282 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN B 47 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN H 109 GLN I 149 ASN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN V 31 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.091216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.083523 restraints weight = 33031.366| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 0.92 r_work: 0.2768 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24334 Z= 0.218 Angle : 0.536 4.839 33189 Z= 0.291 Chirality : 0.050 0.177 4186 Planarity : 0.004 0.036 4209 Dihedral : 4.468 31.970 3427 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.04 % Allowed : 19.32 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.15), residues: 3243 helix: 2.10 (0.17), residues: 1081 sheet: 0.95 (0.19), residues: 713 loop : 1.84 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 132 PHE 0.010 0.001 PHE E 142 TYR 0.015 0.001 TYR G 33 ARG 0.004 0.001 ARG P 59 Details of bonding type rmsd hydrogen bonds : bond 0.04399 ( 1150) hydrogen bonds : angle 4.41139 ( 3381) SS BOND : bond 0.00443 ( 23) SS BOND : angle 1.48017 ( 46) covalent geometry : bond 0.00532 (24311) covalent geometry : angle 0.53369 (33143) *********************** 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 544 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 413 time to evaluate : 2.419 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: A 58 SER cc_start: 0.8358 (m) cc_final: 0.8078 (m) REVERT: A 125 ASN cc_start: 0.8300 (t0) cc_final: 0.7917 (t0) REVERT: B 29 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6948 (tt0) REVERT: B 31 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8190 (pt0) REVERT: B 65 LYS cc_start: 0.8402 (mmtt) cc_final: 0.7527 (mttt) REVERT: B 77 GLU cc_start: 0.8221 (mp0) cc_final: 0.7782 (mp0) REVERT: C 22 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8172 (mp) REVERT: C 124 LEU cc_start: 0.9049 (mt) cc_final: 0.8821 (mp) REVERT: D 65 LYS cc_start: 0.8665 (mmtt) cc_final: 0.8218 (mmtp) REVERT: E 141 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8222 (ptt) REVERT: I 97 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7799 (mm-30) REVERT: J 22 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8058 (mp) REVERT: J 129 ASP cc_start: 0.7252 (m-30) cc_final: 0.6933 (t70) REVERT: K 31 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7764 (pt0) REVERT: L 22 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8299 (mp) REVERT: L 103 ASP cc_start: 0.7891 (p0) cc_final: 0.7423 (p0) REVERT: L 135 LYS cc_start: 0.8179 (tmtt) cc_final: 0.7868 (mtpt) REVERT: M 7 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.7187 (t80) REVERT: M 22 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8180 (mp) REVERT: M 135 LYS cc_start: 0.8847 (mmtt) cc_final: 0.8540 (tttp) REVERT: N 129 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: O 7 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7708 (t80) REVERT: O 129 ASP cc_start: 0.8365 (t70) cc_final: 0.7851 (t0) REVERT: P 22 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8366 (mp) REVERT: P 135 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8172 (tttp) REVERT: Q 31 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8011 (pt0) REVERT: Q 77 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8028 (mt-10) REVERT: Q 135 LYS cc_start: 0.8255 (tptt) cc_final: 0.7768 (tttm) REVERT: R 135 LYS cc_start: 0.8447 (tptt) cc_final: 0.7892 (ttpp) REVERT: S 22 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8389 (mp) REVERT: S 103 ASP cc_start: 0.8199 (p0) cc_final: 0.7982 (p0) REVERT: T 31 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8242 (pt0) REVERT: V 135 LYS cc_start: 0.8509 (mptt) cc_final: 0.8241 (mttt) REVERT: W 10 ILE cc_start: 0.8661 (mt) cc_final: 0.8460 (mm) outliers start: 131 outliers final: 100 residues processed: 509 average time/residue: 0.3311 time to fit residues: 270.1255 Evaluate side-chains 522 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 407 time to evaluate : 2.688 ------------------------------------------------------------------------------- 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 29 GLN Chi-restraints excluded: chain B residue 31 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 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 112 THR Chi-restraints excluded: chain E residue 141 MET 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 F residue 141 MET 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 73 SER Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 29 GLN 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 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 110 THR 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 N residue 129 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 8 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 31 GLN 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 76 THR 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 129 ASP Chi-restraints excluded: chain R residue 148 ASP 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 S residue 141 MET Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 31 GLN 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 112 THR Chi-restraints excluded: chain T residue 125 ASN Chi-restraints excluded: chain T residue 141 MET Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 74 THR 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 85 ASP Chi-restraints excluded: chain V residue 91 VAL Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 112 THR 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 82 VAL Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 135 LYS Chi-restraints excluded: chain W residue 148 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 126 optimal weight: 0.9990 chunk 208 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 320 optimal weight: 0.8980 chunk 317 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN B 47 ASN B 109 GLN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN G 109 GLN H 31 GLN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 ASN M 109 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.095257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.087507 restraints weight = 32554.625| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 0.94 r_work: 0.2830 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2754 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= 0.105 Angle : 0.438 4.596 33189 Z= 0.235 Chirality : 0.046 0.145 4186 Planarity : 0.003 0.029 4209 Dihedral : 3.906 27.439 3427 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.23 % Allowed : 20.70 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.15), residues: 3243 helix: 2.42 (0.17), residues: 1081 sheet: 0.98 (0.19), residues: 713 loop : 2.02 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 132 PHE 0.006 0.001 PHE W 108 TYR 0.009 0.001 TYR B 30 ARG 0.003 0.000 ARG P 59 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 1150) hydrogen bonds : angle 4.06859 ( 3381) SS BOND : bond 0.00091 ( 23) SS BOND : angle 0.71446 ( 46) covalent geometry : bond 0.00236 (24311) covalent geometry : angle 0.43782 (33143) *********************** 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 551 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 441 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.8347 (m) cc_final: 0.8083 (m) REVERT: A 85 ASP cc_start: 0.8126 (p0) cc_final: 0.7799 (p0) REVERT: A 125 ASN cc_start: 0.8171 (t0) cc_final: 0.7765 (t0) REVERT: B 65 LYS cc_start: 0.8357 (mmtt) cc_final: 0.7461 (mttt) REVERT: B 77 GLU cc_start: 0.8147 (mp0) cc_final: 0.7740 (mp0) REVERT: C 22 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8232 (mp) REVERT: C 77 GLU cc_start: 0.8234 (mp0) cc_final: 0.7781 (mp0) REVERT: C 124 LEU cc_start: 0.8991 (mt) cc_final: 0.8777 (mp) REVERT: D 65 LYS cc_start: 0.8663 (mmtt) cc_final: 0.8173 (mmtp) REVERT: E 141 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8213 (ptt) REVERT: G 85 ASP cc_start: 0.8283 (p0) cc_final: 0.8003 (p0) REVERT: H 31 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7213 (pt0) REVERT: I 97 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7790 (mm-30) REVERT: J 22 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8096 (mp) REVERT: J 129 ASP cc_start: 0.7129 (m-30) cc_final: 0.6818 (t70) REVERT: K 31 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7686 (pt0) REVERT: L 103 ASP cc_start: 0.7854 (p0) cc_final: 0.7348 (p0) REVERT: L 135 LYS cc_start: 0.8135 (tmtt) cc_final: 0.7832 (mtpt) REVERT: M 7 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.7106 (t80) REVERT: M 22 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8079 (mp) REVERT: M 67 LYS cc_start: 0.8451 (mtmt) cc_final: 0.8165 (mtmt) REVERT: N 87 ASN cc_start: 0.9102 (t0) cc_final: 0.8833 (t0) REVERT: N 129 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: O 7 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7720 (t80) REVERT: O 129 ASP cc_start: 0.8334 (t70) cc_final: 0.7867 (t0) REVERT: P 135 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8131 (tttp) REVERT: Q 77 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8047 (mt-10) REVERT: Q 135 LYS cc_start: 0.8254 (tptt) cc_final: 0.7710 (tttm) REVERT: R 135 LYS cc_start: 0.8376 (tptt) cc_final: 0.7773 (ttpp) REVERT: S 22 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8411 (mp) REVERT: T 31 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8157 (pt0) REVERT: V 103 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7746 (p0) REVERT: V 135 LYS cc_start: 0.8524 (mptt) cc_final: 0.8229 (mttt) REVERT: W 77 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7696 (mt-10) outliers start: 110 outliers final: 80 residues processed: 520 average time/residue: 0.3194 time to fit residues: 265.7571 Evaluate side-chains 521 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 429 time to evaluate : 2.445 ------------------------------------------------------------------------------- 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 82 VAL Chi-restraints excluded: chain B residue 109 GLN 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 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 29 GLN Chi-restraints excluded: chain F residue 31 GLN 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 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 K residue 8 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 29 GLN 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 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 M residue 141 MET Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 129 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 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 8 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 76 THR 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 129 ASP 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 S residue 141 MET Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 52 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 T residue 141 MET Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 73 SER 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 103 ASP 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 216 optimal weight: 7.9990 chunk 224 optimal weight: 4.9990 chunk 215 optimal weight: 0.0670 chunk 303 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 300 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 overall best weight: 1.9524 ------------------------------------------------------------------------------- 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 ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN G 109 GLN H 31 GLN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 ASN K 149 ASN M 109 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.093700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.085913 restraints weight = 32685.981| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 0.94 r_work: 0.2810 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 2.35 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24334 Z= 0.142 Angle : 0.478 11.362 33189 Z= 0.256 Chirality : 0.047 0.156 4186 Planarity : 0.004 0.029 4209 Dihedral : 4.072 28.593 3427 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.62 % Allowed : 20.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.15), residues: 3243 helix: 2.34 (0.17), residues: 1081 sheet: 0.93 (0.19), residues: 713 loop : 1.98 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 132 PHE 0.006 0.001 PHE W 108 TYR 0.011 0.001 TYR G 33 ARG 0.004 0.000 ARG S 126 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 1150) hydrogen bonds : angle 4.14404 ( 3381) SS BOND : bond 0.00334 ( 23) SS BOND : angle 1.57978 ( 46) covalent geometry : bond 0.00334 (24311) covalent geometry : angle 0.47497 (33143) *********************** 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 545 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 425 time to evaluate : 2.718 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 58 SER cc_start: 0.8397 (m) cc_final: 0.8115 (m) REVERT: A 125 ASN cc_start: 0.8216 (t0) cc_final: 0.7781 (t0) REVERT: B 65 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7434 (mttt) REVERT: B 77 GLU cc_start: 0.8156 (mp0) cc_final: 0.7726 (mp0) REVERT: C 22 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8147 (mp) REVERT: D 65 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8124 (mmtp) REVERT: E 141 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8234 (ptt) REVERT: H 31 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7349 (pt0) REVERT: I 97 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7747 (mm-30) REVERT: J 22 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8014 (mp) REVERT: J 129 ASP cc_start: 0.7152 (m-30) cc_final: 0.6786 (t70) REVERT: K 31 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7705 (pt0) REVERT: L 22 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8252 (mp) REVERT: L 103 ASP cc_start: 0.7836 (p0) cc_final: 0.7315 (p0) REVERT: L 135 LYS cc_start: 0.8115 (tmtt) cc_final: 0.7802 (mtpt) REVERT: M 7 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7147 (t80) REVERT: M 22 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8084 (mp) REVERT: N 129 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7294 (m-30) REVERT: O 7 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7780 (t80) REVERT: O 129 ASP cc_start: 0.8330 (t70) cc_final: 0.7822 (t0) REVERT: P 7 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7906 (t80) REVERT: P 22 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8257 (mp) REVERT: P 135 LYS cc_start: 0.8345 (mmtt) cc_final: 0.8116 (tttp) REVERT: Q 31 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7966 (pt0) REVERT: Q 77 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8048 (mt-10) REVERT: Q 135 LYS cc_start: 0.8260 (tptt) cc_final: 0.7668 (tttm) REVERT: R 135 LYS cc_start: 0.8382 (tptt) cc_final: 0.7743 (ttpp) REVERT: S 22 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8349 (mp) REVERT: T 31 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: V 22 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8473 (mp) REVERT: V 103 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7771 (p0) REVERT: V 135 LYS cc_start: 0.8518 (mptt) cc_final: 0.8192 (mttt) outliers start: 120 outliers final: 91 residues processed: 515 average time/residue: 0.3191 time to fit residues: 264.2577 Evaluate side-chains 529 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 421 time to evaluate : 2.455 ------------------------------------------------------------------------------- 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 82 VAL 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 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 112 THR Chi-restraints excluded: chain E residue 141 MET 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 K residue 8 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 29 GLN 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 K residue 149 ASN 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 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 M residue 141 MET 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 N residue 129 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 Q residue 8 THR Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR 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 76 THR 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 129 ASP 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 S residue 141 MET Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 52 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 T residue 141 MET Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 73 SER 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 22 LEU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 103 ASP 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 83 GLU Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 135 LYS Chi-restraints excluded: chain W residue 148 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 161 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 199 optimal weight: 0.9990 chunk 237 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 189 optimal weight: 8.9990 chunk 303 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 109 GLN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN G 29 GLN G 109 GLN H 29 GLN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN K 87 ASN M 109 GLN Q 87 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.094275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.086500 restraints weight = 32802.023| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 0.95 r_work: 0.2818 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24334 Z= 0.122 Angle : 0.460 8.856 33189 Z= 0.246 Chirality : 0.046 0.151 4186 Planarity : 0.003 0.029 4209 Dihedral : 4.000 27.800 3427 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.58 % Allowed : 20.39 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.15), residues: 3243 helix: 2.38 (0.17), residues: 1081 sheet: 0.93 (0.19), residues: 713 loop : 2.03 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 132 PHE 0.006 0.001 PHE N 108 TYR 0.009 0.001 TYR G 33 ARG 0.004 0.000 ARG P 59 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 1150) hydrogen bonds : angle 4.09067 ( 3381) SS BOND : bond 0.00200 ( 23) SS BOND : angle 1.37970 ( 46) covalent geometry : bond 0.00284 (24311) covalent geometry : angle 0.45773 (33143) *********************** 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 545 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 426 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.8293 (m) cc_final: 0.8003 (m) REVERT: A 125 ASN cc_start: 0.8209 (t0) cc_final: 0.7800 (t0) REVERT: B 65 LYS cc_start: 0.8367 (mmtt) cc_final: 0.7480 (mttt) REVERT: B 77 GLU cc_start: 0.8158 (mp0) cc_final: 0.7790 (mp0) REVERT: C 22 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8179 (mp) REVERT: C 124 LEU cc_start: 0.8954 (mt) cc_final: 0.8749 (mp) REVERT: D 65 LYS cc_start: 0.8661 (mmtt) cc_final: 0.8167 (mmtp) REVERT: E 141 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8233 (ptt) REVERT: I 97 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7773 (mm-30) REVERT: J 22 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8029 (mp) REVERT: J 67 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8458 (mmtt) REVERT: J 129 ASP cc_start: 0.7160 (m-30) cc_final: 0.6862 (t70) REVERT: K 31 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7703 (pt0) REVERT: L 22 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8271 (mp) REVERT: L 103 ASP cc_start: 0.7816 (p0) cc_final: 0.7303 (p0) REVERT: L 135 LYS cc_start: 0.8131 (tmtt) cc_final: 0.7839 (mtpt) REVERT: M 7 PHE cc_start: 0.7427 (OUTLIER) cc_final: 0.7138 (t80) REVERT: M 22 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8071 (mp) REVERT: N 87 ASN cc_start: 0.9088 (t0) cc_final: 0.8806 (t0) REVERT: N 129 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: O 7 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7805 (t80) REVERT: O 129 ASP cc_start: 0.8358 (t70) cc_final: 0.7882 (t0) REVERT: P 7 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7904 (t80) REVERT: P 22 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8283 (mp) REVERT: P 135 LYS cc_start: 0.8359 (mmtt) cc_final: 0.8138 (tttp) REVERT: Q 31 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7963 (pt0) REVERT: Q 77 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8042 (mt-10) REVERT: Q 135 LYS cc_start: 0.8240 (tptt) cc_final: 0.7685 (tttm) REVERT: R 135 LYS cc_start: 0.8368 (tptt) cc_final: 0.7775 (ttpp) REVERT: S 22 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8395 (mp) REVERT: T 31 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8194 (pt0) REVERT: V 22 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8509 (mp) REVERT: V 103 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7762 (p0) REVERT: V 135 LYS cc_start: 0.8521 (mptt) cc_final: 0.8215 (mttt) REVERT: W 77 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7724 (mt-10) outliers start: 119 outliers final: 93 residues processed: 518 average time/residue: 0.3313 time to fit residues: 275.7099 Evaluate side-chains 531 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 422 time to evaluate : 2.641 ------------------------------------------------------------------------------- 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 82 VAL Chi-restraints excluded: chain B residue 138 GLN 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 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 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 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 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 I residue 124 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 29 GLN 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 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 M residue 141 MET 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 N residue 129 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 Q residue 8 THR Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR 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 76 THR 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 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 S residue 141 MET Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 52 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 T residue 141 MET Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 31 GLN 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 U residue 149 ASN Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 103 ASP 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 Chi-restraints excluded: chain W residue 135 LYS Chi-restraints excluded: chain W residue 148 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 248 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 chunk 246 optimal weight: 0.9990 chunk 318 optimal weight: 0.2980 chunk 268 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- 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 ** 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 ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN K 87 ASN K 149 ASN M 87 ASN M 109 GLN T 149 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.092162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.084359 restraints weight = 32987.226| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 0.95 r_work: 0.2782 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 24334 Z= 0.189 Angle : 0.517 8.734 33189 Z= 0.278 Chirality : 0.049 0.163 4186 Planarity : 0.004 0.033 4209 Dihedral : 4.353 30.441 3427 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.66 % Allowed : 20.58 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.15), residues: 3243 helix: 2.18 (0.17), residues: 1081 sheet: 0.82 (0.19), residues: 713 loop : 1.88 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 132 PHE 0.008 0.001 PHE E 142 TYR 0.013 0.001 TYR G 33 ARG 0.004 0.001 ARG P 59 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 1150) hydrogen bonds : angle 4.27593 ( 3381) SS BOND : bond 0.00301 ( 23) SS BOND : angle 1.66089 ( 46) covalent geometry : bond 0.00456 (24311) covalent geometry : angle 0.51385 (33143) ********************** 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 533 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 412 time to evaluate : 2.469 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: 0.8287 (m) cc_final: 0.7995 (m) REVERT: A 125 ASN cc_start: 0.8268 (t0) cc_final: 0.7901 (t0) REVERT: B 65 LYS cc_start: 0.8386 (mmtt) cc_final: 0.7489 (mttt) REVERT: B 77 GLU cc_start: 0.8181 (mp0) cc_final: 0.7796 (mp0) REVERT: C 22 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8154 (mp) REVERT: D 65 LYS cc_start: 0.8658 (mmtt) cc_final: 0.8174 (mmtp) REVERT: E 141 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8271 (ptt) REVERT: G 141 MET cc_start: 0.8459 (ptp) cc_final: 0.8153 (ptm) REVERT: I 97 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7773 (mm-30) REVERT: J 22 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8037 (mp) REVERT: J 67 LYS cc_start: 0.8746 (mmtt) cc_final: 0.8450 (mmtt) REVERT: J 129 ASP cc_start: 0.7180 (m-30) cc_final: 0.6851 (t70) REVERT: K 31 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7753 (pt0) REVERT: L 22 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8280 (mp) REVERT: L 103 ASP cc_start: 0.7857 (p0) cc_final: 0.7347 (p0) REVERT: L 135 LYS cc_start: 0.8145 (tmtt) cc_final: 0.7839 (mtpt) REVERT: M 7 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.7194 (t80) REVERT: M 22 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8131 (mp) REVERT: M 67 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8222 (mttp) REVERT: M 135 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8524 (tttp) REVERT: N 129 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7321 (m-30) REVERT: O 129 ASP cc_start: 0.8344 (t70) cc_final: 0.7846 (t0) REVERT: P 7 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7869 (t80) REVERT: P 22 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8329 (mp) REVERT: P 135 LYS cc_start: 0.8341 (mmtt) cc_final: 0.8129 (tttp) REVERT: Q 31 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7997 (pt0) REVERT: Q 77 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8064 (mt-10) REVERT: Q 135 LYS cc_start: 0.8290 (tptt) cc_final: 0.7704 (tttm) REVERT: R 135 LYS cc_start: 0.8441 (tptt) cc_final: 0.7843 (ttpp) REVERT: S 22 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8365 (mp) REVERT: T 31 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8267 (pt0) REVERT: V 22 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8488 (mp) REVERT: V 135 LYS cc_start: 0.8509 (mptt) cc_final: 0.8204 (mttt) outliers start: 121 outliers final: 93 residues processed: 507 average time/residue: 0.3123 time to fit residues: 254.4717 Evaluate side-chains 515 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 408 time to evaluate : 2.429 ------------------------------------------------------------------------------- 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 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 112 THR Chi-restraints excluded: chain E residue 141 MET 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 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 I residue 124 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 73 SER 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 29 GLN 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 K residue 149 ASN 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 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 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 N residue 129 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 74 THR Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR 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 76 THR 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 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 S residue 141 MET Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 52 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 T residue 141 MET Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 31 GLN 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 U residue 149 ASN Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 103 ASP 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 83 GLU Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 135 LYS Chi-restraints excluded: chain W residue 148 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 250 optimal weight: 7.9990 chunk 241 optimal weight: 2.9990 chunk 155 optimal weight: 0.4980 chunk 106 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 319 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 31 GLN G 109 GLN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN I 29 GLN K 87 ASN M 109 GLN O 149 ASN Q 87 ASN T 149 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.096211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.088459 restraints weight = 32386.351| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 0.94 r_work: 0.2847 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2839 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 : 0.436 6.819 33189 Z= 0.233 Chirality : 0.046 0.148 4186 Planarity : 0.003 0.028 4209 Dihedral : 3.847 25.061 3427 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.46 % Allowed : 21.78 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.15), residues: 3243 helix: 2.51 (0.17), residues: 1081 sheet: 0.92 (0.19), residues: 713 loop : 2.07 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 132 PHE 0.006 0.001 PHE W 7 TYR 0.007 0.001 TYR I 33 ARG 0.004 0.000 ARG P 59 Details of bonding type rmsd hydrogen bonds : bond 0.03071 ( 1150) hydrogen bonds : angle 3.97698 ( 3381) SS BOND : bond 0.00110 ( 23) SS BOND : angle 1.08005 ( 46) covalent geometry : bond 0.00196 (24311) covalent geometry : angle 0.43427 (33143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10591.33 seconds wall clock time: 185 minutes 32.68 seconds (11132.68 seconds total)