Starting phenix.real_space_refine on Thu Sep 18 09:37:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hze_52523/09_2025/9hze_52523.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hze_52523/09_2025/9hze_52523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hze_52523/09_2025/9hze_52523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hze_52523/09_2025/9hze_52523.map" model { file = "/net/cci-nas-00/data/ceres_data/9hze_52523/09_2025/9hze_52523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hze_52523/09_2025/9hze_52523.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 48 5.16 5 C 10344 2.51 5 N 2568 2.21 5 O 3192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16152 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 673 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Restraints were copied for chains: D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z Time building chain proxies: 1.61, per 1000 atoms: 0.10 Number of scatterers: 16152 At special positions: 0 Unit cell: (68.11, 68.11, 294.68, 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 48 16.00 O 3192 8.00 N 2568 7.00 C 10344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.43 Conformation dependent library (CDL) restraints added in 849.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3984 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 48 sheets defined 10.5% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 23 through 26 removed outlier: 3.863A pdb=" N ALA C 26 " --> pdb=" O THR C 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 23 through 26' Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA D 26 " --> pdb=" O THR D 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 23 through 26' Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'E' and resid 18 through 20 No H-bonds generated for 'chain 'E' and resid 18 through 20' Processing helix chain 'E' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA E 26 " --> pdb=" O THR E 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 23 through 26' Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'F' and resid 18 through 20 No H-bonds generated for 'chain 'F' and resid 18 through 20' Processing helix chain 'F' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA F 26 " --> pdb=" O THR F 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 23 through 26' Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'G' and resid 18 through 20 No H-bonds generated for 'chain 'G' and resid 18 through 20' Processing helix chain 'G' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA G 26 " --> pdb=" O THR G 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 23 through 26' Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'H' and resid 18 through 20 No H-bonds generated for 'chain 'H' and resid 18 through 20' Processing helix chain 'H' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA H 26 " --> pdb=" O THR H 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 23 through 26' Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'I' and resid 18 through 20 No H-bonds generated for 'chain 'I' and resid 18 through 20' Processing helix chain 'I' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA I 26 " --> pdb=" O THR I 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 23 through 26' Processing helix chain 'I' and resid 32 through 34 No H-bonds generated for 'chain 'I' and resid 32 through 34' Processing helix chain 'J' and resid 18 through 20 No H-bonds generated for 'chain 'J' and resid 18 through 20' Processing helix chain 'J' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA J 26 " --> pdb=" O THR J 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 23 through 26' Processing helix chain 'J' and resid 32 through 34 No H-bonds generated for 'chain 'J' and resid 32 through 34' Processing helix chain 'K' and resid 18 through 20 No H-bonds generated for 'chain 'K' and resid 18 through 20' Processing helix chain 'K' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA K 26 " --> pdb=" O THR K 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 23 through 26' Processing helix chain 'K' and resid 32 through 34 No H-bonds generated for 'chain 'K' and resid 32 through 34' Processing helix chain 'L' and resid 18 through 20 No H-bonds generated for 'chain 'L' and resid 18 through 20' Processing helix chain 'L' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA L 26 " --> pdb=" O THR L 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 23 through 26' Processing helix chain 'L' and resid 32 through 34 No H-bonds generated for 'chain 'L' and resid 32 through 34' Processing helix chain 'M' and resid 18 through 20 No H-bonds generated for 'chain 'M' and resid 18 through 20' Processing helix chain 'M' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA M 26 " --> pdb=" O THR M 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 23 through 26' Processing helix chain 'M' and resid 32 through 34 No H-bonds generated for 'chain 'M' and resid 32 through 34' Processing helix chain 'N' and resid 18 through 20 No H-bonds generated for 'chain 'N' and resid 18 through 20' Processing helix chain 'N' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA N 26 " --> pdb=" O THR N 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 23 through 26' Processing helix chain 'N' and resid 32 through 34 No H-bonds generated for 'chain 'N' and resid 32 through 34' Processing helix chain 'O' and resid 18 through 20 No H-bonds generated for 'chain 'O' and resid 18 through 20' Processing helix chain 'O' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA O 26 " --> pdb=" O THR O 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 23 through 26' Processing helix chain 'O' and resid 32 through 34 No H-bonds generated for 'chain 'O' and resid 32 through 34' Processing helix chain 'P' and resid 18 through 20 No H-bonds generated for 'chain 'P' and resid 18 through 20' Processing helix chain 'P' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA P 26 " --> pdb=" O THR P 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 23 through 26' Processing helix chain 'P' and resid 32 through 34 No H-bonds generated for 'chain 'P' and resid 32 through 34' Processing helix chain 'Q' and resid 18 through 20 No H-bonds generated for 'chain 'Q' and resid 18 through 20' Processing helix chain 'Q' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA Q 26 " --> pdb=" O THR Q 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 23 through 26' Processing helix chain 'Q' and resid 32 through 34 No H-bonds generated for 'chain 'Q' and resid 32 through 34' Processing helix chain 'R' and resid 18 through 20 No H-bonds generated for 'chain 'R' and resid 18 through 20' Processing helix chain 'R' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA R 26 " --> pdb=" O THR R 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 23 through 26' Processing helix chain 'R' and resid 32 through 34 No H-bonds generated for 'chain 'R' and resid 32 through 34' Processing helix chain 'S' and resid 18 through 20 No H-bonds generated for 'chain 'S' and resid 18 through 20' Processing helix chain 'S' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA S 26 " --> pdb=" O THR S 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 23 through 26' Processing helix chain 'S' and resid 32 through 34 No H-bonds generated for 'chain 'S' and resid 32 through 34' Processing helix chain 'T' and resid 18 through 20 No H-bonds generated for 'chain 'T' and resid 18 through 20' Processing helix chain 'T' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA T 26 " --> pdb=" O THR T 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 23 through 26' Processing helix chain 'T' and resid 32 through 34 No H-bonds generated for 'chain 'T' and resid 32 through 34' Processing helix chain 'U' and resid 18 through 20 No H-bonds generated for 'chain 'U' and resid 18 through 20' Processing helix chain 'U' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA U 26 " --> pdb=" O THR U 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 23 through 26' Processing helix chain 'U' and resid 32 through 34 No H-bonds generated for 'chain 'U' and resid 32 through 34' Processing helix chain 'V' and resid 18 through 20 No H-bonds generated for 'chain 'V' and resid 18 through 20' Processing helix chain 'V' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA V 26 " --> pdb=" O THR V 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 23 through 26' Processing helix chain 'V' and resid 32 through 34 No H-bonds generated for 'chain 'V' and resid 32 through 34' Processing helix chain 'W' and resid 18 through 20 No H-bonds generated for 'chain 'W' and resid 18 through 20' Processing helix chain 'W' and resid 23 through 26 removed outlier: 3.863A pdb=" N ALA W 26 " --> pdb=" O THR W 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 23 through 26' Processing helix chain 'W' and resid 32 through 34 No H-bonds generated for 'chain 'W' and resid 32 through 34' Processing helix chain 'X' and resid 18 through 20 No H-bonds generated for 'chain 'X' and resid 18 through 20' Processing helix chain 'X' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA X 26 " --> pdb=" O THR X 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 23 through 26' Processing helix chain 'X' and resid 32 through 34 No H-bonds generated for 'chain 'X' and resid 32 through 34' Processing helix chain 'Y' and resid 18 through 20 No H-bonds generated for 'chain 'Y' and resid 18 through 20' Processing helix chain 'Y' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA Y 26 " --> pdb=" O THR Y 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 23 through 26' Processing helix chain 'Y' and resid 32 through 34 No H-bonds generated for 'chain 'Y' and resid 32 through 34' Processing helix chain 'Z' and resid 18 through 20 No H-bonds generated for 'chain 'Z' and resid 18 through 20' Processing helix chain 'Z' and resid 23 through 26 removed outlier: 3.864A pdb=" N ALA Z 26 " --> pdb=" O THR Z 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 23 through 26' Processing helix chain 'Z' and resid 32 through 34 No H-bonds generated for 'chain 'Z' and resid 32 through 34' Processing sheet with id=AA1, first strand: chain 'C' and resid 9 through 16 Processing sheet with id=AA2, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AA3, first strand: chain 'D' and resid 9 through 16 Processing sheet with id=AA4, first strand: chain 'D' and resid 28 through 30 Processing sheet with id=AA5, first strand: chain 'E' and resid 9 through 16 Processing sheet with id=AA6, first strand: chain 'E' and resid 28 through 30 Processing sheet with id=AA7, first strand: chain 'F' and resid 9 through 16 Processing sheet with id=AA8, first strand: chain 'F' and resid 28 through 30 Processing sheet with id=AA9, first strand: chain 'G' and resid 9 through 16 Processing sheet with id=AB1, first strand: chain 'G' and resid 28 through 30 Processing sheet with id=AB2, first strand: chain 'H' and resid 9 through 16 Processing sheet with id=AB3, first strand: chain 'H' and resid 28 through 30 Processing sheet with id=AB4, first strand: chain 'I' and resid 9 through 16 Processing sheet with id=AB5, first strand: chain 'I' and resid 28 through 30 Processing sheet with id=AB6, first strand: chain 'J' and resid 9 through 16 Processing sheet with id=AB7, first strand: chain 'J' and resid 28 through 30 Processing sheet with id=AB8, first strand: chain 'K' and resid 9 through 16 Processing sheet with id=AB9, first strand: chain 'K' and resid 28 through 30 Processing sheet with id=AC1, first strand: chain 'L' and resid 9 through 16 Processing sheet with id=AC2, first strand: chain 'L' and resid 28 through 30 Processing sheet with id=AC3, first strand: chain 'M' and resid 9 through 16 Processing sheet with id=AC4, first strand: chain 'M' and resid 28 through 30 Processing sheet with id=AC5, first strand: chain 'N' and resid 9 through 16 Processing sheet with id=AC6, first strand: chain 'N' and resid 28 through 30 Processing sheet with id=AC7, first strand: chain 'O' and resid 9 through 16 Processing sheet with id=AC8, first strand: chain 'O' and resid 28 through 30 Processing sheet with id=AC9, first strand: chain 'P' and resid 9 through 16 Processing sheet with id=AD1, first strand: chain 'P' and resid 28 through 30 Processing sheet with id=AD2, first strand: chain 'Q' and resid 9 through 16 Processing sheet with id=AD3, first strand: chain 'Q' and resid 28 through 30 Processing sheet with id=AD4, first strand: chain 'R' and resid 9 through 16 Processing sheet with id=AD5, first strand: chain 'R' and resid 28 through 30 Processing sheet with id=AD6, first strand: chain 'S' and resid 9 through 16 Processing sheet with id=AD7, first strand: chain 'S' and resid 28 through 30 Processing sheet with id=AD8, first strand: chain 'T' and resid 9 through 16 Processing sheet with id=AD9, first strand: chain 'T' and resid 28 through 30 Processing sheet with id=AE1, first strand: chain 'U' and resid 9 through 16 Processing sheet with id=AE2, first strand: chain 'U' and resid 28 through 30 Processing sheet with id=AE3, first strand: chain 'V' and resid 9 through 16 Processing sheet with id=AE4, first strand: chain 'V' and resid 28 through 30 Processing sheet with id=AE5, first strand: chain 'W' and resid 9 through 16 Processing sheet with id=AE6, first strand: chain 'W' and resid 28 through 30 Processing sheet with id=AE7, first strand: chain 'X' and resid 9 through 16 Processing sheet with id=AE8, first strand: chain 'X' and resid 28 through 30 Processing sheet with id=AE9, first strand: chain 'Y' and resid 9 through 16 Processing sheet with id=AF1, first strand: chain 'Y' and resid 28 through 30 Processing sheet with id=AF2, first strand: chain 'Z' and resid 9 through 16 Processing sheet with id=AF3, first strand: chain 'Z' and resid 28 through 30 384 hydrogen bonds defined for protein. 936 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: 2.53 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5160 1.34 - 1.46: 3852 1.46 - 1.58: 7428 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 16512 Sorted by residual: bond pdb=" C ALA K 38 " pdb=" N GLY K 39 " ideal model delta sigma weight residual 1.324 1.332 -0.007 1.33e-02 5.65e+03 3.01e-01 bond pdb=" C ALA O 38 " pdb=" N GLY O 39 " ideal model delta sigma weight residual 1.324 1.332 -0.007 1.33e-02 5.65e+03 2.98e-01 bond pdb=" C ALA L 38 " pdb=" N GLY L 39 " ideal model delta sigma weight residual 1.324 1.332 -0.007 1.33e-02 5.65e+03 2.95e-01 bond pdb=" C ALA F 38 " pdb=" N GLY F 39 " ideal model delta sigma weight residual 1.324 1.332 -0.007 1.33e-02 5.65e+03 2.95e-01 bond pdb=" C ALA C 38 " pdb=" N GLY C 39 " ideal model delta sigma weight residual 1.324 1.332 -0.007 1.33e-02 5.65e+03 2.92e-01 ... (remaining 16507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.56: 20031 0.56 - 1.12: 2170 1.12 - 1.69: 239 1.69 - 2.25: 96 2.25 - 2.81: 144 Bond angle restraints: 22680 Sorted by residual: angle pdb=" CA GLY Q 39 " pdb=" C GLY Q 39 " pdb=" N THR Q 40 " ideal model delta sigma weight residual 118.67 116.58 2.09 9.80e-01 1.04e+00 4.57e+00 angle pdb=" CA GLY M 39 " pdb=" C GLY M 39 " pdb=" N THR M 40 " ideal model delta sigma weight residual 118.67 116.59 2.08 9.80e-01 1.04e+00 4.53e+00 angle pdb=" CA GLY N 39 " pdb=" C GLY N 39 " pdb=" N THR N 40 " ideal model delta sigma weight residual 118.67 116.59 2.08 9.80e-01 1.04e+00 4.52e+00 angle pdb=" CA GLY K 39 " pdb=" C GLY K 39 " pdb=" N THR K 40 " ideal model delta sigma weight residual 118.67 116.59 2.08 9.80e-01 1.04e+00 4.49e+00 angle pdb=" CA GLY T 39 " pdb=" C GLY T 39 " pdb=" N THR T 40 " ideal model delta sigma weight residual 118.67 116.60 2.07 9.80e-01 1.04e+00 4.47e+00 ... (remaining 22675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 8616 16.23 - 32.46: 744 32.46 - 48.68: 72 48.68 - 64.91: 0 64.91 - 81.14: 24 Dihedral angle restraints: 9456 sinusoidal: 3144 harmonic: 6312 Sorted by residual: dihedral pdb=" CG ARG C 11 " pdb=" CD ARG C 11 " pdb=" NE ARG C 11 " pdb=" CZ ARG C 11 " ideal model delta sinusoidal sigma weight residual -90.00 -128.97 38.97 2 1.50e+01 4.44e-03 8.44e+00 dihedral pdb=" CG ARG H 11 " pdb=" CD ARG H 11 " pdb=" NE ARG H 11 " pdb=" CZ ARG H 11 " ideal model delta sinusoidal sigma weight residual -90.00 -128.97 38.97 2 1.50e+01 4.44e-03 8.44e+00 dihedral pdb=" CG ARG Q 11 " pdb=" CD ARG Q 11 " pdb=" NE ARG Q 11 " pdb=" CZ ARG Q 11 " ideal model delta sinusoidal sigma weight residual -90.00 -128.97 38.97 2 1.50e+01 4.44e-03 8.44e+00 ... (remaining 9453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1598 0.025 - 0.050: 689 0.050 - 0.075: 191 0.075 - 0.100: 186 0.100 - 0.125: 168 Chirality restraints: 2832 Sorted by residual: chirality pdb=" CA ILE W 91 " pdb=" N ILE W 91 " pdb=" C ILE W 91 " pdb=" CB ILE W 91 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA ILE F 91 " pdb=" N ILE F 91 " pdb=" C ILE F 91 " pdb=" CB ILE F 91 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA ILE K 91 " pdb=" N ILE K 91 " pdb=" C ILE K 91 " pdb=" CB ILE K 91 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 2829 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN K 60 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO K 61 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO K 61 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO K 61 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 60 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO D 61 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 61 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 61 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN Q 60 " 0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO Q 61 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO Q 61 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO Q 61 " 0.017 5.00e-02 4.00e+02 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 7237 2.92 - 3.42: 13764 3.42 - 3.91: 26139 3.91 - 4.41: 29719 4.41 - 4.90: 51502 Nonbonded interactions: 128361 Sorted by model distance: nonbonded pdb=" OG1 THR Y 23 " pdb=" OD2 ASP Y 81 " model vdw 2.430 3.040 nonbonded pdb=" OG1 THR J 23 " pdb=" OD2 ASP J 81 " model vdw 2.430 3.040 nonbonded pdb=" OG1 THR C 23 " pdb=" OD2 ASP C 81 " model vdw 2.430 3.040 nonbonded pdb=" OG1 THR S 23 " pdb=" OD2 ASP S 81 " model vdw 2.430 3.040 nonbonded pdb=" OG1 THR F 23 " pdb=" OD2 ASP F 81 " model vdw 2.430 3.040 ... (remaining 128356 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: 0.07 Found NCS groups: ncs_group { reference = 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' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.510 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 0.012 16512 Z= 0.087 Angle : 0.416 2.812 22680 Z= 0.240 Chirality : 0.044 0.125 2832 Planarity : 0.004 0.031 2904 Dihedral : 12.450 81.138 5472 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 17.14 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.19), residues: 2232 helix: None (None), residues: 0 sheet: 0.97 (0.20), residues: 768 loop : 0.06 (0.18), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 11 TYR 0.006 0.001 TYR X 50 PHE 0.005 0.001 PHE R 93 Details of bonding type rmsd covalent geometry : bond 0.00164 (16512) covalent geometry : angle 0.41610 (22680) hydrogen bonds : bond 0.13833 ( 384) hydrogen bonds : angle 6.74916 ( 936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.594 Fit side-chains REVERT: X 8 MET cc_start: 0.7376 (mtp) cc_final: 0.7174 (ttp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.0992 time to fit residues: 24.3346 Evaluate side-chains 104 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.0370 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 GLN E 60 GLN F 60 GLN G 60 GLN H 60 GLN I 60 GLN J 60 GLN K 60 GLN L 60 GLN M 60 GLN N 60 GLN O 60 GLN P 60 GLN Q 60 GLN R 60 GLN T 5 GLN T 60 GLN U 60 GLN V 60 GLN W 60 GLN X 60 GLN Y 60 GLN Z 60 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.032363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.025864 restraints weight = 76469.090| |-----------------------------------------------------------------------------| r_work (start): 0.2489 rms_B_bonded: 3.83 r_work: 0.2376 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 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 : 0.003 0.037 16512 Z= 0.145 Angle : 0.429 3.758 22680 Z= 0.221 Chirality : 0.045 0.183 2832 Planarity : 0.004 0.030 2904 Dihedral : 3.405 11.512 2376 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.26 % Allowed : 17.50 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.18), residues: 2232 helix: None (None), residues: 0 sheet: 1.17 (0.19), residues: 768 loop : 0.07 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 12 TYR 0.008 0.001 TYR P 54 PHE 0.006 0.001 PHE K 93 Details of bonding type rmsd covalent geometry : bond 0.00341 (16512) covalent geometry : angle 0.42861 (22680) hydrogen bonds : bond 0.02484 ( 384) hydrogen bonds : angle 4.89767 ( 936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 108 time to evaluate : 0.559 Fit side-chains REVERT: D 37 ASP cc_start: 0.9162 (p0) cc_final: 0.8780 (p0) REVERT: J 37 ASP cc_start: 0.9152 (p0) cc_final: 0.8908 (p0) REVERT: Q 8 MET cc_start: 0.9196 (ttm) cc_final: 0.8792 (mtp) REVERT: U 37 ASP cc_start: 0.9235 (p0) cc_final: 0.8611 (p0) REVERT: V 8 MET cc_start: 0.9284 (mtm) cc_final: 0.9027 (mtm) REVERT: Y 92 GLU cc_start: 0.9007 (tt0) cc_final: 0.8557 (tt0) outliers start: 38 outliers final: 14 residues processed: 143 average time/residue: 0.0959 time to fit residues: 23.5768 Evaluate side-chains 108 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain Y residue 5 GLN Chi-restraints excluded: chain Z residue 77 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 1 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 52 optimal weight: 0.0770 chunk 58 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 GLN E 5 GLN S 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.030837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.024508 restraints weight = 78368.999| |-----------------------------------------------------------------------------| r_work (start): 0.2450 rms_B_bonded: 3.75 r_work: 0.2345 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16512 Z= 0.250 Angle : 0.484 5.103 22680 Z= 0.245 Chirality : 0.046 0.161 2832 Planarity : 0.004 0.030 2904 Dihedral : 3.953 12.031 2376 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.63 % Allowed : 17.32 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.18), residues: 2232 helix: None (None), residues: 0 sheet: 1.17 (0.18), residues: 768 loop : 0.09 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 12 TYR 0.014 0.001 TYR P 54 PHE 0.008 0.001 PHE K 13 Details of bonding type rmsd covalent geometry : bond 0.00578 (16512) covalent geometry : angle 0.48395 (22680) hydrogen bonds : bond 0.02686 ( 384) hydrogen bonds : angle 4.70523 ( 936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 92 time to evaluate : 0.696 Fit side-chains REVERT: D 37 ASP cc_start: 0.9175 (p0) cc_final: 0.8890 (p0) REVERT: G 37 ASP cc_start: 0.9133 (p0) cc_final: 0.8531 (p0) REVERT: I 35 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9066 (mt) REVERT: I 37 ASP cc_start: 0.9118 (p0) cc_final: 0.8761 (p0) REVERT: K 37 ASP cc_start: 0.9169 (p0) cc_final: 0.8848 (p0) REVERT: M 37 ASP cc_start: 0.9079 (p0) cc_final: 0.8287 (p0) REVERT: N 87 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9149 (mm) REVERT: O 35 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8895 (mt) REVERT: P 35 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8883 (mt) REVERT: P 87 ILE cc_start: 0.9560 (OUTLIER) cc_final: 0.9355 (mm) REVERT: Q 87 ILE cc_start: 0.9561 (OUTLIER) cc_final: 0.9334 (mm) REVERT: R 35 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9056 (mt) REVERT: R 37 ASP cc_start: 0.9109 (p0) cc_final: 0.8805 (p0) REVERT: T 37 ASP cc_start: 0.9005 (p0) cc_final: 0.8531 (p0) REVERT: U 37 ASP cc_start: 0.9268 (p0) cc_final: 0.8819 (p0) REVERT: X 35 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9031 (mt) REVERT: Y 37 ASP cc_start: 0.9257 (p0) cc_final: 0.8518 (p0) outliers start: 61 outliers final: 30 residues processed: 145 average time/residue: 0.0955 time to fit residues: 23.8056 Evaluate side-chains 123 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 85 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain K residue 87 ILE Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 87 ILE Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 87 ILE Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 8 MET Chi-restraints excluded: chain T residue 35 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain W residue 66 SER Chi-restraints excluded: chain X residue 35 LEU Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain Y residue 5 GLN Chi-restraints excluded: chain Y residue 87 ILE Chi-restraints excluded: chain Z residue 35 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 124 optimal weight: 4.9990 chunk 198 optimal weight: 0.0980 chunk 31 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 93 optimal weight: 0.0170 chunk 190 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 overall best weight: 2.2224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.031183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.024875 restraints weight = 78146.881| |-----------------------------------------------------------------------------| r_work (start): 0.2458 rms_B_bonded: 3.71 r_work: 0.2353 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16512 Z= 0.203 Angle : 0.448 4.291 22680 Z= 0.228 Chirality : 0.045 0.150 2832 Planarity : 0.004 0.032 2904 Dihedral : 3.814 11.962 2376 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 2.38 % Allowed : 19.23 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.18), residues: 2232 helix: None (None), residues: 0 sheet: 0.73 (0.17), residues: 888 loop : 0.09 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 12 TYR 0.011 0.001 TYR P 54 PHE 0.009 0.001 PHE F 7 Details of bonding type rmsd covalent geometry : bond 0.00468 (16512) covalent geometry : angle 0.44819 (22680) hydrogen bonds : bond 0.02483 ( 384) hydrogen bonds : angle 4.62654 ( 936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 83 time to evaluate : 0.634 Fit side-chains REVERT: D 37 ASP cc_start: 0.9225 (p0) cc_final: 0.8936 (p0) REVERT: G 37 ASP cc_start: 0.9185 (p0) cc_final: 0.8600 (p0) REVERT: I 35 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9083 (mt) REVERT: I 37 ASP cc_start: 0.9237 (p0) cc_final: 0.9020 (p0) REVERT: K 37 ASP cc_start: 0.9191 (p0) cc_final: 0.8903 (p0) REVERT: M 37 ASP cc_start: 0.9113 (p0) cc_final: 0.8396 (p0) REVERT: O 35 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8946 (mt) REVERT: P 35 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8911 (mt) REVERT: P 87 ILE cc_start: 0.9597 (OUTLIER) cc_final: 0.9393 (mm) REVERT: Q 87 ILE cc_start: 0.9597 (OUTLIER) cc_final: 0.9357 (mm) REVERT: R 37 ASP cc_start: 0.9127 (p0) cc_final: 0.8884 (p0) REVERT: T 37 ASP cc_start: 0.9059 (p0) cc_final: 0.8596 (p0) REVERT: U 37 ASP cc_start: 0.9282 (p0) cc_final: 0.8866 (p0) REVERT: V 37 ASP cc_start: 0.9022 (p0) cc_final: 0.8377 (p0) REVERT: Y 37 ASP cc_start: 0.9264 (p0) cc_final: 0.8608 (p0) outliers start: 40 outliers final: 25 residues processed: 119 average time/residue: 0.0967 time to fit residues: 19.8937 Evaluate side-chains 111 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 87 ILE Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 3 ILE Chi-restraints excluded: chain T residue 35 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain Y residue 5 GLN Chi-restraints excluded: chain Z residue 35 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 178 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 122 optimal weight: 0.0870 chunk 13 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.030587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.024346 restraints weight = 78547.040| |-----------------------------------------------------------------------------| r_work (start): 0.2447 rms_B_bonded: 3.66 r_work: 0.2344 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 16512 Z= 0.270 Angle : 0.493 8.596 22680 Z= 0.245 Chirality : 0.046 0.149 2832 Planarity : 0.004 0.031 2904 Dihedral : 4.048 12.448 2376 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.10 % Allowed : 17.80 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.18), residues: 2232 helix: None (None), residues: 0 sheet: 0.82 (0.18), residues: 816 loop : 0.22 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 12 TYR 0.015 0.001 TYR P 54 PHE 0.008 0.001 PHE K 13 Details of bonding type rmsd covalent geometry : bond 0.00621 (16512) covalent geometry : angle 0.49346 (22680) hydrogen bonds : bond 0.02596 ( 384) hydrogen bonds : angle 4.63945 ( 936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 82 time to evaluate : 0.637 Fit side-chains REVERT: D 37 ASP cc_start: 0.9319 (p0) cc_final: 0.9100 (p0) REVERT: G 8 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8969 (mtt) REVERT: H 84 ASP cc_start: 0.8997 (t70) cc_final: 0.8744 (t0) REVERT: I 35 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9107 (mt) REVERT: K 37 ASP cc_start: 0.9213 (p0) cc_final: 0.8951 (p0) REVERT: M 37 ASP cc_start: 0.9292 (p0) cc_final: 0.8694 (p0) REVERT: N 37 ASP cc_start: 0.9206 (p0) cc_final: 0.8795 (p0) REVERT: O 35 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8926 (mt) REVERT: P 35 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8997 (mt) REVERT: Q 8 MET cc_start: 0.9225 (ttm) cc_final: 0.9010 (mtp) REVERT: Q 87 ILE cc_start: 0.9577 (OUTLIER) cc_final: 0.9363 (mm) REVERT: R 8 MET cc_start: 0.9504 (ttm) cc_final: 0.9295 (ttm) REVERT: R 37 ASP cc_start: 0.9169 (p0) cc_final: 0.8929 (p0) REVERT: T 37 ASP cc_start: 0.9178 (p0) cc_final: 0.8855 (p0) REVERT: U 8 MET cc_start: 0.9320 (mtp) cc_final: 0.8898 (mtt) REVERT: U 37 ASP cc_start: 0.9318 (p0) cc_final: 0.8845 (p0) REVERT: V 37 ASP cc_start: 0.9129 (p0) cc_final: 0.8546 (p0) REVERT: X 35 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9088 (mt) REVERT: Y 37 ASP cc_start: 0.9299 (p0) cc_final: 0.8798 (p0) outliers start: 52 outliers final: 35 residues processed: 130 average time/residue: 0.0986 time to fit residues: 22.1967 Evaluate side-chains 118 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 77 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain Q residue 87 ILE Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 3 ILE Chi-restraints excluded: chain T residue 35 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain X residue 35 LEU Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain Y residue 5 GLN Chi-restraints excluded: chain Z residue 35 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 183 optimal weight: 6.9990 chunk 80 optimal weight: 0.0470 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 overall best weight: 2.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.030940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.024696 restraints weight = 78325.048| |-----------------------------------------------------------------------------| r_work (start): 0.2463 rms_B_bonded: 3.68 r_work: 0.2358 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16512 Z= 0.199 Angle : 0.453 5.359 22680 Z= 0.226 Chirality : 0.045 0.148 2832 Planarity : 0.004 0.032 2904 Dihedral : 3.840 12.138 2376 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 2.32 % Allowed : 18.81 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.18), residues: 2232 helix: None (None), residues: 0 sheet: 0.96 (0.18), residues: 816 loop : 0.38 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Y 11 TYR 0.011 0.001 TYR P 54 PHE 0.005 0.001 PHE K 13 Details of bonding type rmsd covalent geometry : bond 0.00456 (16512) covalent geometry : angle 0.45251 (22680) hydrogen bonds : bond 0.02430 ( 384) hydrogen bonds : angle 4.54531 ( 936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 80 time to evaluate : 0.588 Fit side-chains REVERT: D 37 ASP cc_start: 0.9334 (p0) cc_final: 0.9085 (p0) REVERT: H 8 MET cc_start: 0.8902 (ttm) cc_final: 0.8698 (ttt) REVERT: H 84 ASP cc_start: 0.9027 (t70) cc_final: 0.8751 (t0) REVERT: K 37 ASP cc_start: 0.9206 (p0) cc_final: 0.8959 (p0) REVERT: M 37 ASP cc_start: 0.9308 (p0) cc_final: 0.8755 (p0) REVERT: N 37 ASP cc_start: 0.9230 (p0) cc_final: 0.8948 (p0) REVERT: O 35 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8925 (mt) REVERT: P 35 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8986 (mt) REVERT: Q 87 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9354 (mm) REVERT: R 8 MET cc_start: 0.9409 (ttm) cc_final: 0.9205 (ttm) REVERT: T 37 ASP cc_start: 0.9200 (p0) cc_final: 0.8939 (p0) REVERT: U 37 ASP cc_start: 0.9337 (p0) cc_final: 0.8854 (p0) REVERT: V 37 ASP cc_start: 0.9159 (p0) cc_final: 0.8605 (p0) REVERT: Y 37 ASP cc_start: 0.9264 (p0) cc_final: 0.8806 (p0) outliers start: 39 outliers final: 31 residues processed: 118 average time/residue: 0.0907 time to fit residues: 18.4828 Evaluate side-chains 113 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain Q residue 87 ILE Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 3 ILE Chi-restraints excluded: chain T residue 35 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 66 SER Chi-restraints excluded: chain W residue 66 SER Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain Y residue 5 GLN Chi-restraints excluded: chain Z residue 35 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 193 optimal weight: 5.9990 chunk 167 optimal weight: 0.2980 chunk 210 optimal weight: 5.9990 chunk 213 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.030487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.024396 restraints weight = 77896.908| |-----------------------------------------------------------------------------| r_work (start): 0.2447 rms_B_bonded: 3.58 r_work: 0.2344 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16512 Z= 0.272 Angle : 0.499 6.196 22680 Z= 0.246 Chirality : 0.046 0.148 2832 Planarity : 0.004 0.032 2904 Dihedral : 4.067 12.846 2376 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.50 % Allowed : 18.51 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.18), residues: 2232 helix: None (None), residues: 0 sheet: 0.99 (0.18), residues: 816 loop : 0.46 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 11 TYR 0.012 0.001 TYR P 54 PHE 0.007 0.001 PHE K 13 Details of bonding type rmsd covalent geometry : bond 0.00623 (16512) covalent geometry : angle 0.49909 (22680) hydrogen bonds : bond 0.02490 ( 384) hydrogen bonds : angle 4.62242 ( 936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 77 time to evaluate : 0.621 Fit side-chains REVERT: D 37 ASP cc_start: 0.9367 (p0) cc_final: 0.9164 (p0) REVERT: H 8 MET cc_start: 0.8954 (ttm) cc_final: 0.8742 (ttt) REVERT: H 84 ASP cc_start: 0.9011 (t70) cc_final: 0.8736 (t0) REVERT: I 35 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9122 (mt) REVERT: J 8 MET cc_start: 0.9319 (mmm) cc_final: 0.9102 (mmm) REVERT: K 37 ASP cc_start: 0.9224 (p0) cc_final: 0.8993 (p0) REVERT: O 35 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8960 (mt) REVERT: P 35 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9009 (mt) REVERT: Q 87 ILE cc_start: 0.9567 (OUTLIER) cc_final: 0.9356 (mm) REVERT: R 8 MET cc_start: 0.9461 (ttm) cc_final: 0.9241 (ttm) REVERT: S 8 MET cc_start: 0.9324 (mmm) cc_final: 0.9084 (mmm) REVERT: T 37 ASP cc_start: 0.9238 (p0) cc_final: 0.8985 (p0) REVERT: U 37 ASP cc_start: 0.9327 (p0) cc_final: 0.8895 (p0) REVERT: V 37 ASP cc_start: 0.9177 (p0) cc_final: 0.8645 (p0) REVERT: V 84 ASP cc_start: 0.9036 (t70) cc_final: 0.8549 (t0) REVERT: X 35 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9103 (mt) REVERT: Y 37 ASP cc_start: 0.9327 (p0) cc_final: 0.8742 (p0) REVERT: Y 84 ASP cc_start: 0.8954 (t70) cc_final: 0.8438 (t70) outliers start: 42 outliers final: 35 residues processed: 118 average time/residue: 0.0974 time to fit residues: 19.6784 Evaluate side-chains 115 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 75 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 66 SER Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain Q residue 87 ILE Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 3 ILE Chi-restraints excluded: chain T residue 35 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 66 SER Chi-restraints excluded: chain W residue 66 SER Chi-restraints excluded: chain X residue 35 LEU Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain Y residue 5 GLN Chi-restraints excluded: chain Z residue 35 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 7 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 189 optimal weight: 0.2980 chunk 118 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 197 optimal weight: 0.5980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.031095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.024857 restraints weight = 78374.337| |-----------------------------------------------------------------------------| r_work (start): 0.2463 rms_B_bonded: 3.72 r_work: 0.2357 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16512 Z= 0.160 Angle : 0.435 5.360 22680 Z= 0.217 Chirality : 0.045 0.151 2832 Planarity : 0.004 0.031 2904 Dihedral : 3.727 11.631 2376 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Rotamer: Outliers : 1.96 % Allowed : 18.93 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.18), residues: 2232 helix: None (None), residues: 0 sheet: 1.14 (0.18), residues: 816 loop : 0.57 (0.18), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG Y 11 TYR 0.008 0.001 TYR P 54 PHE 0.005 0.001 PHE C 93 Details of bonding type rmsd covalent geometry : bond 0.00366 (16512) covalent geometry : angle 0.43469 (22680) hydrogen bonds : bond 0.02321 ( 384) hydrogen bonds : angle 4.50731 ( 936) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 79 time to evaluate : 0.610 Fit side-chains REVERT: D 37 ASP cc_start: 0.9370 (p0) cc_final: 0.9150 (p0) REVERT: G 8 MET cc_start: 0.8863 (mtt) cc_final: 0.8281 (mtt) REVERT: H 84 ASP cc_start: 0.8988 (t70) cc_final: 0.8702 (t0) REVERT: J 8 MET cc_start: 0.9294 (mmm) cc_final: 0.9089 (mmm) REVERT: K 37 ASP cc_start: 0.9219 (p0) cc_final: 0.9010 (p0) REVERT: N 37 ASP cc_start: 0.9245 (p0) cc_final: 0.8894 (p0) REVERT: O 35 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8927 (mt) REVERT: R 8 MET cc_start: 0.9405 (ttm) cc_final: 0.9193 (ttm) REVERT: T 37 ASP cc_start: 0.9255 (p0) cc_final: 0.9002 (p0) REVERT: U 37 ASP cc_start: 0.9329 (p0) cc_final: 0.8900 (p0) REVERT: V 37 ASP cc_start: 0.9185 (p0) cc_final: 0.8655 (p0) REVERT: Y 37 ASP cc_start: 0.9323 (p0) cc_final: 0.8728 (p0) REVERT: Y 84 ASP cc_start: 0.8913 (t70) cc_final: 0.8609 (t70) outliers start: 33 outliers final: 28 residues processed: 111 average time/residue: 0.0969 time to fit residues: 18.5586 Evaluate side-chains 107 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 3 ILE Chi-restraints excluded: chain T residue 35 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain V residue 66 SER Chi-restraints excluded: chain W residue 66 SER Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain Y residue 5 GLN Chi-restraints excluded: chain Z residue 35 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 101 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 164 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.030790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.024664 restraints weight = 78108.625| |-----------------------------------------------------------------------------| r_work (start): 0.2453 rms_B_bonded: 3.63 r_work: 0.2348 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16512 Z= 0.215 Angle : 0.463 6.197 22680 Z= 0.228 Chirality : 0.045 0.149 2832 Planarity : 0.004 0.031 2904 Dihedral : 3.851 12.333 2376 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 2.02 % Allowed : 18.93 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.18), residues: 2232 helix: None (None), residues: 0 sheet: 1.18 (0.18), residues: 816 loop : 0.65 (0.18), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 11 TYR 0.010 0.001 TYR P 54 PHE 0.006 0.001 PHE O 7 Details of bonding type rmsd covalent geometry : bond 0.00489 (16512) covalent geometry : angle 0.46328 (22680) hydrogen bonds : bond 0.02316 ( 384) hydrogen bonds : angle 4.56121 ( 936) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 0.616 Fit side-chains REVERT: D 37 ASP cc_start: 0.9374 (p0) cc_final: 0.9158 (p0) REVERT: H 84 ASP cc_start: 0.8938 (t70) cc_final: 0.8644 (t0) REVERT: I 35 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9084 (mt) REVERT: J 8 MET cc_start: 0.9332 (mmm) cc_final: 0.9126 (mmm) REVERT: K 37 ASP cc_start: 0.9226 (p0) cc_final: 0.9018 (p0) REVERT: N 37 ASP cc_start: 0.9257 (p0) cc_final: 0.8895 (p0) REVERT: O 35 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8958 (mt) REVERT: Q 8 MET cc_start: 0.9178 (mtm) cc_final: 0.8913 (mtp) REVERT: R 8 MET cc_start: 0.9442 (ttm) cc_final: 0.9234 (ttm) REVERT: R 37 ASP cc_start: 0.9228 (p0) cc_final: 0.8866 (p0) REVERT: T 37 ASP cc_start: 0.9248 (p0) cc_final: 0.9011 (p0) REVERT: U 37 ASP cc_start: 0.9339 (p0) cc_final: 0.8921 (p0) REVERT: V 37 ASP cc_start: 0.9205 (p0) cc_final: 0.8895 (p0) REVERT: V 84 ASP cc_start: 0.8999 (t70) cc_final: 0.8497 (t0) REVERT: Y 37 ASP cc_start: 0.9327 (p0) cc_final: 0.8718 (p0) REVERT: Y 84 ASP cc_start: 0.8926 (t70) cc_final: 0.8387 (t70) outliers start: 34 outliers final: 31 residues processed: 111 average time/residue: 0.0934 time to fit residues: 17.9117 Evaluate side-chains 110 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 3 ILE Chi-restraints excluded: chain T residue 35 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 66 SER Chi-restraints excluded: chain W residue 66 SER Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain Z residue 35 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 123 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 167 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.030876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.024652 restraints weight = 78480.631| |-----------------------------------------------------------------------------| r_work (start): 0.2459 rms_B_bonded: 3.69 r_work: 0.2354 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16512 Z= 0.211 Angle : 0.462 5.667 22680 Z= 0.227 Chirality : 0.045 0.148 2832 Planarity : 0.004 0.029 2904 Dihedral : 3.858 12.285 2376 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 2.26 % Allowed : 18.63 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.19), residues: 2232 helix: None (None), residues: 0 sheet: 1.21 (0.18), residues: 816 loop : 0.71 (0.18), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 11 TYR 0.010 0.001 TYR P 54 PHE 0.006 0.001 PHE K 13 Details of bonding type rmsd covalent geometry : bond 0.00481 (16512) covalent geometry : angle 0.46209 (22680) hydrogen bonds : bond 0.02283 ( 384) hydrogen bonds : angle 4.57468 ( 936) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 76 time to evaluate : 0.540 Fit side-chains REVERT: D 37 ASP cc_start: 0.9376 (p0) cc_final: 0.9172 (p0) REVERT: H 84 ASP cc_start: 0.8925 (t70) cc_final: 0.8631 (t0) REVERT: I 35 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9055 (mt) REVERT: J 8 MET cc_start: 0.9343 (mmm) cc_final: 0.9136 (mmm) REVERT: K 37 ASP cc_start: 0.9235 (p0) cc_final: 0.9032 (p0) REVERT: N 37 ASP cc_start: 0.9262 (p0) cc_final: 0.8912 (p0) REVERT: O 35 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8909 (mt) REVERT: P 35 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8992 (mt) REVERT: R 8 MET cc_start: 0.9441 (ttm) cc_final: 0.9224 (ttm) REVERT: R 37 ASP cc_start: 0.9295 (p0) cc_final: 0.8964 (p0) REVERT: T 37 ASP cc_start: 0.9254 (p0) cc_final: 0.9021 (p0) REVERT: U 37 ASP cc_start: 0.9338 (p0) cc_final: 0.8940 (p0) REVERT: V 37 ASP cc_start: 0.9206 (p0) cc_final: 0.8900 (p0) REVERT: V 84 ASP cc_start: 0.8989 (t70) cc_final: 0.8470 (t0) REVERT: Y 37 ASP cc_start: 0.9330 (p0) cc_final: 0.8712 (p0) REVERT: Y 84 ASP cc_start: 0.8901 (t70) cc_final: 0.8342 (t70) outliers start: 38 outliers final: 33 residues processed: 112 average time/residue: 0.0949 time to fit residues: 18.3774 Evaluate side-chains 112 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 66 SER Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 66 SER Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 3 ILE Chi-restraints excluded: chain T residue 8 MET Chi-restraints excluded: chain T residue 35 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain U residue 3 ILE Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain V residue 66 SER Chi-restraints excluded: chain W residue 66 SER Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain Z residue 35 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 193 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 206 optimal weight: 0.0030 chunk 95 optimal weight: 0.2980 chunk 151 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.031820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.025579 restraints weight = 76905.424| |-----------------------------------------------------------------------------| r_work (start): 0.2496 rms_B_bonded: 3.69 r_work: 0.2391 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 16512 Z= 0.101 Angle : 0.413 5.934 22680 Z= 0.205 Chirality : 0.045 0.146 2832 Planarity : 0.003 0.029 2904 Dihedral : 3.430 11.077 2376 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 1.13 % Allowed : 19.88 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.19), residues: 2232 helix: None (None), residues: 0 sheet: 1.03 (0.18), residues: 864 loop : 0.59 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG O 11 TYR 0.007 0.001 TYR G 50 PHE 0.006 0.001 PHE C 93 Details of bonding type rmsd covalent geometry : bond 0.00229 (16512) covalent geometry : angle 0.41258 (22680) hydrogen bonds : bond 0.02160 ( 384) hydrogen bonds : angle 4.43540 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2582.13 seconds wall clock time: 45 minutes 33.66 seconds (2733.66 seconds total)