Starting phenix.real_space_refine on Fri Jun 20 08:39:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ewx_50025/06_2025/9ewx_50025.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ewx_50025/06_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_50025/06_2025/9ewx_50025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ewx_50025/06_2025/9ewx_50025.map" model { file = "/net/cci-nas-00/data/ceres_data/9ewx_50025/06_2025/9ewx_50025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ewx_50025/06_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-5710/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: 5.90, per 1000 atoms: 0.25 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: 5.34 Conformation dependent library (CDL) restraints added in 3.0 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: 2.52 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: 6.93 Time building geometry restraints manager: 6.41 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: 0.24 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: 5.060 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: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 41.940 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.370 ------------------------------------------------------------------------------- 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 : 2.416 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: 0.3483 time to fit residues: 343.7053 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 : 2.358 ------------------------------------------------------------------------------- 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 = 28)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.092090 restraints weight = 32285.890| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.16 r_work: 0.2881 rms_B_bonded: 1.66 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: 0.8568 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 4.59809 ( 3381) SS BOND : bond 0.00240 ( 23) SS BOND : angle 0.49200 ( 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 : 2.661 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: 0.8307 (m) REVERT: B 65 LYS cc_start: 0.8286 (mmtt) cc_final: 0.7362 (mttt) REVERT: D 65 LYS cc_start: 0.8608 (mmtt) cc_final: 0.8126 (mmtp) REVERT: I 65 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8261 (mmtm) REVERT: I 70 THR cc_start: 0.8665 (p) cc_final: 0.8458 (m) REVERT: I 97 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7715 (mm-30) REVERT: I 116 LYS cc_start: 0.8158 (mmtm) cc_final: 0.7901 (mmtt) REVERT: I 148 ASP cc_start: 0.7977 (m-30) cc_final: 0.7718 (m-30) REVERT: L 135 LYS cc_start: 0.8206 (tmtt) cc_final: 0.7857 (mtpt) REVERT: M 29 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7433 (mt0) REVERT: N 87 ASN cc_start: 0.9131 (t0) cc_final: 0.8914 (t0) REVERT: N 129 ASP cc_start: 0.7697 (m-30) cc_final: 0.7419 (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: 0.8003 (t70) REVERT: P 135 LYS cc_start: 0.8374 (mmtt) cc_final: 0.7809 (mptt) REVERT: Q 135 LYS cc_start: 0.8093 (tptt) cc_final: 0.7797 (tttm) REVERT: R 135 LYS cc_start: 0.8345 (tptt) cc_final: 0.7821 (ttpp) REVERT: R 141 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8245 (ptm) REVERT: S 91 VAL cc_start: 0.9216 (m) cc_final: 0.8917 (t) REVERT: W 8 THR cc_start: 0.6827 (OUTLIER) cc_final: 0.6446 (m) REVERT: W 91 VAL cc_start: 0.9072 (m) cc_final: 0.8758 (t) REVERT: W 135 LYS cc_start: 0.8365 (tptt) cc_final: 0.8090 (mtpp) outliers start: 92 outliers final: 56 residues processed: 551 average time/residue: 0.3459 time to fit residues: 301.6207 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 : 2.518 ------------------------------------------------------------------------------- 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: 6.9990 chunk 35 optimal weight: 8.9990 chunk 159 optimal weight: 9.9990 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: 6.3990 ------------------------------------------------------------------------------- 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 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** J 149 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** R 125 ASN R 149 ASN S 109 GLN S 149 ASN T 109 GLN T 149 ASN U 109 GLN U 138 GLN U 149 ASN V 149 ASN W 149 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.089824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.080822 restraints weight = 33487.600| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 1.23 r_work: 0.2705 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 24334 Z= 0.384 Angle : 0.688 5.820 33189 Z= 0.377 Chirality : 0.057 0.242 4186 Planarity : 0.005 0.051 4209 Dihedral : 5.139 32.429 3427 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 5.96 % Allowed : 18.35 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.17 (0.15), residues: 3243 helix: 1.59 (0.16), residues: 1081 sheet: 1.16 (0.19), residues: 713 loop : 1.74 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP F 132 PHE 0.020 0.002 PHE E 142 TYR 0.015 0.002 TYR Q 33 ARG 0.007 0.001 ARG Q 59 Details of bonding type rmsd hydrogen bonds : bond 0.05728 ( 1150) hydrogen bonds : angle 4.99171 ( 3381) SS BOND : bond 0.00662 ( 23) SS BOND : angle 2.41071 ( 46) covalent geometry : bond 0.00943 (24311) covalent geometry : angle 0.68292 (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 584 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 429 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 PHE cc_start: 0.7807 (t80) cc_final: 0.7606 (t80) REVERT: A 58 SER cc_start: 0.8386 (m) cc_final: 0.8073 (m) REVERT: A 136 SER cc_start: 0.8682 (t) cc_final: 0.8229 (p) REVERT: B 22 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8624 (mp) REVERT: B 31 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8276 (pt0) REVERT: B 47 ASN cc_start: 0.9018 (m-40) cc_final: 0.8772 (m-40) REVERT: B 65 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7340 (mttt) REVERT: C 22 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8064 (mp) REVERT: D 65 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8087 (mmtp) REVERT: E 141 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8179 (ptt) REVERT: F 22 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8149 (mp) REVERT: G 85 ASP cc_start: 0.8356 (p0) cc_final: 0.8018 (p0) REVERT: G 103 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7358 (p0) REVERT: H 22 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8459 (mp) REVERT: I 65 LYS cc_start: 0.8621 (mmtt) cc_final: 0.8235 (mmtp) REVERT: I 97 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7656 (mm-30) REVERT: I 103 ASP cc_start: 0.8307 (p0) cc_final: 0.8097 (p0) REVERT: I 116 LYS cc_start: 0.8252 (mmtm) cc_final: 0.8041 (mmtt) REVERT: J 22 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8075 (mp) REVERT: J 129 ASP cc_start: 0.7331 (m-30) cc_final: 0.6723 (t70) REVERT: K 31 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7911 (pt0) REVERT: K 98 ASP cc_start: 0.8080 (m-30) cc_final: 0.7863 (m-30) REVERT: L 22 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8307 (mp) REVERT: L 129 ASP cc_start: 0.7678 (t0) cc_final: 0.7455 (t0) REVERT: L 135 LYS cc_start: 0.8202 (tmtt) cc_final: 0.7785 (mtpt) REVERT: M 7 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7227 (t80) REVERT: M 22 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8192 (mp) REVERT: M 135 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8544 (tttp) REVERT: N 22 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8528 (mp) REVERT: N 129 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: O 7 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7678 (t80) REVERT: P 22 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8335 (mp) REVERT: P 135 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8011 (ttmt) REVERT: Q 22 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8325 (mp) REVERT: Q 55 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: Q 87 ASN cc_start: 0.8810 (t0) cc_final: 0.8529 (t0) REVERT: Q 135 LYS cc_start: 0.8300 (tptt) cc_final: 0.7762 (tttm) REVERT: R 135 LYS cc_start: 0.8501 (tptt) cc_final: 0.7821 (ttpp) REVERT: R 141 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8270 (ptm) REVERT: S 7 PHE cc_start: 0.7558 (OUTLIER) cc_final: 0.7321 (t80) REVERT: S 22 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8382 (mp) REVERT: V 109 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8222 (mm-40) REVERT: V 135 LYS cc_start: 0.8503 (mptt) cc_final: 0.8123 (mttt) REVERT: W 7 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.6371 (t80) REVERT: W 135 LYS cc_start: 0.8500 (tptt) cc_final: 0.8012 (ttpp) outliers start: 155 outliers final: 103 residues processed: 541 average time/residue: 0.3362 time to fit residues: 290.7341 Evaluate side-chains 526 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 401 time to evaluate : 2.502 ------------------------------------------------------------------------------- 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 29 GLN 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 22 LEU 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 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 J residue 78 THR Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 141 MET 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 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 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 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 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 55 GLU 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 7 PHE Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 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 7 PHE Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 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 7 PHE 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: 1.9990 chunk 232 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 225 optimal weight: 0.8980 chunk 319 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 318 optimal weight: 0.8980 chunk 180 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN D 125 ASN E 31 GLN G 109 GLN H 109 GLN J 109 GLN J 149 ASN M 29 GLN M 109 GLN M 149 ASN Q 149 ASN U 138 GLN V 31 GLN ** V 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.095109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.086509 restraints weight = 32969.713| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.14 r_work: 0.2800 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2640 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= 0.114 Angle : 0.449 4.547 33189 Z= 0.243 Chirality : 0.046 0.151 4186 Planarity : 0.004 0.030 4209 Dihedral : 4.111 26.866 3427 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.46 % Allowed : 20.78 % Favored : 75.76 % 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: 2.70 (0.15), residues: 3243 helix: 2.26 (0.17), residues: 1081 sheet: 1.22 (0.19), residues: 713 loop : 2.00 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 132 PHE 0.006 0.001 PHE W 108 TYR 0.006 0.001 TYR H 33 ARG 0.003 0.000 ARG P 59 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 1150) hydrogen bonds : angle 4.36529 ( 3381) SS BOND : bond 0.00108 ( 23) SS BOND : angle 0.74185 ( 46) covalent geometry : bond 0.00254 (24311) covalent geometry : angle 0.44831 (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 545 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 455 time to evaluate : 2.606 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: 0.8130 (p0) cc_final: 0.7812 (p0) REVERT: B 65 LYS cc_start: 0.8335 (mmtt) cc_final: 0.7411 (mttt) REVERT: B 77 GLU cc_start: 0.8144 (mp0) cc_final: 0.7713 (mp0) REVERT: C 77 GLU cc_start: 0.8304 (mp0) cc_final: 0.7970 (mp0) REVERT: D 65 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8104 (mmtp) REVERT: E 141 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8198 (ptt) REVERT: G 85 ASP cc_start: 0.8305 (p0) cc_final: 0.8045 (p0) REVERT: I 65 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8406 (mmtm) REVERT: I 97 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7715 (mm-30) REVERT: I 116 LYS cc_start: 0.8223 (mmtm) cc_final: 0.7964 (mmtt) REVERT: J 129 ASP cc_start: 0.7177 (m-30) cc_final: 0.6741 (t70) REVERT: K 31 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7700 (pt0) REVERT: L 103 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7603 (p0) REVERT: L 129 ASP cc_start: 0.7665 (t0) cc_final: 0.7371 (t0) REVERT: L 135 LYS cc_start: 0.8218 (tmtt) cc_final: 0.7852 (mtpt) REVERT: M 7 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.7089 (t80) REVERT: M 135 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8492 (tttp) REVERT: N 129 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7345 (m-30) REVERT: O 7 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7570 (t80) REVERT: O 129 ASP cc_start: 0.8423 (t70) cc_final: 0.7948 (t0) REVERT: P 135 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8128 (tttp) REVERT: Q 87 ASN cc_start: 0.8656 (t0) cc_final: 0.8455 (t0) REVERT: Q 135 LYS cc_start: 0.8270 (tptt) cc_final: 0.7762 (tttm) REVERT: R 135 LYS cc_start: 0.8375 (tptt) cc_final: 0.7721 (ttpp) REVERT: R 141 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8254 (ptm) REVERT: T 135 LYS cc_start: 0.8632 (tppt) cc_final: 0.8268 (mmtm) REVERT: V 103 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7928 (p0) REVERT: V 135 LYS cc_start: 0.8530 (mptt) cc_final: 0.8167 (mttt) REVERT: W 10 ILE cc_start: 0.8523 (mt) cc_final: 0.8263 (mm) REVERT: W 135 LYS cc_start: 0.8497 (tptt) cc_final: 0.8199 (ttpp) outliers start: 90 outliers final: 65 residues processed: 520 average time/residue: 0.3340 time to fit residues: 277.8764 Evaluate side-chains 505 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 432 time to evaluate : 2.618 ------------------------------------------------------------------------------- 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 C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE 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 I residue 112 THR Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 141 MET Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 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 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 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 R residue 141 MET Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 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 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 125 ASN 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 175 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 233 optimal weight: 0.0020 chunk 313 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 252 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 267 optimal weight: 0.6980 chunk 234 optimal weight: 7.9990 chunk 265 optimal weight: 0.9980 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 149 ASN G 109 GLN H 109 GLN L 29 GLN S 109 GLN V 31 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.096705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.088181 restraints weight = 32749.609| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.13 r_work: 0.2825 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 24334 Z= 0.095 Angle : 0.428 4.582 33189 Z= 0.230 Chirality : 0.046 0.145 4186 Planarity : 0.003 0.027 4209 Dihedral : 3.849 24.152 3427 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.62 % Allowed : 21.16 % 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: 2.85 (0.15), residues: 3243 helix: 2.46 (0.17), residues: 1081 sheet: 1.14 (0.19), residues: 713 loop : 2.10 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 132 PHE 0.007 0.001 PHE S 7 TYR 0.007 0.001 TYR H 33 ARG 0.003 0.000 ARG S 126 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 1150) hydrogen bonds : angle 4.10285 ( 3381) SS BOND : bond 0.00227 ( 23) SS BOND : angle 0.69185 ( 46) covalent geometry : bond 0.00209 (24311) covalent geometry : angle 0.42759 (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 542 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 448 time to evaluate : 2.452 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 85 ASP cc_start: 0.8105 (p0) cc_final: 0.7777 (p0) REVERT: A 125 ASN cc_start: 0.8241 (t0) cc_final: 0.7822 (t0) REVERT: B 31 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.8038 (pt0) REVERT: B 65 LYS cc_start: 0.8349 (mmtt) cc_final: 0.7370 (mttt) REVERT: B 77 GLU cc_start: 0.8149 (mp0) cc_final: 0.7801 (mp0) REVERT: C 22 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8209 (mp) REVERT: C 65 LYS cc_start: 0.8648 (mttm) cc_final: 0.8408 (mttm) REVERT: C 77 GLU cc_start: 0.8295 (mp0) cc_final: 0.7944 (mp0) REVERT: D 65 LYS cc_start: 0.8629 (mmtt) cc_final: 0.8111 (mmtp) REVERT: E 141 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8178 (ptt) REVERT: I 97 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7737 (mm-30) REVERT: I 116 LYS cc_start: 0.8218 (mmtm) cc_final: 0.7957 (mmtt) REVERT: J 22 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8077 (mp) REVERT: J 91 VAL cc_start: 0.8752 (m) cc_final: 0.8444 (t) REVERT: J 129 ASP cc_start: 0.7147 (m-30) cc_final: 0.6731 (t70) REVERT: K 31 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7700 (pt0) REVERT: L 103 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7500 (p0) REVERT: L 135 LYS cc_start: 0.8199 (tmtt) cc_final: 0.7851 (mtpt) REVERT: M 7 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.7052 (t80) REVERT: M 22 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8074 (mp) REVERT: N 87 ASN cc_start: 0.9110 (t0) cc_final: 0.8887 (t0) REVERT: N 129 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7305 (m-30) REVERT: O 129 ASP cc_start: 0.8405 (t70) cc_final: 0.7925 (t0) REVERT: P 7 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7804 (t80) REVERT: P 135 LYS cc_start: 0.8388 (mmtt) cc_final: 0.8128 (tttp) REVERT: Q 135 LYS cc_start: 0.8235 (tptt) cc_final: 0.7719 (tttm) REVERT: R 135 LYS cc_start: 0.8364 (tptt) cc_final: 0.7705 (ttpp) REVERT: T 135 LYS cc_start: 0.8618 (tppt) cc_final: 0.8261 (mmtm) REVERT: V 103 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7881 (p0) REVERT: V 135 LYS cc_start: 0.8557 (mptt) cc_final: 0.8195 (mttt) REVERT: W 10 ILE cc_start: 0.8549 (mt) cc_final: 0.8319 (mm) outliers start: 94 outliers final: 69 residues processed: 518 average time/residue: 0.3562 time to fit residues: 299.0936 Evaluate side-chains 514 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 434 time to evaluate : 2.806 ------------------------------------------------------------------------------- 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 31 GLN Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 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 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 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 22 LEU Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 112 THR 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 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 77 GLU Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 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 129 ASP 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 112 THR Chi-restraints excluded: chain T residue 125 ASN 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 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: 9.9990 chunk 298 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 282 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 159 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 297 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN D 125 ASN G 29 GLN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN V 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.094303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.085716 restraints weight = 32836.525| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.14 r_work: 0.2785 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24334 Z= 0.152 Angle : 0.482 11.377 33189 Z= 0.259 Chirality : 0.047 0.158 4186 Planarity : 0.004 0.030 4209 Dihedral : 4.125 27.521 3427 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.73 % Allowed : 19.70 % Favored : 75.57 % 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: 2.33 (0.17), residues: 1081 sheet: 1.01 (0.19), residues: 713 loop : 2.02 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 132 PHE 0.006 0.001 PHE E 142 TYR 0.012 0.001 TYR G 33 ARG 0.003 0.000 ARG P 59 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 1150) hydrogen bonds : angle 4.19393 ( 3381) SS BOND : bond 0.00305 ( 23) SS BOND : angle 1.57547 ( 46) covalent geometry : bond 0.00361 (24311) covalent geometry : angle 0.47922 (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 551 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 428 time to evaluate : 2.676 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 125 ASN cc_start: 0.8275 (t0) cc_final: 0.7892 (t0) REVERT: B 31 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8068 (pt0) REVERT: B 65 LYS cc_start: 0.8323 (mmtt) cc_final: 0.7396 (mttt) REVERT: C 22 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8176 (mp) REVERT: C 77 GLU cc_start: 0.8252 (mp0) cc_final: 0.7826 (mp0) REVERT: D 65 LYS cc_start: 0.8624 (mmtt) cc_final: 0.8105 (mmtp) REVERT: E 141 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8198 (ptt) REVERT: I 65 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8198 (mmtp) REVERT: I 97 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7725 (mm-30) REVERT: I 116 LYS cc_start: 0.8199 (mmtm) cc_final: 0.7924 (mmtt) REVERT: J 13 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8372 (mmm) REVERT: J 22 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8026 (mp) REVERT: J 129 ASP cc_start: 0.7219 (m-30) cc_final: 0.6757 (t70) REVERT: K 31 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7711 (pt0) REVERT: L 22 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8281 (mp) REVERT: L 103 ASP cc_start: 0.7883 (p0) cc_final: 0.7358 (p0) REVERT: L 135 LYS cc_start: 0.8206 (tmtt) cc_final: 0.7841 (mtpt) REVERT: M 7 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.7120 (t80) REVERT: M 22 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8093 (mp) REVERT: M 135 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8501 (tttp) REVERT: N 129 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7336 (m-30) REVERT: O 7 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7595 (t80) REVERT: O 129 ASP cc_start: 0.8297 (t70) cc_final: 0.7791 (t0) REVERT: P 22 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8306 (mp) REVERT: P 135 LYS cc_start: 0.8372 (mmtt) cc_final: 0.8136 (tttp) REVERT: Q 31 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7969 (pt0) REVERT: Q 135 LYS cc_start: 0.8212 (tptt) cc_final: 0.7750 (tttm) REVERT: R 135 LYS cc_start: 0.8405 (tptt) cc_final: 0.7747 (ttpp) REVERT: S 22 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8371 (mp) REVERT: T 31 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8256 (pt0) REVERT: V 103 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7868 (p0) REVERT: V 135 LYS cc_start: 0.8519 (mptt) cc_final: 0.8160 (mttt) REVERT: W 10 ILE cc_start: 0.8608 (mt) cc_final: 0.8397 (mm) outliers start: 123 outliers final: 92 residues processed: 518 average time/residue: 0.3297 time to fit residues: 274.8543 Evaluate side-chains 530 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 422 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain 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 8 THR Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 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 13 MET 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 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 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 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 31 GLN 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 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 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 V residue 7 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 126 optimal weight: 3.9990 chunk 208 optimal weight: 7.9990 chunk 229 optimal weight: 0.0570 chunk 4 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 254 optimal weight: 0.0030 chunk 147 optimal weight: 2.9990 chunk 320 optimal weight: 3.9990 chunk 317 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 overall best weight: 0.5510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 149 ASN G 109 GLN H 31 GLN H 109 GLN H 149 ASN I 149 ASN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.098538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.090012 restraints weight = 32524.263| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.13 r_work: 0.2853 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24334 Z= 0.084 Angle : 0.421 7.285 33189 Z= 0.224 Chirality : 0.045 0.141 4186 Planarity : 0.003 0.026 4209 Dihedral : 3.660 21.427 3427 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.81 % Allowed : 20.85 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.15), residues: 3243 helix: 2.63 (0.17), residues: 1081 sheet: 1.06 (0.19), residues: 713 loop : 2.16 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 132 PHE 0.005 0.001 PHE I 108 TYR 0.006 0.001 TYR G 79 ARG 0.003 0.000 ARG P 59 Details of bonding type rmsd hydrogen bonds : bond 0.02866 ( 1150) hydrogen bonds : angle 3.87747 ( 3381) SS BOND : bond 0.00085 ( 23) SS BOND : angle 0.96758 ( 46) covalent geometry : bond 0.00177 (24311) covalent geometry : angle 0.41976 (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 558 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 459 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8114 (p0) cc_final: 0.7801 (p0) REVERT: A 125 ASN cc_start: 0.8176 (t0) cc_final: 0.7789 (t0) REVERT: B 65 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7405 (mttt) REVERT: B 77 GLU cc_start: 0.8147 (mp0) cc_final: 0.7802 (mp0) REVERT: B 103 ASP cc_start: 0.7554 (p0) cc_final: 0.7316 (p0) REVERT: C 22 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8155 (mp) REVERT: C 65 LYS cc_start: 0.8658 (mttm) cc_final: 0.8166 (mttm) REVERT: C 77 GLU cc_start: 0.8260 (mp0) cc_final: 0.7736 (mp0) REVERT: D 65 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8110 (mmtp) REVERT: E 141 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8155 (ptt) REVERT: H 31 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.7246 (pt0) REVERT: I 97 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7760 (mm-30) REVERT: I 116 LYS cc_start: 0.8211 (mmtm) cc_final: 0.7948 (mmtt) REVERT: J 67 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8408 (mmtt) REVERT: J 129 ASP cc_start: 0.7148 (m-30) cc_final: 0.6753 (t70) REVERT: K 31 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7659 (pt0) REVERT: L 88 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8513 (mmmt) REVERT: L 135 LYS cc_start: 0.8169 (tmtt) cc_final: 0.7837 (mtpt) REVERT: M 7 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7077 (t80) REVERT: M 22 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8039 (mp) REVERT: M 70 THR cc_start: 0.8842 (p) cc_final: 0.8618 (m) REVERT: N 87 ASN cc_start: 0.9065 (t0) cc_final: 0.8855 (t0) REVERT: N 129 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7292 (m-30) REVERT: O 7 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7586 (t80) REVERT: O 43 LEU cc_start: 0.9091 (tp) cc_final: 0.8799 (tp) REVERT: O 129 ASP cc_start: 0.8421 (t70) cc_final: 0.7976 (t0) REVERT: P 7 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7796 (t80) REVERT: P 135 LYS cc_start: 0.8387 (mmtt) cc_final: 0.8124 (tttp) REVERT: Q 31 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7875 (pt0) REVERT: Q 135 LYS cc_start: 0.8208 (tptt) cc_final: 0.7686 (tttm) REVERT: R 135 LYS cc_start: 0.8370 (tptt) cc_final: 0.7704 (ttpp) REVERT: S 22 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8471 (mp) REVERT: T 31 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8117 (pt0) REVERT: T 135 LYS cc_start: 0.8618 (tppt) cc_final: 0.8237 (mmtm) REVERT: V 103 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7804 (p0) REVERT: V 135 LYS cc_start: 0.8489 (mptt) cc_final: 0.8154 (mttt) REVERT: W 77 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7723 (mt-10) outliers start: 99 outliers final: 67 residues processed: 533 average time/residue: 0.3897 time to fit residues: 333.0828 Evaluate side-chains 520 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 440 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 22 LEU 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 8 THR 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 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 73 SER Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 148 ASP Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 92 ILE 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 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 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 73 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 85 ASP 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 73 SER Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 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 Chi-restraints excluded: chain W residue 112 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 216 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 303 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 300 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 149 ASN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 GLN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN I 149 ASN J 149 ASN ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 138 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 = 0.2945 r_free = 0.2945 target = 0.091293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.082295 restraints weight = 33306.327| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 1.23 r_work: 0.2734 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 24334 Z= 0.269 Angle : 0.579 8.318 33189 Z= 0.313 Chirality : 0.052 0.184 4186 Planarity : 0.004 0.040 4209 Dihedral : 4.630 30.595 3427 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.50 % Allowed : 20.16 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.15), residues: 3243 helix: 2.04 (0.17), residues: 1081 sheet: 0.83 (0.18), residues: 713 loop : 1.81 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 132 PHE 0.012 0.002 PHE E 142 TYR 0.013 0.001 TYR H 30 ARG 0.004 0.001 ARG Q 59 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 1150) hydrogen bonds : angle 4.41876 ( 3381) SS BOND : bond 0.00419 ( 23) SS BOND : angle 2.01479 ( 46) covalent geometry : bond 0.00659 (24311) covalent geometry : angle 0.57407 (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 523 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 406 time to evaluate : 2.879 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: 0.8333 (m) cc_final: 0.8039 (m) REVERT: A 125 ASN cc_start: 0.8302 (t0) cc_final: 0.7876 (t0) REVERT: B 65 LYS cc_start: 0.8278 (mmtt) cc_final: 0.7317 (mttt) REVERT: C 22 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8090 (mp) REVERT: C 124 LEU cc_start: 0.9096 (mt) cc_final: 0.8883 (mp) REVERT: D 65 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8041 (mmtp) REVERT: E 141 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8237 (ptt) REVERT: I 65 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8194 (mmtp) REVERT: I 97 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7676 (mm-30) REVERT: J 129 ASP cc_start: 0.7250 (m-30) cc_final: 0.6751 (t70) REVERT: K 31 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7820 (pt0) REVERT: L 22 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8240 (mp) REVERT: L 135 LYS cc_start: 0.8200 (tmtt) cc_final: 0.7826 (mtpt) REVERT: M 7 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.7213 (t80) REVERT: M 22 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8138 (mp) REVERT: M 77 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7987 (mt-10) REVERT: M 135 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8526 (tttp) REVERT: N 129 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7289 (m-30) REVERT: O 7 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7823 (t80) REVERT: O 129 ASP cc_start: 0.8258 (t70) cc_final: 0.7713 (t0) REVERT: P 22 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8378 (mp) REVERT: P 135 LYS cc_start: 0.8319 (mmtt) cc_final: 0.8080 (tttp) REVERT: Q 31 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.8043 (pt0) REVERT: Q 135 LYS cc_start: 0.8342 (tptt) cc_final: 0.7820 (tttm) REVERT: R 135 LYS cc_start: 0.8479 (tptt) cc_final: 0.7826 (ttpp) REVERT: S 22 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8355 (mp) REVERT: T 31 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8347 (pt0) REVERT: V 22 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8421 (mp) REVERT: V 97 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: V 135 LYS cc_start: 0.8527 (mptt) cc_final: 0.8123 (mttt) outliers start: 117 outliers final: 89 residues processed: 499 average time/residue: 0.3405 time to fit residues: 273.9818 Evaluate side-chains 504 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 401 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 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 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 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 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 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 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 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 22 LEU 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 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 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 31 GLN 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 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 97 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 161 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 121 optimal weight: 0.0050 chunk 76 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- 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 G 109 GLN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 149 ASN K 87 ASN K 149 ASN M 109 GLN T 149 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 = 0.094484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.085521 restraints weight = 32928.529| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.23 r_work: 0.2781 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24334 Z= 0.126 Angle : 0.466 6.511 33189 Z= 0.251 Chirality : 0.047 0.151 4186 Planarity : 0.004 0.029 4209 Dihedral : 4.170 27.676 3427 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.00 % Allowed : 20.97 % 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: 2.58 (0.15), residues: 3243 helix: 2.31 (0.17), residues: 1081 sheet: 0.84 (0.19), residues: 713 loop : 1.97 (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 W 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 0.03542 ( 1150) hydrogen bonds : angle 4.14234 ( 3381) SS BOND : bond 0.00140 ( 23) SS BOND : angle 1.15731 ( 46) covalent geometry : bond 0.00293 (24311) covalent geometry : angle 0.46430 (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 523 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 419 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 SER cc_start: 0.8332 (m) cc_final: 0.8039 (m) REVERT: A 125 ASN cc_start: 0.8225 (t0) cc_final: 0.7783 (t0) REVERT: B 65 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7312 (mttt) REVERT: B 77 GLU cc_start: 0.8093 (mp0) cc_final: 0.7768 (mp0) REVERT: C 22 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8187 (mp) REVERT: C 65 LYS cc_start: 0.8613 (mttm) cc_final: 0.8100 (mttm) REVERT: C 77 GLU cc_start: 0.8255 (mp0) cc_final: 0.7693 (mp0) REVERT: C 124 LEU cc_start: 0.9024 (mt) cc_final: 0.8820 (mp) REVERT: D 65 LYS cc_start: 0.8598 (mmtt) cc_final: 0.8051 (mmtp) REVERT: E 141 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8234 (ptt) REVERT: G 141 MET cc_start: 0.8529 (ptp) cc_final: 0.8217 (ptm) REVERT: I 65 LYS cc_start: 0.8598 (mmtt) cc_final: 0.8193 (mmtp) REVERT: I 97 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7689 (mm-30) REVERT: J 91 VAL cc_start: 0.8690 (m) cc_final: 0.8374 (t) REVERT: J 129 ASP cc_start: 0.7163 (m-30) cc_final: 0.6695 (t70) REVERT: K 31 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7716 (pt0) REVERT: L 22 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8243 (mp) REVERT: L 103 ASP cc_start: 0.8087 (m-30) cc_final: 0.7819 (m-30) REVERT: L 135 LYS cc_start: 0.8137 (tmtt) cc_final: 0.7769 (mtpt) REVERT: M 7 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7169 (t80) REVERT: M 22 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8044 (mp) REVERT: N 87 ASN cc_start: 0.9174 (t0) cc_final: 0.8826 (t0) REVERT: N 129 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: O 7 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7853 (t80) REVERT: O 129 ASP cc_start: 0.8414 (t70) cc_final: 0.7882 (t0) REVERT: P 7 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7866 (t80) REVERT: P 22 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8305 (mp) REVERT: P 135 LYS cc_start: 0.8338 (mmtt) cc_final: 0.8074 (tttp) REVERT: Q 31 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7958 (pt0) REVERT: Q 135 LYS cc_start: 0.8295 (tptt) cc_final: 0.7766 (tttm) REVERT: R 135 LYS cc_start: 0.8397 (tptt) cc_final: 0.7702 (ttpp) REVERT: S 22 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8377 (mp) REVERT: T 31 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8264 (pt0) REVERT: V 22 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8473 (mp) REVERT: V 97 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7462 (mp0) REVERT: V 103 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7940 (p0) REVERT: V 135 LYS cc_start: 0.8523 (mptt) cc_final: 0.8131 (mttt) REVERT: W 77 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7689 (mt-10) outliers start: 104 outliers final: 79 residues processed: 499 average time/residue: 0.3318 time to fit residues: 266.4849 Evaluate side-chains 511 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 416 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 109 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 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 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 103 ASP 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 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 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 22 LEU 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 73 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 141 MET Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 141 MET Chi-restraints excluded: chain T residue 149 ASN Chi-restraints excluded: chain U residue 8 THR 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 V residue 22 LEU Chi-restraints excluded: chain V residue 76 THR Chi-restraints excluded: chain V residue 97 GLU 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 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: 6.9990 chunk 33 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 253 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 318 optimal weight: 0.8980 chunk 268 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 ASN K 149 ASN M 87 ASN M 109 GLN T 149 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.094572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.086090 restraints weight = 32807.866| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.13 r_work: 0.2792 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2884 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= 0.133 Angle : 0.472 6.114 33189 Z= 0.254 Chirality : 0.047 0.154 4186 Planarity : 0.003 0.029 4209 Dihedral : 4.144 26.383 3427 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.00 % Allowed : 20.93 % 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: 2.59 (0.15), residues: 3243 helix: 2.32 (0.17), residues: 1081 sheet: 0.82 (0.19), residues: 713 loop : 1.99 (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 W 7 TYR 0.010 0.001 TYR G 33 ARG 0.004 0.000 ARG P 59 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 1150) hydrogen bonds : angle 4.11322 ( 3381) SS BOND : bond 0.00166 ( 23) SS BOND : angle 1.21048 ( 46) covalent geometry : bond 0.00313 (24311) covalent geometry : angle 0.47017 (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 519 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 415 time to evaluate : 2.441 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: 0.8314 (m) cc_final: 0.8036 (m) REVERT: A 125 ASN cc_start: 0.8217 (t0) cc_final: 0.7777 (t0) REVERT: B 65 LYS cc_start: 0.8324 (mmtt) cc_final: 0.7393 (mttt) REVERT: C 22 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8171 (mp) REVERT: C 65 LYS cc_start: 0.8636 (mttm) cc_final: 0.8120 (mttm) REVERT: C 77 GLU cc_start: 0.8243 (mp0) cc_final: 0.7704 (mp0) REVERT: C 124 LEU cc_start: 0.9049 (mt) cc_final: 0.8841 (mp) REVERT: D 65 LYS cc_start: 0.8638 (mmtt) cc_final: 0.8114 (mmtp) REVERT: E 141 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8250 (ptt) REVERT: G 141 MET cc_start: 0.8500 (ptp) cc_final: 0.8197 (ptm) REVERT: I 65 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8223 (mmtp) REVERT: I 97 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7739 (mm-30) REVERT: J 67 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8488 (mmtt) REVERT: J 91 VAL cc_start: 0.8695 (m) cc_final: 0.8401 (t) REVERT: J 129 ASP cc_start: 0.7179 (m-30) cc_final: 0.6809 (t70) REVERT: K 31 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7712 (pt0) REVERT: L 22 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8249 (mp) REVERT: L 103 ASP cc_start: 0.8053 (m-30) cc_final: 0.7787 (m-30) REVERT: L 135 LYS cc_start: 0.8143 (tmtt) cc_final: 0.7804 (mtpt) REVERT: M 7 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.7156 (t80) REVERT: M 22 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8042 (mp) REVERT: N 87 ASN cc_start: 0.9158 (t0) cc_final: 0.8807 (t0) REVERT: O 129 ASP cc_start: 0.8417 (t70) cc_final: 0.7893 (t0) REVERT: P 7 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7870 (t80) REVERT: P 22 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8320 (mp) REVERT: P 135 LYS cc_start: 0.8335 (mmtt) cc_final: 0.8078 (tttp) REVERT: Q 31 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7971 (pt0) REVERT: R 135 LYS cc_start: 0.8403 (tptt) cc_final: 0.7748 (ttpp) REVERT: S 22 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8383 (mp) REVERT: T 31 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8236 (pt0) REVERT: V 22 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8472 (mp) REVERT: V 97 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: V 103 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7895 (p0) REVERT: V 135 LYS cc_start: 0.8516 (mptt) cc_final: 0.8173 (mttt) REVERT: W 77 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7729 (mt-10) outliers start: 104 outliers final: 84 residues processed: 494 average time/residue: 0.3726 time to fit residues: 296.8059 Evaluate side-chains 512 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 414 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 109 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 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 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 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 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 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 73 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 141 MET Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 141 MET Chi-restraints excluded: chain T residue 149 ASN Chi-restraints excluded: chain U residue 8 THR 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 76 THR Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 97 GLU 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 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: 6.9990 chunk 241 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 319 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 GLN K 87 ASN M 87 ASN M 109 GLN Q 87 ASN T 149 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.093975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.085476 restraints weight = 32839.230| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.13 r_work: 0.2782 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24334 Z= 0.154 Angle : 0.488 6.091 33189 Z= 0.263 Chirality : 0.048 0.157 4186 Planarity : 0.004 0.031 4209 Dihedral : 4.224 26.147 3427 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.04 % Allowed : 20.97 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.52 (0.15), residues: 3243 helix: 2.26 (0.17), residues: 1081 sheet: 0.78 (0.19), residues: 713 loop : 1.96 (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 P 59 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 1150) hydrogen bonds : angle 4.15914 ( 3381) SS BOND : bond 0.00211 ( 23) SS BOND : angle 1.31548 ( 46) covalent geometry : bond 0.00367 (24311) covalent geometry : angle 0.48541 (33143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10835.37 seconds wall clock time: 190 minutes 22.27 seconds (11422.27 seconds total)