Starting phenix.real_space_refine on Sun Sep 29 21:21:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ewx_50025/09_2024/9ewx_50025.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ewx_50025/09_2024/9ewx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ewx_50025/09_2024/9ewx_50025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ewx_50025/09_2024/9ewx_50025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ewx_50025/09_2024/9ewx_50025.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ewx_50025/09_2024/9ewx_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-5461/modules/chem_data/mon_lib" Total number of atoms: 23989 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V Time building chain proxies: 6.44, per 1000 atoms: 0.27 Number of scatterers: 23989 At special positions: 0 Unit cell: (71.688, 71.688, 319.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 4853 8.00 N 3933 7.00 C 15111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=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: 5.69 Conformation dependent library (CDL) restraints added in 3.3 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: 2.67 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: 7.05 Time building geometry restraints manager: 6.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7843 1.35 - 1.46: 4991 1.46 - 1.58: 11339 1.58 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 24311 Sorted by residual: bond pdb=" CG GLN K 109 " pdb=" CD GLN K 109 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.54e-01 bond pdb=" CG GLN F 109 " pdb=" CD GLN F 109 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.47e-01 bond pdb=" CG GLN J 109 " pdb=" CD GLN J 109 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.36e-01 bond pdb=" CG GLN O 109 " pdb=" CD GLN O 109 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.35e-01 bond pdb=" CG GLN P 109 " pdb=" CD GLN P 109 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.30e-01 ... (remaining 24306 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 32130 0.91 - 1.81: 682 1.81 - 2.72: 216 2.72 - 3.63: 92 3.63 - 4.54: 23 Bond angle restraints: 33143 Sorted by residual: angle pdb=" CB GLN E 109 " pdb=" CG GLN E 109 " pdb=" CD GLN E 109 " ideal model delta sigma weight residual 112.60 115.48 -2.88 1.70e+00 3.46e-01 2.87e+00 angle pdb=" CB GLN R 109 " pdb=" CG GLN R 109 " pdb=" CD GLN R 109 " ideal model delta sigma weight residual 112.60 115.47 -2.87 1.70e+00 3.46e-01 2.86e+00 angle pdb=" CB GLN H 109 " pdb=" CG GLN H 109 " pdb=" CD GLN H 109 " ideal model delta sigma weight residual 112.60 115.46 -2.86 1.70e+00 3.46e-01 2.84e+00 angle pdb=" CB GLN P 109 " pdb=" CG GLN P 109 " pdb=" CD GLN P 109 " ideal model delta sigma weight residual 112.60 115.46 -2.86 1.70e+00 3.46e-01 2.83e+00 angle pdb=" CB GLN N 109 " pdb=" CG GLN N 109 " pdb=" CD GLN N 109 " ideal model delta sigma weight residual 112.60 115.45 -2.85 1.70e+00 3.46e-01 2.81e+00 ... (remaining 33138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 42.560 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.480 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 23 poor density : 616 time to evaluate : 2.739 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: 0.3454 time to fit residues: 340.2805 Evaluate side-chains 454 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 451 time to evaluate : 2.690 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 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 fitting. rotamer outliers: 88 poor density : 487 time to evaluate : 2.652 Fit side-chains revert: symmetry clash REVERT: A 82 VAL cc_start: 0.8726 (m) cc_final: 0.8417 (m) REVERT: B 43 LEU cc_start: 0.9090 (tp) cc_final: 0.8868 (tp) REVERT: B 65 LYS cc_start: 0.8348 (mmtt) cc_final: 0.7663 (mttt) REVERT: C 135 LYS cc_start: 0.8204 (tptt) cc_final: 0.7972 (mttp) REVERT: D 65 LYS cc_start: 0.8676 (mmtt) cc_final: 0.8288 (mmtp) REVERT: I 91 VAL cc_start: 0.9196 (m) cc_final: 0.8970 (t) REVERT: I 97 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7765 (mm-30) REVERT: I 116 LYS cc_start: 0.8020 (mmtm) cc_final: 0.7802 (mmtt) REVERT: I 148 ASP cc_start: 0.7926 (m-30) cc_final: 0.7496 (t0) REVERT: K 91 VAL cc_start: 0.9002 (m) cc_final: 0.8753 (t) REVERT: L 135 LYS cc_start: 0.8364 (tmtt) cc_final: 0.7957 (mtpt) REVERT: M 29 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7483 (mt0) REVERT: N 87 ASN cc_start: 0.9100 (t0) cc_final: 0.8896 (t0) REVERT: N 129 ASP cc_start: 0.7606 (m-30) cc_final: 0.7353 (m-30) REVERT: O 43 LEU cc_start: 0.9016 (tp) cc_final: 0.8715 (tp) REVERT: P 135 LYS cc_start: 0.8412 (mmtt) cc_final: 0.7849 (mptt) REVERT: Q 135 LYS cc_start: 0.8040 (tptt) cc_final: 0.7746 (tttm) REVERT: R 135 LYS cc_start: 0.8305 (tptt) cc_final: 0.7801 (ttpp) REVERT: R 141 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8309 (ptm) REVERT: W 8 THR cc_start: 0.6786 (OUTLIER) cc_final: 0.6375 (m) REVERT: W 135 LYS cc_start: 0.8476 (tptt) cc_final: 0.8147 (mtpp) outliers start: 88 outliers final: 58 residues processed: 544 average time/residue: 0.3354 time to fit residues: 289.6583 Evaluate side-chains 496 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 435 time to evaluate : 2.555 ------------------------------------------------------------------------------- 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 162 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 292 optimal weight: 5.9990 chunk 316 optimal weight: 7.9990 chunk 260 optimal weight: 7.9990 chunk 290 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 E 149 ASN F 149 ASN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN H 31 GLN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 149 ASN I 149 ASN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 GLN O 149 ASN P 149 ASN ** R 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 125 ASN R 149 ASN T 109 GLN T 149 ASN U 109 GLN U 138 GLN U 149 ASN W 149 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 24311 Z= 0.535 Angle : 0.638 5.121 33143 Z= 0.348 Chirality : 0.055 0.222 4186 Planarity : 0.005 0.048 4209 Dihedral : 4.858 28.325 3427 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.58 % Allowed : 18.78 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.15), residues: 3243 helix: 1.80 (0.17), residues: 1081 sheet: 1.18 (0.19), residues: 713 loop : 1.92 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 132 PHE 0.018 0.002 PHE E 142 TYR 0.014 0.002 TYR U 33 ARG 0.006 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 570 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 425 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8587 (mp) REVERT: B 31 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8147 (pt0) REVERT: B 65 LYS cc_start: 0.8438 (mmtt) cc_final: 0.7773 (mttt) REVERT: C 22 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8097 (mp) REVERT: C 135 LYS cc_start: 0.8383 (tptt) cc_final: 0.8047 (mptt) REVERT: C 148 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7279 (m-30) REVERT: D 65 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8316 (mmtp) REVERT: E 141 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8225 (ptt) REVERT: F 22 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8208 (mp) REVERT: I 91 VAL cc_start: 0.9306 (m) cc_final: 0.9081 (t) REVERT: I 97 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7784 (mm-30) REVERT: J 22 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8120 (mp) REVERT: K 31 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7863 (pt0) REVERT: L 22 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8421 (mp) REVERT: L 129 ASP cc_start: 0.7793 (t0) cc_final: 0.7582 (t0) REVERT: L 135 LYS cc_start: 0.8244 (tmtt) cc_final: 0.7873 (mtpt) REVERT: M 7 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.7015 (t80) REVERT: M 22 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8236 (mp) REVERT: M 29 GLN cc_start: 0.8296 (tt0) cc_final: 0.7750 (mt0) REVERT: M 135 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8597 (tttp) REVERT: N 129 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7428 (m-30) REVERT: O 7 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7583 (t80) REVERT: O 129 ASP cc_start: 0.8393 (t70) cc_final: 0.7872 (t0) REVERT: P 22 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8407 (mp) REVERT: Q 22 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8317 (mp) REVERT: Q 87 ASN cc_start: 0.8677 (t0) cc_final: 0.8428 (t0) REVERT: Q 135 LYS cc_start: 0.8119 (tptt) cc_final: 0.7718 (tttm) REVERT: R 135 LYS cc_start: 0.8498 (tptt) cc_final: 0.7897 (ttpp) REVERT: R 141 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8338 (ptm) REVERT: S 22 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8432 (mp) REVERT: T 135 LYS cc_start: 0.8459 (tptt) cc_final: 0.8109 (mmtm) REVERT: U 103 ASP cc_start: 0.8442 (p0) cc_final: 0.8155 (p0) REVERT: V 135 LYS cc_start: 0.8584 (mptt) cc_final: 0.8200 (mttt) REVERT: W 135 LYS cc_start: 0.8554 (tptt) cc_final: 0.8278 (ttpp) outliers start: 145 outliers final: 95 residues processed: 530 average time/residue: 0.3318 time to fit residues: 280.9798 Evaluate side-chains 514 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 402 time to evaluate : 2.440 ------------------------------------------------------------------------------- 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 80 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain 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 76 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 31 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 112 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 141 MET Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 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 91 VAL Chi-restraints excluded: chain T residue 103 ASP Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 125 ASN Chi-restraints excluded: chain T residue 141 MET Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 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 289 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 293 optimal weight: 0.9990 chunk 311 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 278 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 138 GLN D 109 GLN D 125 ASN G 109 GLN H 109 GLN J 109 GLN M 109 GLN P 29 GLN R 109 GLN S 109 GLN U 138 GLN V 31 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24311 Z= 0.175 Angle : 0.453 5.208 33143 Z= 0.245 Chirality : 0.047 0.153 4186 Planarity : 0.004 0.029 4209 Dihedral : 4.110 25.552 3427 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.73 % Allowed : 21.01 % Favored : 75.26 % 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: 2.29 (0.17), residues: 1081 sheet: 1.18 (0.19), residues: 713 loop : 2.06 (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 0.011 0.001 TYR G 33 ARG 0.003 0.000 ARG S 126 *********************** 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 531 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 434 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8220 (p0) cc_final: 0.7981 (p0) REVERT: B 65 LYS cc_start: 0.8429 (mmtt) cc_final: 0.7769 (mttt) REVERT: B 77 GLU cc_start: 0.8346 (mp0) cc_final: 0.8072 (mp0) REVERT: C 135 LYS cc_start: 0.8383 (tptt) cc_final: 0.8103 (mptt) REVERT: D 65 LYS cc_start: 0.8704 (mmtt) cc_final: 0.8288 (mmtp) REVERT: E 141 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8270 (ptt) REVERT: G 85 ASP cc_start: 0.8412 (p0) cc_final: 0.8149 (p0) REVERT: I 97 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7836 (mm-30) REVERT: J 13 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8291 (mmm) REVERT: K 31 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: K 91 VAL cc_start: 0.8953 (m) cc_final: 0.8723 (t) REVERT: L 103 ASP cc_start: 0.7962 (p0) cc_final: 0.7542 (p0) REVERT: L 135 LYS cc_start: 0.8255 (tmtt) cc_final: 0.7889 (mtpt) REVERT: M 7 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6964 (t80) REVERT: M 29 GLN cc_start: 0.8013 (tt0) cc_final: 0.7565 (mt0) REVERT: M 135 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8602 (tttp) REVERT: N 22 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8536 (mp) REVERT: N 129 ASP cc_start: 0.7556 (m-30) cc_final: 0.7336 (m-30) REVERT: O 129 ASP cc_start: 0.8389 (t70) cc_final: 0.7844 (t0) REVERT: Q 77 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7837 (mt-10) REVERT: Q 135 LYS cc_start: 0.8180 (tptt) cc_final: 0.7764 (tttm) REVERT: R 91 VAL cc_start: 0.9175 (m) cc_final: 0.8961 (t) REVERT: R 135 LYS cc_start: 0.8456 (tptt) cc_final: 0.7787 (ttpp) REVERT: S 91 VAL cc_start: 0.9206 (m) cc_final: 0.8991 (t) REVERT: V 135 LYS cc_start: 0.8566 (mptt) cc_final: 0.8165 (mttt) REVERT: W 10 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8301 (mm) REVERT: W 135 LYS cc_start: 0.8556 (tptt) cc_final: 0.8240 (ttpp) outliers start: 97 outliers final: 66 residues processed: 505 average time/residue: 0.3233 time to fit residues: 260.6321 Evaluate side-chains 483 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 411 time to evaluate : 2.497 ------------------------------------------------------------------------------- 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 82 VAL 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 73 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 H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 13 MET Chi-restraints excluded: chain J residue 73 SER 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 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 8 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 148 ASP Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain V residue 31 GLN Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 259 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 231 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 265 optimal weight: 0.8980 chunk 215 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 279 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 G 109 GLN H 109 GLN I 109 GLN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN V 29 GLN V 31 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 24311 Z= 0.163 Angle : 0.442 6.663 33143 Z= 0.237 Chirality : 0.046 0.149 4186 Planarity : 0.003 0.028 4209 Dihedral : 3.924 24.660 3427 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.42 % Allowed : 20.24 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.15), residues: 3243 helix: 2.42 (0.17), residues: 1081 sheet: 1.08 (0.19), residues: 713 loop : 2.10 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 132 PHE 0.007 0.001 PHE S 7 TYR 0.010 0.001 TYR G 33 ARG 0.004 0.000 ARG S 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 436 time to evaluate : 2.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8200 (p0) cc_final: 0.7930 (p0) REVERT: A 125 ASN cc_start: 0.8119 (t0) cc_final: 0.7886 (t0) REVERT: B 31 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7984 (pt0) REVERT: B 65 LYS cc_start: 0.8433 (mmtt) cc_final: 0.7720 (mttt) REVERT: B 77 GLU cc_start: 0.8357 (mp0) cc_final: 0.8134 (mp0) REVERT: C 22 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8183 (mp) REVERT: C 135 LYS cc_start: 0.8386 (tptt) cc_final: 0.8091 (mptt) REVERT: D 65 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8295 (mmtp) REVERT: E 141 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8249 (ptt) REVERT: I 97 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7848 (mm-30) REVERT: J 13 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8302 (mmm) REVERT: J 22 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8103 (mp) REVERT: J 129 ASP cc_start: 0.7401 (m-30) cc_final: 0.7056 (t70) REVERT: K 31 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7640 (pt0) REVERT: K 91 VAL cc_start: 0.8939 (m) cc_final: 0.8733 (t) REVERT: L 103 ASP cc_start: 0.7920 (p0) cc_final: 0.7502 (p0) REVERT: L 135 LYS cc_start: 0.8281 (tmtt) cc_final: 0.7922 (mtpt) REVERT: M 7 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.6945 (t80) REVERT: M 22 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8090 (mp) REVERT: M 29 GLN cc_start: 0.7996 (tt0) cc_final: 0.7548 (mt0) REVERT: M 135 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8573 (tttp) REVERT: N 87 ASN cc_start: 0.9052 (t0) cc_final: 0.8793 (t0) REVERT: N 129 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: O 7 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7542 (t80) REVERT: O 129 ASP cc_start: 0.8396 (t70) cc_final: 0.7881 (t0) REVERT: Q 77 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7875 (mt-10) REVERT: Q 135 LYS cc_start: 0.8189 (tptt) cc_final: 0.7804 (tttm) REVERT: R 135 LYS cc_start: 0.8435 (tptt) cc_final: 0.7753 (ttpp) REVERT: S 22 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8422 (mp) REVERT: S 135 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8356 (mttp) REVERT: V 135 LYS cc_start: 0.8552 (mptt) cc_final: 0.8163 (mttt) REVERT: W 135 LYS cc_start: 0.8567 (tptt) cc_final: 0.8329 (mtpp) outliers start: 115 outliers final: 86 residues processed: 519 average time/residue: 0.3212 time to fit residues: 265.2675 Evaluate side-chains 515 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 418 time to evaluate : 2.455 ------------------------------------------------------------------------------- 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 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 8 THR 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 103 ASP Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 13 MET 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 K residue 22 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 148 ASP Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 141 MET Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 104 optimal weight: 8.9990 chunk 280 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 182 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 311 optimal weight: 0.9990 chunk 258 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 163 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN G 109 GLN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN R 109 GLN S 109 GLN V 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24311 Z= 0.172 Angle : 0.446 6.037 33143 Z= 0.239 Chirality : 0.046 0.149 4186 Planarity : 0.003 0.027 4209 Dihedral : 3.891 24.615 3427 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.58 % Allowed : 20.28 % Favored : 75.14 % 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: 2.81 (0.15), residues: 3243 helix: 2.47 (0.17), residues: 1081 sheet: 1.00 (0.19), residues: 713 loop : 2.11 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 132 PHE 0.005 0.001 PHE B 108 TYR 0.009 0.001 TYR G 33 ARG 0.004 0.000 ARG A 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 546 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 427 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8177 (p0) cc_final: 0.7918 (p0) REVERT: B 31 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.8002 (pt0) REVERT: B 65 LYS cc_start: 0.8422 (mmtt) cc_final: 0.7743 (mttt) REVERT: B 77 GLU cc_start: 0.8383 (mp0) cc_final: 0.8137 (mp0) REVERT: B 103 ASP cc_start: 0.7625 (p0) cc_final: 0.7379 (p0) REVERT: C 22 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8177 (mp) REVERT: C 77 GLU cc_start: 0.8219 (mp0) cc_final: 0.7981 (mp0) REVERT: C 135 LYS cc_start: 0.8423 (tptt) cc_final: 0.8222 (mptt) REVERT: D 65 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8286 (mmtp) REVERT: E 141 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8250 (ptt) REVERT: I 97 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7852 (mm-30) REVERT: J 13 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8307 (mmm) REVERT: J 22 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8109 (mp) REVERT: J 129 ASP cc_start: 0.7406 (m-30) cc_final: 0.6986 (t70) REVERT: K 31 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7611 (pt0) REVERT: K 91 VAL cc_start: 0.8950 (m) cc_final: 0.8709 (t) REVERT: L 22 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8320 (mp) REVERT: L 103 ASP cc_start: 0.7795 (p0) cc_final: 0.7322 (p0) REVERT: L 135 LYS cc_start: 0.8264 (tmtt) cc_final: 0.7889 (mtpt) REVERT: M 7 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6978 (t80) REVERT: M 22 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8105 (mp) REVERT: M 29 GLN cc_start: 0.7999 (tt0) cc_final: 0.7550 (mt0) REVERT: M 135 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8583 (tttp) REVERT: N 87 ASN cc_start: 0.9055 (t0) cc_final: 0.8818 (t0) REVERT: N 129 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7245 (m-30) REVERT: O 7 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7608 (t80) REVERT: O 129 ASP cc_start: 0.8390 (t70) cc_final: 0.7852 (t0) REVERT: P 22 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8289 (mp) REVERT: Q 31 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7941 (pt0) REVERT: Q 77 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7899 (mt-10) REVERT: R 135 LYS cc_start: 0.8407 (tptt) cc_final: 0.7742 (ttpp) REVERT: S 135 LYS cc_start: 0.8708 (mmtt) cc_final: 0.8390 (mttp) REVERT: V 103 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7598 (p0) REVERT: V 135 LYS cc_start: 0.8530 (mptt) cc_final: 0.8157 (mttt) REVERT: W 135 LYS cc_start: 0.8576 (tptt) cc_final: 0.8314 (mtpp) outliers start: 119 outliers final: 93 residues processed: 519 average time/residue: 0.3284 time to fit residues: 271.2921 Evaluate side-chains 522 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 415 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 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 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 13 MET Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR 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 85 ASP Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 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 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain 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 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 148 ASP Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 141 MET Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 78 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 U residue 8 THR Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 148 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 300 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 262 optimal weight: 4.9990 chunk 173 optimal weight: 0.0770 chunk 310 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.7938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 149 ASN G 109 GLN H 29 GLN H 31 GLN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN P 149 ASN Q 149 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 24311 Z= 0.131 Angle : 0.424 5.582 33143 Z= 0.226 Chirality : 0.045 0.142 4186 Planarity : 0.003 0.025 4209 Dihedral : 3.656 20.794 3427 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 4.23 % Allowed : 20.89 % 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: 2.94 (0.15), residues: 3243 helix: 2.62 (0.17), residues: 1081 sheet: 1.02 (0.19), residues: 713 loop : 2.19 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 132 PHE 0.005 0.001 PHE I 108 TYR 0.005 0.001 TYR B 33 ARG 0.003 0.000 ARG P 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 441 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8201 (p0) cc_final: 0.7942 (p0) REVERT: B 65 LYS cc_start: 0.8416 (mmtt) cc_final: 0.7733 (mttt) REVERT: B 77 GLU cc_start: 0.8370 (mp0) cc_final: 0.8142 (mp0) REVERT: C 22 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8115 (mp) REVERT: C 77 GLU cc_start: 0.8237 (mp0) cc_final: 0.7994 (mp0) REVERT: C 135 LYS cc_start: 0.8420 (tptt) cc_final: 0.8208 (mptt) REVERT: D 65 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8279 (mmtp) REVERT: E 141 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8225 (ptt) REVERT: H 31 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.7109 (pt0) REVERT: I 97 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7878 (mm-30) REVERT: J 67 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8596 (mmtt) REVERT: J 129 ASP cc_start: 0.7396 (m-30) cc_final: 0.6995 (t70) REVERT: K 31 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7596 (pt0) REVERT: K 91 VAL cc_start: 0.8903 (m) cc_final: 0.8686 (t) REVERT: L 22 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8273 (mp) REVERT: L 135 LYS cc_start: 0.8265 (tmtt) cc_final: 0.7881 (mtpt) REVERT: M 7 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6975 (t80) REVERT: M 29 GLN cc_start: 0.7807 (tt0) cc_final: 0.7392 (mt0) REVERT: N 87 ASN cc_start: 0.9021 (t0) cc_final: 0.8814 (t0) REVERT: O 7 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7596 (t80) REVERT: O 43 LEU cc_start: 0.9070 (tp) cc_final: 0.8745 (tp) REVERT: O 129 ASP cc_start: 0.8412 (t70) cc_final: 0.7896 (t0) REVERT: P 7 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7818 (t80) REVERT: Q 31 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7876 (pt0) REVERT: Q 77 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7962 (mt-10) REVERT: R 135 LYS cc_start: 0.8396 (tptt) cc_final: 0.7714 (ttpp) REVERT: S 22 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8452 (mp) REVERT: S 135 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8410 (mttp) REVERT: V 103 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7501 (p0) REVERT: V 109 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7758 (mm-40) REVERT: V 135 LYS cc_start: 0.8529 (mptt) cc_final: 0.8160 (mttt) REVERT: W 77 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7622 (mt-10) REVERT: W 135 LYS cc_start: 0.8557 (tptt) cc_final: 0.8289 (mtpp) outliers start: 110 outliers final: 83 residues processed: 523 average time/residue: 0.3235 time to fit residues: 270.2900 Evaluate side-chains 511 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 417 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 82 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 8 THR 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 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 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 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 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 74 THR 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 R residue 8 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 141 MET Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 192 optimal weight: 0.4980 chunk 123 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 211 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN G 29 GLN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 109 GLN ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2751 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= 0.167 Angle : 0.446 5.459 33143 Z= 0.237 Chirality : 0.046 0.149 4186 Planarity : 0.003 0.026 4209 Dihedral : 3.779 21.229 3427 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.35 % Allowed : 20.89 % 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: 2.89 (0.15), residues: 3243 helix: 2.56 (0.17), residues: 1081 sheet: 1.02 (0.19), residues: 713 loop : 2.17 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 132 PHE 0.005 0.001 PHE J 108 TYR 0.007 0.001 TYR I 33 ARG 0.004 0.000 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 539 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 426 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8202 (p0) cc_final: 0.7906 (p0) REVERT: B 31 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7953 (pt0) REVERT: B 65 LYS cc_start: 0.8419 (mmtt) cc_final: 0.7745 (mttt) REVERT: C 22 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8130 (mp) REVERT: C 77 GLU cc_start: 0.8226 (mp0) cc_final: 0.7997 (mp0) REVERT: C 135 LYS cc_start: 0.8449 (tptt) cc_final: 0.8229 (mptt) REVERT: D 65 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8331 (mmtp) REVERT: E 141 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8230 (ptt) REVERT: I 97 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7886 (mm-30) REVERT: J 103 ASP cc_start: 0.7823 (p0) cc_final: 0.7357 (p0) REVERT: J 129 ASP cc_start: 0.7421 (m-30) cc_final: 0.7009 (t70) REVERT: K 31 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7622 (pt0) REVERT: L 22 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8251 (mp) REVERT: L 135 LYS cc_start: 0.8277 (tmtt) cc_final: 0.7912 (mtpt) REVERT: M 7 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.7008 (t80) REVERT: M 22 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8024 (mp) REVERT: M 29 GLN cc_start: 0.7950 (tt0) cc_final: 0.7515 (mt0) REVERT: N 87 ASN cc_start: 0.9043 (t0) cc_final: 0.8810 (t0) REVERT: O 7 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7624 (t80) REVERT: O 129 ASP cc_start: 0.8413 (t70) cc_final: 0.7879 (t0) REVERT: P 7 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7846 (t80) REVERT: P 22 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8289 (mp) REVERT: Q 31 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7867 (pt0) REVERT: Q 77 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7965 (mt-10) REVERT: R 135 LYS cc_start: 0.8415 (tptt) cc_final: 0.7726 (ttpp) REVERT: S 22 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8441 (mp) REVERT: S 135 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8420 (mttp) REVERT: V 103 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7499 (p0) REVERT: V 109 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7794 (mm-40) REVERT: V 135 LYS cc_start: 0.8517 (mptt) cc_final: 0.8145 (mttt) REVERT: W 77 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7635 (mt-10) REVERT: W 135 LYS cc_start: 0.8564 (tptt) cc_final: 0.8297 (mtpp) outliers start: 113 outliers final: 92 residues processed: 510 average time/residue: 0.3275 time to fit residues: 267.7740 Evaluate side-chains 524 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 419 time to evaluate : 2.482 ------------------------------------------------------------------------------- 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 A residue 112 THR Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 8 THR 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 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 85 ASP 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 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 110 THR 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 78 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 141 MET Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 112 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 297 optimal weight: 0.8980 chunk 271 optimal weight: 5.9990 chunk 289 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 chunk 88 optimal weight: 0.0370 chunk 261 optimal weight: 7.9990 chunk 273 optimal weight: 2.9990 chunk 288 optimal weight: 0.9990 chunk 189 optimal weight: 0.8980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 31 GLN G 29 GLN G 109 GLN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 24311 Z= 0.127 Angle : 0.425 5.267 33143 Z= 0.225 Chirality : 0.045 0.142 4186 Planarity : 0.003 0.025 4209 Dihedral : 3.588 17.848 3427 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 4.16 % Allowed : 21.28 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.15), residues: 3243 helix: 2.69 (0.17), residues: 1081 sheet: 1.07 (0.19), residues: 713 loop : 2.22 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 132 PHE 0.006 0.001 PHE I 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 542 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 434 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8179 (p0) cc_final: 0.7894 (p0) REVERT: B 31 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7909 (pt0) REVERT: B 65 LYS cc_start: 0.8426 (mmtt) cc_final: 0.7745 (mttt) REVERT: C 22 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8151 (mp) REVERT: C 77 GLU cc_start: 0.8218 (mp0) cc_final: 0.7910 (mp0) REVERT: C 135 LYS cc_start: 0.8443 (tptt) cc_final: 0.8224 (mptt) REVERT: D 65 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8290 (mmtp) REVERT: G 141 MET cc_start: 0.8462 (ptp) cc_final: 0.8201 (ptm) REVERT: J 67 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8549 (mmtt) REVERT: J 91 VAL cc_start: 0.8699 (m) cc_final: 0.8413 (t) REVERT: J 129 ASP cc_start: 0.7386 (m-30) cc_final: 0.6993 (t70) REVERT: K 31 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7595 (pt0) REVERT: K 91 VAL cc_start: 0.8876 (m) cc_final: 0.8646 (t) REVERT: K 103 ASP cc_start: 0.7449 (p0) cc_final: 0.7246 (p0) REVERT: L 22 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8232 (mp) REVERT: L 103 ASP cc_start: 0.7978 (m-30) cc_final: 0.7756 (m-30) REVERT: L 135 LYS cc_start: 0.8278 (tmtt) cc_final: 0.7905 (mtpt) REVERT: M 7 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.7004 (t80) REVERT: M 22 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7999 (mp) REVERT: M 29 GLN cc_start: 0.7827 (tt0) cc_final: 0.7408 (mt0) REVERT: N 87 ASN cc_start: 0.9002 (t0) cc_final: 0.8802 (t0) REVERT: O 7 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.7691 (t80) REVERT: O 43 LEU cc_start: 0.9039 (tp) cc_final: 0.8741 (tp) REVERT: O 129 ASP cc_start: 0.8411 (t70) cc_final: 0.7912 (t0) REVERT: P 7 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7815 (t80) REVERT: P 22 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8262 (mp) REVERT: P 148 ASP cc_start: 0.7529 (t70) cc_final: 0.7276 (t70) REVERT: Q 31 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7840 (pt0) REVERT: Q 77 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7936 (mt-10) REVERT: R 135 LYS cc_start: 0.8407 (tptt) cc_final: 0.7714 (ttpp) REVERT: S 22 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8471 (mp) REVERT: S 135 LYS cc_start: 0.8746 (mmtt) cc_final: 0.8429 (mttp) REVERT: T 135 LYS cc_start: 0.8498 (tptt) cc_final: 0.8260 (mptt) REVERT: U 129 ASP cc_start: 0.7211 (m-30) cc_final: 0.6850 (m-30) REVERT: V 22 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8647 (mp) REVERT: V 103 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7467 (p0) REVERT: V 109 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7676 (mm-40) REVERT: V 135 LYS cc_start: 0.8505 (mptt) cc_final: 0.8131 (mttt) REVERT: W 77 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7635 (mt-10) REVERT: W 135 LYS cc_start: 0.8549 (tptt) cc_final: 0.8272 (mtpp) outliers start: 108 outliers final: 84 residues processed: 512 average time/residue: 0.3223 time to fit residues: 262.7033 Evaluate side-chains 520 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 423 time to evaluate : 2.562 ------------------------------------------------------------------------------- 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 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 B residue 138 GLN Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 31 GLN Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 141 MET 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 103 ASP Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 110 THR 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 78 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 141 MET Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 212 optimal weight: 0.3980 chunk 320 optimal weight: 0.9990 chunk 295 optimal weight: 1.9990 chunk 255 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 202 optimal weight: 9.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 E 31 GLN G 29 GLN G 109 GLN ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24311 Z= 0.149 Angle : 0.437 5.298 33143 Z= 0.232 Chirality : 0.046 0.145 4186 Planarity : 0.003 0.026 4209 Dihedral : 3.662 17.709 3427 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.08 % Allowed : 21.28 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.15), residues: 3243 helix: 2.65 (0.17), residues: 1081 sheet: 1.08 (0.19), residues: 713 loop : 2.20 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 132 PHE 0.006 0.001 PHE I 108 TYR 0.006 0.001 TYR I 33 ARG 0.005 0.000 ARG S 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 427 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASP cc_start: 0.8176 (p0) cc_final: 0.7892 (p0) REVERT: B 31 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7907 (pt0) REVERT: B 65 LYS cc_start: 0.8414 (mmtt) cc_final: 0.7745 (mttt) REVERT: C 22 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8118 (mp) REVERT: C 77 GLU cc_start: 0.8223 (mp0) cc_final: 0.7987 (mp0) REVERT: C 135 LYS cc_start: 0.8449 (tptt) cc_final: 0.8215 (mptt) REVERT: D 65 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8299 (mmtp) REVERT: J 67 LYS cc_start: 0.8838 (mmtt) cc_final: 0.8578 (mmtt) REVERT: J 91 VAL cc_start: 0.8730 (m) cc_final: 0.8434 (t) REVERT: J 129 ASP cc_start: 0.7409 (m-30) cc_final: 0.6971 (t70) REVERT: K 31 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7629 (pt0) REVERT: L 22 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8224 (mp) REVERT: L 135 LYS cc_start: 0.8265 (tmtt) cc_final: 0.7901 (mtpt) REVERT: M 7 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6961 (t80) REVERT: M 22 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8042 (mp) REVERT: M 29 GLN cc_start: 0.7868 (tt0) cc_final: 0.7439 (mt0) REVERT: N 87 ASN cc_start: 0.9023 (t0) cc_final: 0.8801 (t0) REVERT: O 7 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7662 (t80) REVERT: O 43 LEU cc_start: 0.9083 (tp) cc_final: 0.8747 (tp) REVERT: O 129 ASP cc_start: 0.8413 (t70) cc_final: 0.7888 (t0) REVERT: P 7 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7801 (t80) REVERT: P 22 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8284 (mp) REVERT: P 148 ASP cc_start: 0.7512 (t70) cc_final: 0.7270 (t70) REVERT: Q 31 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7848 (pt0) REVERT: Q 77 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7943 (mt-10) REVERT: R 135 LYS cc_start: 0.8400 (tptt) cc_final: 0.7703 (ttpp) REVERT: S 22 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8450 (mp) REVERT: S 135 LYS cc_start: 0.8746 (mmtt) cc_final: 0.8421 (mttp) REVERT: T 135 LYS cc_start: 0.8492 (tptt) cc_final: 0.8262 (mptt) REVERT: U 129 ASP cc_start: 0.7230 (m-30) cc_final: 0.6877 (m-30) REVERT: V 22 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8645 (mp) REVERT: V 103 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7432 (p0) REVERT: V 109 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7722 (mm-40) REVERT: V 135 LYS cc_start: 0.8511 (mptt) cc_final: 0.8135 (mttt) REVERT: W 77 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7639 (mt-10) REVERT: W 135 LYS cc_start: 0.8552 (tptt) cc_final: 0.8280 (mtpp) outliers start: 106 outliers final: 83 residues processed: 506 average time/residue: 0.3318 time to fit residues: 268.8410 Evaluate side-chains 519 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 423 time to evaluate : 2.667 ------------------------------------------------------------------------------- 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 31 GLN Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 141 MET 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 103 ASP Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 110 THR 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 78 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 141 MET Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 31 GLN Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 272 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 262 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN G 29 GLN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 GLN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 GLN M 109 GLN Q 87 ASN ** S 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.093368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.084873 restraints weight = 33608.108| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.17 r_work: 0.2781 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24311 Z= 0.261 Angle : 0.499 5.803 33143 Z= 0.267 Chirality : 0.048 0.189 4186 Planarity : 0.003 0.032 4209 Dihedral : 4.165 24.957 3427 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.31 % Allowed : 21.28 % Favored : 74.41 % 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: 2.71 (0.15), residues: 3243 helix: 2.36 (0.17), residues: 1081 sheet: 0.94 (0.19), residues: 713 loop : 2.08 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 132 PHE 0.008 0.001 PHE E 142 TYR 0.013 0.001 TYR G 33 ARG 0.004 0.001 ARG P 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5652.45 seconds wall clock time: 101 minutes 57.85 seconds (6117.85 seconds total)