Starting phenix.real_space_refine on Sat Jan 25 15:28:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ewx_50025/01_2025/9ewx_50025.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ewx_50025/01_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_50025/01_2025/9ewx_50025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ewx_50025/01_2025/9ewx_50025.map" model { file = "/net/cci-nas-00/data/ceres_data/9ewx_50025/01_2025/9ewx_50025.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ewx_50025/01_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 7.05, per 1000 atoms: 0.29 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 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: 5.23 Conformation dependent library (CDL) restraints added in 3.4 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: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 30 through 47 Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 30 through 47 Processing helix chain 'B' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 30 through 47 Processing helix chain 'C' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR C 52 " --> pdb=" O PRO C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 30 through 47 Processing helix chain 'D' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'E' and resid 8 through 23 Processing helix chain 'E' and resid 30 through 47 Processing helix chain 'E' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR E 52 " --> pdb=" O PRO E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'F' and resid 8 through 23 Processing helix chain 'F' and resid 30 through 47 Processing helix chain 'F' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR F 52 " --> pdb=" O PRO F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 47 Processing helix chain 'G' and resid 48 through 59 removed outlier: 3.596A pdb=" N THR G 52 " --> pdb=" O PRO G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'H' and resid 8 through 23 Processing helix chain 'H' and resid 30 through 47 Processing helix chain 'H' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR H 52 " --> pdb=" O PRO H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'I' and resid 8 through 23 Processing helix chain 'I' and resid 30 through 47 Processing helix chain 'I' and resid 48 through 59 removed outlier: 3.594A pdb=" N THR I 52 " --> pdb=" O PRO I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'J' and resid 8 through 23 Processing helix chain 'J' and resid 30 through 47 Processing helix chain 'J' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR J 52 " --> pdb=" O PRO J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'K' and resid 8 through 23 Processing helix chain 'K' and resid 30 through 47 Processing helix chain 'K' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR K 52 " --> pdb=" O PRO K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'L' and resid 8 through 23 Processing helix chain 'L' and resid 30 through 47 Processing helix chain 'L' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR L 52 " --> pdb=" O PRO L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'M' and resid 8 through 23 Processing helix chain 'M' and resid 30 through 47 Processing helix chain 'M' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR M 52 " --> pdb=" O PRO M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 64 No H-bonds generated for 'chain 'M' and resid 62 through 64' Processing helix chain 'N' and resid 8 through 23 Processing helix chain 'N' and resid 30 through 47 Processing helix chain 'N' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR N 52 " --> pdb=" O PRO N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'O' and resid 8 through 23 Processing helix chain 'O' and resid 30 through 47 Processing helix chain 'O' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR O 52 " --> pdb=" O PRO O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 64 No H-bonds generated for 'chain 'O' and resid 62 through 64' Processing helix chain 'P' and resid 8 through 23 Processing helix chain 'P' and resid 30 through 47 Processing helix chain 'P' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR P 52 " --> pdb=" O PRO P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 64 No H-bonds generated for 'chain 'P' and resid 62 through 64' Processing helix chain 'Q' and resid 8 through 23 Processing helix chain 'Q' and resid 30 through 47 Processing helix chain 'Q' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR Q 52 " --> pdb=" O PRO Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 64 No H-bonds generated for 'chain 'Q' and resid 62 through 64' Processing helix chain 'R' and resid 8 through 23 Processing helix chain 'R' and resid 30 through 47 Processing helix chain 'R' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR R 52 " --> pdb=" O PRO R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 64 No H-bonds generated for 'chain 'R' and resid 62 through 64' Processing helix chain 'S' and resid 8 through 23 Processing helix chain 'S' and resid 30 through 47 Processing helix chain 'S' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR S 52 " --> pdb=" O PRO S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'T' and resid 8 through 23 Processing helix chain 'T' and resid 30 through 47 Processing helix chain 'T' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR T 52 " --> pdb=" O PRO T 48 " (cutoff:3.500A) Processing helix chain 'T' and resid 62 through 64 No H-bonds generated for 'chain 'T' and resid 62 through 64' Processing helix chain 'U' and resid 8 through 23 Processing helix chain 'U' and resid 30 through 47 Processing helix chain 'U' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR U 52 " --> pdb=" O PRO U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 62 through 64 No H-bonds generated for 'chain 'U' and resid 62 through 64' Processing helix chain 'V' and resid 8 through 23 Processing helix chain 'V' and resid 30 through 47 Processing helix chain 'V' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR V 52 " --> pdb=" O PRO V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 62 through 64 No H-bonds generated for 'chain 'V' and resid 62 through 64' Processing helix chain 'W' and resid 8 through 23 Processing helix chain 'W' and resid 30 through 47 Processing helix chain 'W' and resid 48 through 59 removed outlier: 3.594A pdb=" N THR W 52 " --> pdb=" O PRO W 48 " (cutoff:3.500A) Processing helix chain 'W' and resid 62 through 64 No H-bonds generated for 'chain 'W' and resid 62 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 96 Processing sheet with id=AA3, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 96 Processing sheet with id=AA5, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 96 Processing sheet with id=AA7, first strand: chain 'D' and resid 66 through 67 Processing sheet with id=AA8, first strand: chain 'D' and resid 90 through 96 Processing sheet with id=AA9, first strand: chain 'E' and resid 66 through 67 Processing sheet with id=AB1, first strand: chain 'E' and resid 90 through 96 Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 67 Processing sheet with id=AB3, first strand: chain 'F' and resid 90 through 96 Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 67 Processing sheet with id=AB5, first strand: chain 'G' and resid 90 through 96 Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 67 Processing sheet with id=AB7, first strand: chain 'H' and resid 90 through 96 Processing sheet with id=AB8, first strand: chain 'I' and resid 66 through 67 Processing sheet with id=AB9, first strand: chain 'I' and resid 90 through 96 Processing sheet with id=AC1, first strand: chain 'J' and resid 66 through 67 Processing sheet with id=AC2, first strand: chain 'J' and resid 90 through 96 Processing sheet with id=AC3, first strand: chain 'K' and resid 66 through 67 Processing sheet with id=AC4, first strand: chain 'K' and resid 90 through 96 Processing sheet with id=AC5, first strand: chain 'L' and resid 66 through 67 Processing sheet with id=AC6, first strand: chain 'L' and resid 90 through 96 Processing sheet with id=AC7, first strand: chain 'M' and resid 66 through 67 Processing sheet with id=AC8, first strand: chain 'M' and resid 90 through 96 Processing sheet with id=AC9, first strand: chain 'N' and resid 66 through 67 Processing sheet with id=AD1, first strand: chain 'N' and resid 90 through 96 Processing sheet with id=AD2, first strand: chain 'O' and resid 66 through 67 Processing sheet with id=AD3, first strand: chain 'O' and resid 90 through 96 Processing sheet with id=AD4, first strand: chain 'P' and resid 66 through 67 Processing sheet with id=AD5, first strand: chain 'P' and resid 90 through 96 Processing sheet with id=AD6, first strand: chain 'Q' and resid 66 through 67 Processing sheet with id=AD7, first strand: chain 'Q' and resid 90 through 96 Processing sheet with id=AD8, first strand: chain 'R' and resid 66 through 67 Processing sheet with id=AD9, first strand: chain 'R' and resid 90 through 96 Processing sheet with id=AE1, first strand: chain 'S' and resid 66 through 67 Processing sheet with id=AE2, first strand: chain 'S' and resid 90 through 96 Processing sheet with id=AE3, first strand: chain 'T' and resid 66 through 67 Processing sheet with id=AE4, first strand: chain 'T' and resid 90 through 96 Processing sheet with id=AE5, first strand: chain 'U' and resid 66 through 67 Processing sheet with id=AE6, first strand: chain 'U' and resid 90 through 96 Processing sheet with id=AE7, first strand: chain 'V' and resid 66 through 67 Processing sheet with id=AE8, first strand: chain 'V' and resid 90 through 96 Processing sheet with id=AE9, first strand: chain 'W' and resid 66 through 67 Processing sheet with id=AF1, first strand: chain 'W' and resid 90 through 96 1150 hydrogen bonds defined for protein. 3381 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.68 Time building geometry restraints manager: 6.16 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: 12721 16.52 - 33.04: 1426 33.04 - 49.56: 369 49.56 - 66.07: 46 66.07 - 82.59: 115 Dihedral angle restraints: 14677 sinusoidal: 5316 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 14674 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: 2.03 - 2.60: 137 2.60 - 3.18: 21554 3.18 - 3.75: 36500 3.75 - 4.33: 53745 4.33 - 4.90: 90824 Nonbonded interactions: 202760 Sorted by model distance: nonbonded pdb=" SG CYS P 134 " pdb=" SG CYS P 147 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS W 134 " pdb=" SG CYS W 147 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS D 134 " pdb=" SG CYS D 147 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS O 134 " pdb=" SG CYS O 147 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS M 134 " pdb=" SG CYS M 147 " model vdw 2.032 3.760 ... (remaining 202755 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: 0.25 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: 9.180 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: 0.000 Extract box with map and model: 0.960 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 44.020 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.960 ------------------------------------------------------------------------------- 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 24311 Z= 0.136 Angle : 0.416 4.536 33143 Z= 0.226 Chirality : 0.044 0.131 4186 Planarity : 0.003 0.017 4209 Dihedral : 17.574 82.593 8648 Min Nonbonded Distance : 2.031 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 *********************** 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 : 2.972 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: 0.3704 time to fit residues: 364.9291 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 : 2.762 ------------------------------------------------------------------------------- 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: 7.9990 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 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 149 ASN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 149 ASN E 31 GLN E 149 ASN F 29 GLN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN G 109 GLN G 149 ASN H 149 ASN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 ASN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 149 ASN K 29 GLN K 149 ASN L 29 GLN L 87 ASN L 149 ASN M 29 GLN M 109 GLN M 149 ASN N 149 ASN O 87 ASN O 149 ASN P 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 149 ASN V 149 ASN W 149 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.099798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.091237 restraints weight = 33056.464| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.17 r_work: 0.2874 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 24311 Z= 0.142 Angle : 0.442 4.543 33143 Z= 0.238 Chirality : 0.046 0.146 4186 Planarity : 0.003 0.020 4209 Dihedral : 3.497 14.534 3430 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 3.39 % Allowed : 21.16 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.18 (0.15), residues: 3243 helix: 2.50 (0.17), residues: 1081 sheet: 1.33 (0.20), residues: 713 loop : 2.51 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 132 PHE 0.006 0.001 PHE R 108 TYR 0.008 0.001 TYR G 33 ARG 0.002 0.000 ARG R 126 *********************** 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 575 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 487 time to evaluate : 2.719 Fit side-chains revert: symmetry clash REVERT: A 82 VAL cc_start: 0.8591 (m) cc_final: 0.8303 (m) REVERT: B 43 LEU cc_start: 0.9084 (tp) cc_final: 0.8871 (tp) REVERT: B 65 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7305 (mttt) REVERT: C 135 LYS cc_start: 0.8138 (tptt) cc_final: 0.7885 (mttp) REVERT: D 65 LYS cc_start: 0.8594 (mmtt) cc_final: 0.8108 (mmtp) REVERT: I 70 THR cc_start: 0.8682 (p) cc_final: 0.8438 (m) REVERT: I 91 VAL cc_start: 0.9193 (m) cc_final: 0.8924 (t) REVERT: I 97 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7686 (mm-30) REVERT: I 116 LYS cc_start: 0.8147 (mmtm) cc_final: 0.7876 (mmtt) REVERT: I 148 ASP cc_start: 0.7929 (m-30) cc_final: 0.7505 (t0) REVERT: K 91 VAL cc_start: 0.9006 (m) cc_final: 0.8724 (t) REVERT: L 135 LYS cc_start: 0.8229 (tmtt) cc_final: 0.7856 (mtpt) REVERT: M 29 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7526 (mt0) REVERT: N 129 ASP cc_start: 0.7683 (m-30) cc_final: 0.7394 (m-30) REVERT: O 43 LEU cc_start: 0.8999 (tp) cc_final: 0.8732 (tp) REVERT: P 135 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7805 (mptt) REVERT: Q 135 LYS cc_start: 0.7997 (tptt) cc_final: 0.7704 (tttm) REVERT: R 135 LYS cc_start: 0.8262 (tptt) cc_final: 0.7793 (ttpp) REVERT: R 141 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8256 (ptm) REVERT: W 8 THR cc_start: 0.6777 (OUTLIER) cc_final: 0.6350 (m) REVERT: W 135 LYS cc_start: 0.8404 (tptt) cc_final: 0.8118 (mtpp) outliers start: 88 outliers final: 58 residues processed: 544 average time/residue: 0.3480 time to fit residues: 300.2088 Evaluate side-chains 497 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 436 time to evaluate : 2.720 ------------------------------------------------------------------------------- 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 73 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 19 ILE 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 M residue 147 CYS Chi-restraints excluded: chain N residue 73 SER 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 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: 4.9990 chunk 129 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 chunk 318 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 136 optimal weight: 0.8980 chunk 305 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 138 GLN B 149 ASN ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN D 31 GLN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN F 149 ASN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN I 109 GLN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN O 29 GLN O 149 ASN P 149 ASN R 109 GLN R 125 ASN S 109 GLN T 109 GLN U 109 GLN U 138 GLN U 149 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.091841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.083192 restraints weight = 33524.148| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 1.17 r_work: 0.2742 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 24311 Z= 0.385 Angle : 0.563 4.840 33143 Z= 0.307 Chirality : 0.051 0.209 4186 Planarity : 0.004 0.038 4209 Dihedral : 4.532 25.038 3427 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.04 % Allowed : 19.85 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.15), residues: 3243 helix: 2.04 (0.17), residues: 1081 sheet: 1.28 (0.19), residues: 713 loop : 2.07 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 132 PHE 0.013 0.002 PHE E 142 TYR 0.012 0.002 TYR I 30 ARG 0.004 0.001 ARG Q 59 *********************** 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 571 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 440 time to evaluate : 2.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8610 (mp) REVERT: B 31 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8203 (pt0) REVERT: B 65 LYS cc_start: 0.8307 (mmtt) cc_final: 0.7379 (mttt) REVERT: C 22 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8124 (mp) REVERT: C 135 LYS cc_start: 0.8305 (tptt) cc_final: 0.8025 (mptt) REVERT: C 148 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7145 (m-30) REVERT: D 65 LYS cc_start: 0.8574 (mmtt) cc_final: 0.8093 (mmtp) REVERT: E 141 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8137 (ptt) REVERT: F 22 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8084 (mp) REVERT: I 91 VAL cc_start: 0.9284 (m) cc_final: 0.9066 (t) REVERT: I 97 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7732 (mm-30) REVERT: I 148 ASP cc_start: 0.8002 (m-30) cc_final: 0.7661 (m-30) REVERT: J 22 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8076 (mp) REVERT: K 31 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7845 (pt0) REVERT: L 22 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8285 (mp) REVERT: L 135 LYS cc_start: 0.8154 (tmtt) cc_final: 0.7819 (mtpt) REVERT: M 7 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.7009 (t80) REVERT: M 22 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8122 (mp) REVERT: M 135 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8496 (tttp) REVERT: N 87 ASN cc_start: 0.9076 (t0) cc_final: 0.8755 (t0) REVERT: N 129 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7402 (m-30) REVERT: O 7 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7537 (t80) REVERT: O 129 ASP cc_start: 0.8330 (t70) cc_final: 0.7800 (t0) REVERT: P 22 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8394 (mp) REVERT: P 135 LYS cc_start: 0.8388 (mmtt) cc_final: 0.8182 (tttp) REVERT: Q 22 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8320 (mp) REVERT: Q 87 ASN cc_start: 0.8670 (t0) cc_final: 0.8433 (t0) REVERT: Q 135 LYS cc_start: 0.8033 (tptt) cc_final: 0.7672 (tttm) REVERT: R 135 LYS cc_start: 0.8405 (tptt) cc_final: 0.7747 (ttpp) REVERT: S 22 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8392 (mp) REVERT: T 135 LYS cc_start: 0.8479 (tptt) cc_final: 0.8130 (mmtm) outliers start: 131 outliers final: 85 residues processed: 536 average time/residue: 0.3483 time to fit residues: 297.5247 Evaluate side-chains 517 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 416 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 31 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 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 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 M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain N residue 147 CYS Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 112 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 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 91 VAL 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 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 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 U residue 147 CYS Chi-restraints excluded: chain V residue 139 ASP Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 112 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 201 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 282 optimal weight: 0.8980 chunk 94 optimal weight: 0.0670 chunk 236 optimal weight: 9.9990 chunk 225 optimal weight: 0.9990 chunk 319 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 318 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 138 GLN D 109 GLN D 125 ASN G 109 GLN H 109 GLN J 109 GLN M 109 GLN P 149 ASN U 29 GLN U 138 GLN V 31 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.094318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.085748 restraints weight = 33587.674| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.16 r_work: 0.2783 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24311 Z= 0.207 Angle : 0.465 5.203 33143 Z= 0.251 Chirality : 0.047 0.156 4186 Planarity : 0.003 0.028 4209 Dihedral : 4.096 25.002 3427 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 4.27 % Allowed : 20.85 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.15), residues: 3243 helix: 2.30 (0.17), residues: 1081 sheet: 1.19 (0.19), residues: 713 loop : 2.09 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 132 PHE 0.007 0.001 PHE W 108 TYR 0.007 0.001 TYR B 33 ARG 0.002 0.000 ARG E 59 *********************** 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 543 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 432 time to evaluate : 3.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8082 (p0) cc_final: 0.7776 (p0) REVERT: B 31 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8104 (pt0) REVERT: B 65 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7403 (mttt) REVERT: B 77 GLU cc_start: 0.8174 (mp0) cc_final: 0.7782 (mp0) REVERT: C 77 GLU cc_start: 0.8254 (mp0) cc_final: 0.7910 (mp0) REVERT: C 135 LYS cc_start: 0.8358 (tptt) cc_final: 0.8022 (mptt) REVERT: D 65 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8101 (mmtp) REVERT: E 141 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8174 (ptt) REVERT: I 97 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7760 (mm-30) REVERT: I 148 ASP cc_start: 0.8038 (m-30) cc_final: 0.7688 (m-30) REVERT: J 13 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8321 (mmm) REVERT: K 22 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8063 (mp) REVERT: K 31 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7718 (pt0) REVERT: K 91 VAL cc_start: 0.9002 (m) cc_final: 0.8729 (t) REVERT: L 103 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7535 (p0) REVERT: L 129 ASP cc_start: 0.7617 (t0) cc_final: 0.7377 (t0) REVERT: L 135 LYS cc_start: 0.8169 (tmtt) cc_final: 0.7837 (mtpt) REVERT: M 7 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6985 (t80) REVERT: M 29 GLN cc_start: 0.8144 (tt0) cc_final: 0.7571 (mt0) REVERT: M 135 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8506 (tttp) REVERT: N 22 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8571 (mp) REVERT: N 129 ASP cc_start: 0.7647 (m-30) cc_final: 0.7345 (m-30) REVERT: O 7 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7576 (t80) REVERT: O 129 ASP cc_start: 0.8321 (t70) cc_final: 0.7754 (t0) REVERT: P 135 LYS cc_start: 0.8397 (mmtt) cc_final: 0.8185 (tttp) REVERT: Q 77 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8058 (mt-10) REVERT: Q 87 ASN cc_start: 0.8624 (t0) cc_final: 0.8420 (t0) REVERT: Q 135 LYS cc_start: 0.8081 (tptt) cc_final: 0.7677 (tttm) REVERT: R 135 LYS cc_start: 0.8387 (tptt) cc_final: 0.7778 (ttpp) REVERT: S 7 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.7257 (t80) REVERT: S 91 VAL cc_start: 0.9221 (m) cc_final: 0.8985 (t) REVERT: T 135 LYS cc_start: 0.8497 (tptt) cc_final: 0.8136 (mmtm) REVERT: W 10 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8179 (mm) outliers start: 111 outliers final: 80 residues processed: 511 average time/residue: 0.3584 time to fit residues: 292.9084 Evaluate side-chains 502 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 411 time to evaluate : 2.747 ------------------------------------------------------------------------------- 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 11 GLU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 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 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 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 73 SER Chi-restraints excluded: chain J residue 103 ASP 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 103 ASP Chi-restraints excluded: chain L residue 112 THR 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 92 ILE Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain 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 78 THR Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain S residue 7 PHE Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 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 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 110 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain V residue 31 GLN Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 135 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 175 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 233 optimal weight: 0.0060 chunk 313 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 252 optimal weight: 0.0980 chunk 35 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 chunk 267 optimal weight: 8.9990 chunk 234 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 overall best weight: 3.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 138 GLN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 149 ASN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 GLN I 109 GLN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 GLN P 149 ASN R 109 GLN T 87 ASN T 149 ASN V 31 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.092010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.083124 restraints weight = 33831.938| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.25 r_work: 0.2737 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 24311 Z= 0.319 Angle : 0.519 7.368 33143 Z= 0.281 Chirality : 0.049 0.174 4186 Planarity : 0.004 0.034 4209 Dihedral : 4.429 31.196 3427 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.43 % Allowed : 19.35 % 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: 2.49 (0.15), residues: 3243 helix: 2.10 (0.17), residues: 1081 sheet: 0.96 (0.19), residues: 713 loop : 1.94 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 132 PHE 0.010 0.001 PHE E 142 TYR 0.014 0.001 TYR G 33 ARG 0.003 0.001 ARG S 59 *********************** 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 557 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 416 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8154 (pt0) REVERT: B 65 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7367 (mttt) REVERT: B 77 GLU cc_start: 0.8201 (mp0) cc_final: 0.7860 (mp0) REVERT: C 22 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8146 (mp) REVERT: C 135 LYS cc_start: 0.8248 (tptt) cc_final: 0.7936 (mptt) REVERT: D 65 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8059 (mmtp) REVERT: E 141 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8218 (ptt) REVERT: F 22 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8090 (mp) REVERT: H 31 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: I 97 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7675 (mm-30) REVERT: I 129 ASP cc_start: 0.8099 (t70) cc_final: 0.7877 (t70) REVERT: J 22 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8035 (mp) REVERT: J 129 ASP cc_start: 0.7564 (m-30) cc_final: 0.6816 (t70) REVERT: K 22 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8016 (mp) REVERT: K 31 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7770 (pt0) REVERT: L 22 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8239 (mp) REVERT: L 103 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7554 (p0) REVERT: L 135 LYS cc_start: 0.8164 (tmtt) cc_final: 0.7800 (mtpt) REVERT: M 7 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.7003 (t80) REVERT: M 22 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8091 (mp) REVERT: M 135 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8535 (tttp) REVERT: N 22 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8540 (mp) REVERT: N 129 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7349 (m-30) REVERT: O 7 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7770 (t80) REVERT: O 11 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: O 129 ASP cc_start: 0.8302 (t70) cc_final: 0.7720 (t0) REVERT: P 22 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8338 (mp) REVERT: P 135 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8197 (tttp) REVERT: Q 31 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.8016 (pt0) REVERT: Q 77 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8113 (mt-10) REVERT: Q 87 ASN cc_start: 0.8685 (t0) cc_final: 0.8448 (t0) REVERT: Q 135 LYS cc_start: 0.8196 (tptt) cc_final: 0.7718 (tttm) REVERT: R 135 LYS cc_start: 0.8450 (tptt) cc_final: 0.7828 (ttpp) REVERT: R 141 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8288 (ptm) REVERT: S 7 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.7324 (t80) REVERT: S 22 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8359 (mp) REVERT: S 91 VAL cc_start: 0.9173 (m) cc_final: 0.8928 (t) REVERT: T 135 LYS cc_start: 0.8517 (tptt) cc_final: 0.8199 (mmtm) REVERT: V 135 LYS cc_start: 0.8533 (mptt) cc_final: 0.8123 (mttt) REVERT: W 10 ILE cc_start: 0.8522 (mt) cc_final: 0.8296 (mm) REVERT: W 31 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7831 (pt0) outliers start: 141 outliers final: 103 residues processed: 518 average time/residue: 0.3408 time to fit residues: 282.6507 Evaluate side-chains 531 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 406 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 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 112 THR Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR 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 L residue 8 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain L residue 112 THR 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 22 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 74 THR 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 11 GLU 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 92 ILE 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 77 GLU 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 82 VAL Chi-restraints excluded: chain Q residue 85 ASP 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 141 MET Chi-restraints excluded: chain R residue 148 ASP Chi-restraints excluded: chain S residue 7 PHE Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 87 ASN Chi-restraints excluded: chain T residue 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 110 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain U residue 141 MET 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 V residue 139 ASP Chi-restraints excluded: chain W residue 31 GLN 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 Chi-restraints excluded: chain W residue 135 LYS Chi-restraints excluded: chain W residue 148 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 139 optimal weight: 8.9990 chunk 298 optimal weight: 0.9980 chunk 137 optimal weight: 9.9990 chunk 282 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 190 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 297 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN B 47 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN T 87 ASN V 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.091610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.083106 restraints weight = 33717.269| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.16 r_work: 0.2745 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 24311 Z= 0.315 Angle : 0.520 7.277 33143 Z= 0.282 Chirality : 0.049 0.168 4186 Planarity : 0.004 0.033 4209 Dihedral : 4.493 32.943 3427 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.50 % Allowed : 19.43 % 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: 2.36 (0.15), residues: 3243 helix: 2.06 (0.17), residues: 1081 sheet: 0.79 (0.18), residues: 713 loop : 1.86 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 132 PHE 0.009 0.001 PHE E 142 TYR 0.013 0.001 TYR G 33 ARG 0.004 0.001 ARG P 59 *********************** 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 556 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 413 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8173 (pt0) REVERT: B 65 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7416 (mttt) REVERT: B 77 GLU cc_start: 0.8165 (mp0) cc_final: 0.7669 (mp0) REVERT: C 22 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8174 (mp) REVERT: C 135 LYS cc_start: 0.8229 (tptt) cc_final: 0.7880 (mttp) REVERT: D 65 LYS cc_start: 0.8628 (mmtt) cc_final: 0.8106 (mmtp) REVERT: E 141 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8210 (ptt) REVERT: F 22 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8148 (mp) REVERT: H 31 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7464 (pt0) REVERT: I 97 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7708 (mm-30) REVERT: I 129 ASP cc_start: 0.8077 (t70) cc_final: 0.7823 (t70) REVERT: J 22 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8058 (mp) REVERT: J 129 ASP cc_start: 0.7549 (m-30) cc_final: 0.6904 (t70) REVERT: K 22 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8032 (mp) REVERT: K 31 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7764 (pt0) REVERT: L 22 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8274 (mp) REVERT: L 103 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7465 (p0) REVERT: L 135 LYS cc_start: 0.8138 (tmtt) cc_final: 0.7749 (mtpt) REVERT: M 7 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.7000 (t80) REVERT: M 22 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8100 (mp) REVERT: M 135 LYS cc_start: 0.8868 (mmtt) cc_final: 0.8526 (tttp) REVERT: N 22 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8531 (mp) REVERT: N 129 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7376 (m-30) REVERT: O 11 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: O 129 ASP cc_start: 0.8323 (t70) cc_final: 0.7747 (t0) REVERT: P 22 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8331 (mp) REVERT: P 135 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8193 (tttp) REVERT: Q 31 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8020 (pt0) REVERT: Q 77 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8087 (mt-10) REVERT: Q 87 ASN cc_start: 0.8679 (t0) cc_final: 0.8442 (t0) REVERT: Q 135 LYS cc_start: 0.8269 (tptt) cc_final: 0.7832 (tttm) REVERT: R 135 LYS cc_start: 0.8438 (tptt) cc_final: 0.7844 (ttpp) REVERT: R 141 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8285 (ptm) REVERT: S 22 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8352 (mp) REVERT: S 91 VAL cc_start: 0.9213 (m) cc_final: 0.8948 (t) REVERT: T 135 LYS cc_start: 0.8479 (tptt) cc_final: 0.8177 (mmtm) REVERT: V 135 LYS cc_start: 0.8522 (mptt) cc_final: 0.8179 (mttt) REVERT: W 31 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7832 (pt0) outliers start: 143 outliers final: 109 residues processed: 519 average time/residue: 0.3469 time to fit residues: 287.9852 Evaluate side-chains 534 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 405 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 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 112 THR Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR 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 78 THR Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 148 ASP Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 11 GLU 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 22 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 74 THR 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 11 GLU 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 92 ILE 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 77 GLU 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 82 VAL Chi-restraints excluded: chain Q residue 85 ASP 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 141 MET 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 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 87 ASN 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 110 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain U residue 149 ASN 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 V residue 139 ASP Chi-restraints excluded: chain W residue 31 GLN 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 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: 2.9990 chunk 208 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 254 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 320 optimal weight: 7.9990 chunk 317 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 209 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.094048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.085529 restraints weight = 33475.806| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.16 r_work: 0.2784 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24311 Z= 0.192 Angle : 0.461 6.319 33143 Z= 0.248 Chirality : 0.047 0.149 4186 Planarity : 0.004 0.031 4209 Dihedral : 4.119 29.752 3427 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.69 % Allowed : 20.39 % 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: 2.57 (0.15), residues: 3243 helix: 2.32 (0.17), residues: 1081 sheet: 0.81 (0.18), residues: 713 loop : 1.97 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 132 PHE 0.006 0.001 PHE W 108 TYR 0.009 0.001 TYR G 33 ARG 0.003 0.000 ARG S 126 *********************** 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 546 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 424 time to evaluate : 2.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8262 (t0) cc_final: 0.7898 (t0) REVERT: B 31 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8094 (pt0) REVERT: B 65 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7436 (mttt) REVERT: B 77 GLU cc_start: 0.8169 (mp0) cc_final: 0.7729 (mp0) REVERT: C 22 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8184 (mp) REVERT: C 77 GLU cc_start: 0.8207 (mp0) cc_final: 0.7918 (mp0) REVERT: C 135 LYS cc_start: 0.8226 (tptt) cc_final: 0.7991 (mtmm) REVERT: D 65 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8100 (mmtp) REVERT: E 141 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8199 (ptt) REVERT: H 31 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7349 (pt0) REVERT: I 97 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7708 (mm-30) REVERT: I 129 ASP cc_start: 0.8034 (t70) cc_final: 0.7813 (t70) REVERT: J 22 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8063 (mp) REVERT: J 129 ASP cc_start: 0.7503 (m-30) cc_final: 0.6856 (t70) REVERT: K 22 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8031 (mp) REVERT: K 31 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7709 (pt0) REVERT: L 22 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8291 (mp) REVERT: L 103 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7383 (p0) REVERT: L 135 LYS cc_start: 0.8130 (tmtt) cc_final: 0.7755 (mtpt) REVERT: M 7 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.7031 (t80) REVERT: M 22 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8043 (mp) REVERT: M 29 GLN cc_start: 0.8134 (tt0) cc_final: 0.7577 (mt0) REVERT: M 67 LYS cc_start: 0.8449 (mtmt) cc_final: 0.8192 (mtmt) REVERT: M 135 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8490 (tttp) REVERT: N 22 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8511 (mp) REVERT: N 129 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7282 (m-30) REVERT: O 129 ASP cc_start: 0.8326 (t70) cc_final: 0.7767 (t0) REVERT: Q 77 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8132 (mt-10) REVERT: Q 135 LYS cc_start: 0.8262 (tptt) cc_final: 0.7820 (tttm) REVERT: R 135 LYS cc_start: 0.8428 (tptt) cc_final: 0.7846 (ttpp) REVERT: R 141 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8244 (ptm) REVERT: S 22 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8419 (mp) REVERT: S 91 VAL cc_start: 0.9195 (m) cc_final: 0.8973 (t) REVERT: T 135 LYS cc_start: 0.8466 (tptt) cc_final: 0.8157 (mmtm) REVERT: V 135 LYS cc_start: 0.8520 (mptt) cc_final: 0.8157 (mttt) REVERT: W 31 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7787 (pt0) outliers start: 122 outliers final: 89 residues processed: 514 average time/residue: 0.3363 time to fit residues: 276.4402 Evaluate side-chains 518 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 413 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 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 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 29 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 112 THR Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain L residue 112 THR 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 11 GLU 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 22 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 92 ILE 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 74 THR Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 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 141 MET 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 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 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 78 THR Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 13 MET Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain W residue 31 GLN 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 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: 4.9990 chunk 215 optimal weight: 4.9990 chunk 303 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 300 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 D 149 ASN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 149 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.091302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.082826 restraints weight = 33743.635| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.16 r_work: 0.2741 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24311 Z= 0.345 Angle : 0.536 8.316 33143 Z= 0.290 Chirality : 0.050 0.173 4186 Planarity : 0.004 0.033 4209 Dihedral : 4.587 33.116 3427 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.31 % Allowed : 19.85 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.15), residues: 3243 helix: 2.03 (0.17), residues: 1081 sheet: 0.66 (0.18), residues: 713 loop : 1.81 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 132 PHE 0.010 0.001 PHE E 142 TYR 0.014 0.001 TYR G 33 ARG 0.004 0.001 ARG P 59 *********************** 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 546 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 408 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.8282 (t0) cc_final: 0.7871 (t0) REVERT: B 31 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8208 (pt0) REVERT: B 65 LYS cc_start: 0.8354 (mmtt) cc_final: 0.7442 (mttt) REVERT: B 77 GLU cc_start: 0.8177 (mp0) cc_final: 0.7754 (mp0) REVERT: C 22 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8120 (mp) REVERT: C 135 LYS cc_start: 0.8256 (tptt) cc_final: 0.7990 (mtmm) REVERT: D 65 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8108 (mmtp) REVERT: E 141 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8234 (ptt) REVERT: H 31 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7496 (pt0) REVERT: I 97 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7717 (mm-30) REVERT: J 22 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8066 (mp) REVERT: J 129 ASP cc_start: 0.7541 (m-30) cc_final: 0.6959 (t70) REVERT: K 22 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8035 (mp) REVERT: K 31 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7808 (pt0) REVERT: L 22 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8255 (mp) REVERT: L 103 ASP cc_start: 0.7919 (p0) cc_final: 0.7460 (p0) REVERT: L 129 ASP cc_start: 0.7891 (t0) cc_final: 0.7616 (t0) REVERT: L 135 LYS cc_start: 0.8141 (tmtt) cc_final: 0.7771 (mtpt) REVERT: M 7 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.7009 (t80) REVERT: M 22 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8121 (mp) REVERT: M 67 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8261 (mtmt) REVERT: M 135 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8547 (tttp) REVERT: N 129 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7313 (m-30) REVERT: O 129 ASP cc_start: 0.8314 (t70) cc_final: 0.7729 (t0) REVERT: P 7 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7889 (t80) REVERT: P 22 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8335 (mp) REVERT: Q 31 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8027 (pt0) REVERT: Q 77 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8116 (mt-10) REVERT: Q 135 LYS cc_start: 0.8207 (tptt) cc_final: 0.7776 (tttm) REVERT: R 135 LYS cc_start: 0.8433 (tptt) cc_final: 0.7870 (ttpp) REVERT: R 141 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8283 (ptm) REVERT: S 22 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8402 (mp) REVERT: S 91 VAL cc_start: 0.9194 (m) cc_final: 0.8928 (t) REVERT: T 135 LYS cc_start: 0.8451 (tptt) cc_final: 0.8163 (mmtm) REVERT: V 22 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8430 (mp) REVERT: V 97 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: V 135 LYS cc_start: 0.8520 (mptt) cc_final: 0.8151 (mttt) REVERT: W 31 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7891 (pt0) outliers start: 138 outliers final: 109 residues processed: 512 average time/residue: 0.3441 time to fit residues: 280.3024 Evaluate side-chains 529 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 401 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 109 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 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 D residue 149 ASN 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 76 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 141 MET Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 148 ASP Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain K residue 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 112 THR Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 148 ASP Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 11 GLU 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 22 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 116 LYS 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 82 VAL Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 141 MET 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 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 73 SER Chi-restraints excluded: chain U residue 78 THR 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 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 31 GLN 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 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: 2.9990 chunk 10 optimal weight: 1.9990 chunk 121 optimal weight: 0.0270 chunk 76 optimal weight: 5.9990 chunk 108 optimal weight: 0.0970 chunk 199 optimal weight: 0.8980 chunk 237 optimal weight: 0.9980 chunk 292 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 189 optimal weight: 6.9990 chunk 303 optimal weight: 6.9990 overall best weight: 0.5836 ------------------------------------------------------------------------------- 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 G 29 GLN G 109 GLN I 31 GLN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 ASN Q 87 ASN Q 149 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.097196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.088732 restraints weight = 33266.511| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.16 r_work: 0.2831 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24311 Z= 0.125 Angle : 0.434 7.877 33143 Z= 0.232 Chirality : 0.046 0.146 4186 Planarity : 0.003 0.029 4209 Dihedral : 3.848 25.569 3427 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.27 % Allowed : 21.97 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.15), residues: 3243 helix: 2.47 (0.17), residues: 1081 sheet: 0.84 (0.19), residues: 713 loop : 2.02 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 132 PHE 0.005 0.001 PHE B 108 TYR 0.008 0.001 TYR I 33 ARG 0.004 0.000 ARG P 59 *********************** 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 527 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 442 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8026 (p0) cc_final: 0.7680 (p0) REVERT: A 125 ASN cc_start: 0.8170 (t0) cc_final: 0.7811 (t0) REVERT: B 65 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7418 (mttt) REVERT: B 77 GLU cc_start: 0.8131 (mp0) cc_final: 0.7775 (mp0) REVERT: C 22 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8174 (mp) REVERT: C 77 GLU cc_start: 0.8214 (mp0) cc_final: 0.7855 (mp0) REVERT: C 135 LYS cc_start: 0.8239 (tptt) cc_final: 0.7978 (mtmm) REVERT: D 65 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8059 (mmtp) REVERT: E 141 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8181 (ptt) REVERT: G 85 ASP cc_start: 0.8267 (p0) cc_final: 0.7971 (p0) REVERT: G 141 MET cc_start: 0.8466 (ptp) cc_final: 0.8177 (ptm) REVERT: H 31 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7229 (pt0) REVERT: I 97 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7738 (mm-30) REVERT: J 67 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8486 (mmtt) REVERT: J 129 ASP cc_start: 0.7496 (m-30) cc_final: 0.6859 (t70) REVERT: K 31 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7651 (pt0) REVERT: K 65 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8336 (mmtp) REVERT: K 91 VAL cc_start: 0.8950 (m) cc_final: 0.8697 (t) REVERT: L 135 LYS cc_start: 0.8159 (tmtt) cc_final: 0.7768 (mtpt) REVERT: M 7 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6948 (t80) REVERT: M 22 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8014 (mp) REVERT: M 29 GLN cc_start: 0.8021 (tt0) cc_final: 0.7479 (mt0) REVERT: M 67 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8200 (mtmt) REVERT: M 135 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8519 (tttp) REVERT: N 22 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8495 (mp) REVERT: N 87 ASN cc_start: 0.9135 (t0) cc_final: 0.8897 (t0) REVERT: O 43 LEU cc_start: 0.9016 (tp) cc_final: 0.8740 (tp) REVERT: O 129 ASP cc_start: 0.8405 (t70) cc_final: 0.7932 (t0) REVERT: P 7 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7849 (t80) REVERT: Q 77 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8128 (mt-10) REVERT: Q 135 LYS cc_start: 0.8213 (tptt) cc_final: 0.7813 (tttm) REVERT: R 135 LYS cc_start: 0.8346 (tptt) cc_final: 0.7759 (ttpp) REVERT: S 91 VAL cc_start: 0.9225 (m) cc_final: 0.9015 (t) REVERT: T 135 LYS cc_start: 0.8436 (tptt) cc_final: 0.8110 (mmtm) REVERT: V 22 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8482 (mp) REVERT: V 97 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: V 103 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7858 (p0) REVERT: V 135 LYS cc_start: 0.8492 (mptt) cc_final: 0.8156 (mttt) REVERT: W 77 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7688 (mt-10) outliers start: 85 outliers final: 56 residues processed: 502 average time/residue: 0.3436 time to fit residues: 274.7982 Evaluate side-chains 489 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 422 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 78 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 22 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain 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 11 GLU 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 22 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 82 VAL 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 29 GLN Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 141 MET 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 78 THR 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 141 MET Chi-restraints excluded: chain V residue 7 PHE 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 W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 248 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 253 optimal weight: 8.9990 chunk 246 optimal weight: 2.9990 chunk 318 optimal weight: 0.1980 chunk 268 optimal weight: 4.9990 chunk 90 optimal weight: 0.0980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 109 GLN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN G 29 GLN G 109 GLN H 29 GLN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN T 149 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.095563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.087077 restraints weight = 33406.185| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.16 r_work: 0.2815 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24311 Z= 0.164 Angle : 0.450 7.593 33143 Z= 0.240 Chirality : 0.046 0.147 4186 Planarity : 0.003 0.030 4209 Dihedral : 3.890 23.596 3427 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.81 % Allowed : 22.82 % Favored : 74.37 % 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: 2.74 (0.15), residues: 3243 helix: 2.50 (0.17), residues: 1081 sheet: 0.86 (0.19), residues: 713 loop : 2.05 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 132 PHE 0.006 0.001 PHE W 7 TYR 0.009 0.001 TYR I 33 ARG 0.003 0.000 ARG P 59 ********************** 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 499 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 426 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8002 (p0) cc_final: 0.7651 (p0) REVERT: A 125 ASN cc_start: 0.8204 (t0) cc_final: 0.7836 (t0) REVERT: B 65 LYS cc_start: 0.8345 (mmtt) cc_final: 0.7420 (mttt) REVERT: B 77 GLU cc_start: 0.8131 (mp0) cc_final: 0.7749 (mp0) REVERT: C 22 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8126 (mp) REVERT: C 77 GLU cc_start: 0.8190 (mp0) cc_final: 0.7923 (mp0) REVERT: C 135 LYS cc_start: 0.8265 (tptt) cc_final: 0.8013 (mtmm) REVERT: D 65 LYS cc_start: 0.8622 (mmtt) cc_final: 0.8073 (mmtp) REVERT: E 141 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8214 (ptt) REVERT: G 141 MET cc_start: 0.8458 (ptp) cc_final: 0.8161 (ptm) REVERT: H 31 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7271 (pt0) REVERT: I 97 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7766 (mm-30) REVERT: J 67 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8495 (mmtt) REVERT: J 129 ASP cc_start: 0.7523 (m-30) cc_final: 0.6900 (t70) REVERT: K 31 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7702 (pt0) REVERT: K 65 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8329 (mmtp) REVERT: L 135 LYS cc_start: 0.8152 (tmtt) cc_final: 0.7795 (mtpt) REVERT: M 7 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.6938 (t80) REVERT: M 22 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8002 (mp) REVERT: M 29 GLN cc_start: 0.8120 (tt0) cc_final: 0.7564 (mt0) REVERT: M 67 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8211 (mtmt) REVERT: M 135 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8516 (tttp) REVERT: N 87 ASN cc_start: 0.9136 (t0) cc_final: 0.8873 (t0) REVERT: O 129 ASP cc_start: 0.8358 (t70) cc_final: 0.7845 (t0) REVERT: P 7 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7895 (t80) REVERT: Q 77 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8136 (mt-10) REVERT: Q 135 LYS cc_start: 0.8183 (tptt) cc_final: 0.7617 (tttm) REVERT: R 135 LYS cc_start: 0.8382 (tptt) cc_final: 0.7753 (ttpp) REVERT: S 91 VAL cc_start: 0.9221 (m) cc_final: 0.8987 (t) REVERT: T 135 LYS cc_start: 0.8403 (tptt) cc_final: 0.8101 (mmtm) REVERT: V 22 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8487 (mp) REVERT: V 97 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: V 103 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7863 (p0) REVERT: V 135 LYS cc_start: 0.8495 (mptt) cc_final: 0.8153 (mttt) REVERT: W 77 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7690 (mt-10) outliers start: 73 outliers final: 59 residues processed: 479 average time/residue: 0.3426 time to fit residues: 260.5507 Evaluate side-chains 488 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 419 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 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 11 GLU 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 22 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 82 VAL 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 41 SER Chi-restraints excluded: chain R residue 78 THR 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 78 THR 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 78 THR Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain V residue 7 PHE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 250 optimal weight: 7.9990 chunk 241 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 174 optimal weight: 8.9990 chunk 319 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 F 31 GLN G 29 GLN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN Q 149 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.092483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.084000 restraints weight = 33612.784| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.16 r_work: 0.2760 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24311 Z= 0.276 Angle : 0.509 7.841 33143 Z= 0.274 Chirality : 0.049 0.161 4186 Planarity : 0.004 0.031 4209 Dihedral : 4.312 26.743 3427 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.96 % Allowed : 22.66 % Favored : 74.37 % 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: 2.50 (0.15), residues: 3243 helix: 2.27 (0.17), residues: 1081 sheet: 0.71 (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 0.008 0.001 PHE E 142 TYR 0.013 0.001 TYR H 33 ARG 0.007 0.001 ARG P 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10461.38 seconds wall clock time: 189 minutes 54.69 seconds (11394.69 seconds total)