Starting phenix.real_space_refine on Sat Jun 14 04:47:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hze_52523/06_2025/9hze_52523.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hze_52523/06_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_52523/06_2025/9hze_52523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hze_52523/06_2025/9hze_52523.map" model { file = "/net/cci-nas-00/data/ceres_data/9hze_52523/06_2025/9hze_52523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hze_52523/06_2025/9hze_52523.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, Y, X, Z Time building chain proxies: 3.66, per 1000 atoms: 0.23 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: 3.37 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.06 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: 4.39 Time building geometry restraints manager: 4.10 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: 0.16 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 29.720 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.570 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 PHE 0.005 0.001 PHE R 93 TYR 0.006 0.001 TYR X 50 ARG 0.001 0.000 ARG L 11 Details of bonding type rmsd hydrogen bonds : bond 0.13833 ( 384) hydrogen bonds : angle 6.74916 ( 936) covalent geometry : bond 0.00164 (16512) covalent geometry : angle 0.41610 (22680) *********************** 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 : 1.818 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: 0.2171 time to fit residues: 52.8117 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 : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 GLN D 60 GLN E 60 GLN F 60 GLN ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 S 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.031001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.024679 restraints weight = 77959.232| |-----------------------------------------------------------------------------| r_work (start): 0.2450 rms_B_bonded: 3.74 r_work: 0.2344 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 16512 Z= 0.283 Angle : 0.511 5.107 22680 Z= 0.261 Chirality : 0.046 0.195 2832 Planarity : 0.004 0.030 2904 Dihedral : 3.963 12.021 2376 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.46 % Allowed : 15.48 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.18), residues: 2232 helix: None (None), residues: 0 sheet: 0.97 (0.19), residues: 768 loop : 0.02 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE K 13 TYR 0.015 0.001 TYR P 54 ARG 0.002 0.001 ARG Z 12 Details of bonding type rmsd hydrogen bonds : bond 0.02786 ( 384) hydrogen bonds : angle 4.87351 ( 936) covalent geometry : bond 0.00660 (16512) covalent geometry : angle 0.51063 (22680) *********************** 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 178 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 103 time to evaluate : 1.572 Fit side-chains REVERT: D 37 ASP cc_start: 0.9133 (p0) cc_final: 0.8831 (p0) REVERT: F 8 MET cc_start: 0.9383 (mtm) cc_final: 0.9151 (mtt) REVERT: F 87 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9179 (mm) REVERT: G 37 ASP cc_start: 0.9090 (p0) cc_final: 0.8459 (p0) REVERT: I 37 ASP cc_start: 0.9104 (p0) cc_final: 0.8756 (p0) REVERT: J 37 ASP cc_start: 0.9156 (p0) cc_final: 0.8877 (p0) REVERT: M 37 ASP cc_start: 0.9069 (p0) cc_final: 0.8293 (p0) REVERT: N 87 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9112 (mm) REVERT: P 35 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8873 (mt) REVERT: P 87 ILE cc_start: 0.9532 (OUTLIER) cc_final: 0.9322 (mm) REVERT: Q 87 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9282 (mm) REVERT: R 35 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9005 (mt) REVERT: T 37 ASP cc_start: 0.9019 (p0) cc_final: 0.8554 (p0) REVERT: U 5 GLN cc_start: 0.9419 (mt0) cc_final: 0.9193 (mt0) REVERT: U 37 ASP cc_start: 0.9302 (p0) cc_final: 0.8758 (p0) REVERT: V 8 MET cc_start: 0.9256 (mtm) cc_final: 0.8898 (mtm) REVERT: X 87 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9162 (mm) outliers start: 75 outliers final: 35 residues processed: 175 average time/residue: 0.1943 time to fit residues: 58.2532 Evaluate side-chains 134 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 92 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 77 ILE 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 F residue 87 ILE 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 J residue 66 SER Chi-restraints excluded: chain K residue 87 ILE Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 66 SER 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 N residue 87 ILE Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain P residue 87 ILE Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 66 SER 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 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 W residue 66 SER Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 87 ILE Chi-restraints excluded: chain Y residue 5 GLN Chi-restraints excluded: chain Y residue 63 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 30 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 125 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 5 GLN G 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.031961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.025635 restraints weight = 75869.758| |-----------------------------------------------------------------------------| r_work (start): 0.2491 rms_B_bonded: 3.67 r_work: 0.2385 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16512 Z= 0.114 Angle : 0.410 3.120 22680 Z= 0.211 Chirality : 0.045 0.157 2832 Planarity : 0.004 0.031 2904 Dihedral : 3.486 10.712 2376 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 2.14 % Allowed : 18.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.18), residues: 2232 helix: None (None), residues: 0 sheet: 0.61 (0.17), residues: 888 loop : 0.05 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE K 93 TYR 0.007 0.001 TYR P 54 ARG 0.001 0.000 ARG E 12 Details of bonding type rmsd hydrogen bonds : bond 0.02355 ( 384) hydrogen bonds : angle 4.64178 ( 936) covalent geometry : bond 0.00263 (16512) covalent geometry : angle 0.41036 (22680) *********************** 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 141 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 1.641 Fit side-chains REVERT: D 37 ASP cc_start: 0.9140 (p0) cc_final: 0.8792 (p0) REVERT: G 37 ASP cc_start: 0.9142 (p0) cc_final: 0.8510 (p0) REVERT: I 37 ASP cc_start: 0.9171 (p0) cc_final: 0.8944 (p0) REVERT: J 37 ASP cc_start: 0.9120 (p0) cc_final: 0.8892 (p0) REVERT: M 37 ASP cc_start: 0.9031 (p0) cc_final: 0.8281 (p0) REVERT: P 35 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8831 (mt) REVERT: Q 87 ILE cc_start: 0.9604 (OUTLIER) cc_final: 0.9341 (mm) REVERT: T 37 ASP cc_start: 0.8979 (p0) cc_final: 0.8542 (p0) REVERT: U 5 GLN cc_start: 0.9386 (mt0) cc_final: 0.9178 (mt0) REVERT: U 37 ASP cc_start: 0.9245 (p0) cc_final: 0.8735 (p0) REVERT: Y 92 GLU cc_start: 0.8894 (tt0) cc_final: 0.8491 (tt0) outliers start: 36 outliers final: 21 residues processed: 136 average time/residue: 0.1993 time to fit residues: 46.1903 Evaluate side-chains 121 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 37 ASP 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 P residue 35 LEU Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 87 ILE Chi-restraints excluded: chain S residue 83 LEU 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 V residue 63 VAL Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain Y residue 5 GLN Chi-restraints excluded: chain Y residue 63 VAL Chi-restraints excluded: chain Z residue 35 LEU Chi-restraints excluded: chain Z residue 77 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 120 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 215 optimal weight: 0.0770 chunk 135 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 167 optimal weight: 0.0010 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.5146 ------------------------------------------------------------------------------- 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 = 0.2765 r_free = 0.2765 target = 0.033168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.026999 restraints weight = 75255.587| |-----------------------------------------------------------------------------| r_work (start): 0.2525 rms_B_bonded: 3.68 r_work: 0.2415 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 16512 Z= 0.073 Angle : 0.394 4.807 22680 Z= 0.199 Chirality : 0.045 0.150 2832 Planarity : 0.004 0.031 2904 Dihedral : 3.127 9.903 2376 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 1.55 % Allowed : 20.18 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 2232 helix: None (None), residues: 0 sheet: 0.86 (0.17), residues: 888 loop : 0.13 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.000 PHE D 7 TYR 0.005 0.001 TYR G 50 ARG 0.001 0.000 ARG X 11 Details of bonding type rmsd hydrogen bonds : bond 0.02196 ( 384) hydrogen bonds : angle 4.40556 ( 936) covalent geometry : bond 0.00162 (16512) covalent geometry : angle 0.39372 (22680) *********************** 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 135 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 1.630 Fit side-chains REVERT: D 37 ASP cc_start: 0.9162 (p0) cc_final: 0.8878 (p0) REVERT: F 8 MET cc_start: 0.9338 (mtm) cc_final: 0.9119 (mtp) REVERT: G 37 ASP cc_start: 0.9206 (p0) cc_final: 0.8850 (p0) REVERT: I 37 ASP cc_start: 0.9211 (p0) cc_final: 0.8976 (p0) REVERT: K 8 MET cc_start: 0.9230 (ttm) cc_final: 0.8627 (mmm) REVERT: M 37 ASP cc_start: 0.9078 (p0) cc_final: 0.8363 (p0) REVERT: O 8 MET cc_start: 0.9362 (mtp) cc_final: 0.9145 (mtm) REVERT: P 37 ASP cc_start: 0.9252 (p0) cc_final: 0.8871 (p0) REVERT: T 37 ASP cc_start: 0.9074 (p0) cc_final: 0.8768 (p0) REVERT: U 5 GLN cc_start: 0.9425 (mt0) cc_final: 0.9221 (mt0) REVERT: U 37 ASP cc_start: 0.9263 (p0) cc_final: 0.8777 (p0) REVERT: Y 92 GLU cc_start: 0.8892 (tt0) cc_final: 0.8533 (tt0) outliers start: 26 outliers final: 16 residues processed: 129 average time/residue: 0.2056 time to fit residues: 45.1440 Evaluate side-chains 120 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain Y residue 63 VAL Chi-restraints excluded: chain Z residue 35 LEU Chi-restraints excluded: chain Z residue 77 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 6 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 178 optimal weight: 0.0050 chunk 206 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 173 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 overall best weight: 3.2002 ------------------------------------------------------------------------------- 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 = 0.2679 r_free = 0.2679 target = 0.030657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.024477 restraints weight = 78859.039| |-----------------------------------------------------------------------------| r_work (start): 0.2442 rms_B_bonded: 3.66 r_work: 0.2339 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 16512 Z= 0.285 Angle : 0.503 5.809 22680 Z= 0.249 Chirality : 0.046 0.166 2832 Planarity : 0.004 0.031 2904 Dihedral : 3.990 12.547 2376 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 1.67 % Allowed : 20.12 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 2232 helix: None (None), residues: 0 sheet: 0.92 (0.17), residues: 888 loop : 0.25 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE K 13 TYR 0.016 0.001 TYR P 54 ARG 0.002 0.000 ARG E 12 Details of bonding type rmsd hydrogen bonds : bond 0.02649 ( 384) hydrogen bonds : angle 4.58728 ( 936) covalent geometry : bond 0.00654 (16512) covalent geometry : angle 0.50261 (22680) *********************** 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 118 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 1.652 Fit side-chains REVERT: C 37 ASP cc_start: 0.9213 (p0) cc_final: 0.8769 (p0) REVERT: D 37 ASP cc_start: 0.9230 (p0) cc_final: 0.8953 (p0) REVERT: G 37 ASP cc_start: 0.9214 (p0) cc_final: 0.8673 (p0) REVERT: I 35 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9113 (mt) REVERT: K 37 ASP cc_start: 0.9175 (p0) cc_final: 0.8823 (p0) REVERT: M 37 ASP cc_start: 0.9176 (p0) cc_final: 0.8562 (p0) REVERT: N 37 ASP cc_start: 0.9191 (p0) cc_final: 0.8800 (p0) REVERT: P 35 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8917 (mt) REVERT: P 37 ASP cc_start: 0.9285 (p0) cc_final: 0.8888 (p0) REVERT: Q 37 ASP cc_start: 0.9291 (p0) cc_final: 0.8856 (p0) REVERT: R 37 ASP cc_start: 0.9213 (p0) cc_final: 0.8846 (p0) REVERT: T 37 ASP cc_start: 0.9237 (p0) cc_final: 0.8799 (p0) REVERT: U 37 ASP cc_start: 0.9302 (p0) cc_final: 0.8870 (p0) REVERT: V 37 ASP cc_start: 0.9160 (p0) cc_final: 0.8484 (p0) REVERT: X 87 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.9261 (mm) REVERT: Y 37 ASP cc_start: 0.9329 (p0) cc_final: 0.8747 (p0) outliers start: 28 outliers final: 20 residues processed: 116 average time/residue: 0.2089 time to fit residues: 41.5229 Evaluate side-chains 103 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain G residue 5 GLN 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 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 P residue 35 LEU Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 63 VAL 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 X residue 87 ILE Chi-restraints excluded: chain Y residue 63 VAL 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 58 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 176 optimal weight: 20.0000 chunk 161 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 15 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.031031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.024790 restraints weight = 77673.617| |-----------------------------------------------------------------------------| r_work (start): 0.2448 rms_B_bonded: 3.70 r_work: 0.2340 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16512 Z= 0.196 Angle : 0.450 5.609 22680 Z= 0.224 Chirality : 0.045 0.159 2832 Planarity : 0.004 0.030 2904 Dihedral : 3.775 11.774 2376 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 1.67 % Allowed : 20.42 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.18), residues: 2232 helix: None (None), residues: 0 sheet: 1.05 (0.18), residues: 888 loop : 0.40 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE K 13 TYR 0.011 0.001 TYR P 54 ARG 0.001 0.000 ARG H 11 Details of bonding type rmsd hydrogen bonds : bond 0.02417 ( 384) hydrogen bonds : angle 4.53332 ( 936) covalent geometry : bond 0.00449 (16512) covalent geometry : angle 0.45001 (22680) *********************** 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 118 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 1.721 Fit side-chains REVERT: C 37 ASP cc_start: 0.9226 (p0) cc_final: 0.8812 (p0) REVERT: D 37 ASP cc_start: 0.9301 (p0) cc_final: 0.9066 (p0) REVERT: G 37 ASP cc_start: 0.9257 (p0) cc_final: 0.8668 (p0) REVERT: I 35 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9079 (mt) REVERT: K 37 ASP cc_start: 0.9204 (p0) cc_final: 0.8933 (p0) REVERT: M 37 ASP cc_start: 0.9280 (p0) cc_final: 0.8724 (p0) REVERT: N 37 ASP cc_start: 0.9203 (p0) cc_final: 0.8899 (p0) REVERT: P 35 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8909 (mt) REVERT: P 37 ASP cc_start: 0.9340 (p0) cc_final: 0.8968 (p0) REVERT: Q 37 ASP cc_start: 0.9306 (p0) cc_final: 0.8905 (p0) REVERT: R 37 ASP cc_start: 0.9223 (p0) cc_final: 0.8892 (p0) REVERT: T 37 ASP cc_start: 0.9274 (p0) cc_final: 0.8994 (p0) REVERT: U 37 ASP cc_start: 0.9331 (p0) cc_final: 0.8854 (p0) REVERT: V 37 ASP cc_start: 0.9137 (p0) cc_final: 0.8567 (p0) REVERT: V 84 ASP cc_start: 0.9022 (t70) cc_final: 0.8574 (t0) REVERT: X 87 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9226 (mm) REVERT: Y 37 ASP cc_start: 0.9302 (p0) cc_final: 0.8780 (p0) REVERT: Y 84 ASP cc_start: 0.8975 (t70) cc_final: 0.8660 (t70) outliers start: 28 outliers final: 22 residues processed: 115 average time/residue: 0.2055 time to fit residues: 40.5928 Evaluate side-chains 113 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 1.784 ------------------------------------------------------------------------------- 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 77 ILE Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain G residue 5 GLN 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 M residue 3 ILE Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain P residue 8 MET Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain S residue 83 LEU 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 X residue 63 VAL Chi-restraints excluded: chain X residue 87 ILE Chi-restraints excluded: chain Y residue 63 VAL 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 151 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.2668 r_free = 0.2668 target = 0.030364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.024199 restraints weight = 78245.066| |-----------------------------------------------------------------------------| r_work (start): 0.2426 rms_B_bonded: 3.62 r_work: 0.2322 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 16512 Z= 0.320 Angle : 0.534 7.318 22680 Z= 0.261 Chirality : 0.046 0.159 2832 Planarity : 0.004 0.029 2904 Dihedral : 4.177 13.061 2376 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.08 % Allowed : 19.88 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.18), residues: 2232 helix: None (None), residues: 0 sheet: 1.11 (0.19), residues: 816 loop : 0.44 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE K 13 TYR 0.016 0.001 TYR P 54 ARG 0.002 0.000 ARG E 12 Details of bonding type rmsd hydrogen bonds : bond 0.02556 ( 384) hydrogen bonds : angle 4.65161 ( 936) covalent geometry : bond 0.00734 (16512) covalent geometry : angle 0.53376 (22680) *********************** 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 116 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 81 time to evaluate : 1.671 Fit side-chains REVERT: C 37 ASP cc_start: 0.9231 (p0) cc_final: 0.8840 (p0) REVERT: D 37 ASP cc_start: 0.9360 (p0) cc_final: 0.9157 (p0) REVERT: H 84 ASP cc_start: 0.9022 (t70) cc_final: 0.8748 (t0) REVERT: I 8 MET cc_start: 0.9101 (mtp) cc_final: 0.8801 (mtp) REVERT: I 35 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9138 (mt) REVERT: K 37 ASP cc_start: 0.9229 (p0) cc_final: 0.8968 (p0) REVERT: P 35 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9038 (mt) REVERT: Q 37 ASP cc_start: 0.9333 (p0) cc_final: 0.8973 (p0) REVERT: Q 87 ILE cc_start: 0.9569 (OUTLIER) cc_final: 0.9358 (mm) REVERT: R 37 ASP cc_start: 0.9253 (p0) cc_final: 0.8967 (p0) REVERT: U 37 ASP cc_start: 0.9332 (p0) cc_final: 0.8897 (p0) REVERT: V 37 ASP cc_start: 0.9163 (p0) cc_final: 0.8623 (p0) REVERT: V 84 ASP cc_start: 0.9012 (t70) cc_final: 0.8594 (t0) REVERT: X 87 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9261 (mm) REVERT: Y 37 ASP cc_start: 0.9384 (p0) cc_final: 0.8742 (p0) REVERT: Y 84 ASP cc_start: 0.8986 (t70) cc_final: 0.8470 (t70) REVERT: Z 8 MET cc_start: 0.9273 (ttm) cc_final: 0.9010 (ttm) outliers start: 35 outliers final: 27 residues processed: 113 average time/residue: 0.2045 time to fit residues: 39.6063 Evaluate side-chains 110 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 1.653 ------------------------------------------------------------------------------- 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 G residue 5 GLN Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain I residue 35 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 5 GLN Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain P residue 8 MET Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 87 ILE Chi-restraints excluded: chain S residue 83 LEU 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 63 VAL Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain W residue 66 SER Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 87 ILE Chi-restraints excluded: chain Y residue 63 VAL 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 60 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 170 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 61 optimal weight: 0.0970 chunk 159 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.2733 r_free = 0.2733 target = 0.032048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.025761 restraints weight = 76776.920| |-----------------------------------------------------------------------------| r_work (start): 0.2498 rms_B_bonded: 3.73 r_work: 0.2391 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16512 Z= 0.084 Angle : 0.413 5.664 22680 Z= 0.206 Chirality : 0.045 0.154 2832 Planarity : 0.003 0.029 2904 Dihedral : 3.367 10.784 2376 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.43 % Allowed : 20.36 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 2232 helix: None (None), residues: 0 sheet: 1.02 (0.19), residues: 864 loop : 0.39 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE K 93 TYR 0.007 0.001 TYR G 50 ARG 0.001 0.000 ARG V 11 Details of bonding type rmsd hydrogen bonds : bond 0.02207 ( 384) hydrogen bonds : angle 4.43035 ( 936) covalent geometry : bond 0.00190 (16512) covalent geometry : angle 0.41337 (22680) *********************** 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 121 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.597 Fit side-chains REVERT: C 37 ASP cc_start: 0.9211 (p0) cc_final: 0.8818 (p0) REVERT: D 37 ASP cc_start: 0.9311 (p0) cc_final: 0.9069 (p0) REVERT: E 5 GLN cc_start: 0.9406 (mt0) cc_final: 0.8942 (mp10) REVERT: G 37 ASP cc_start: 0.9157 (p0) cc_final: 0.8860 (p0) REVERT: I 8 MET cc_start: 0.9026 (mtp) cc_final: 0.8805 (mtp) REVERT: K 37 ASP cc_start: 0.9191 (p0) cc_final: 0.8959 (p0) REVERT: N 37 ASP cc_start: 0.9237 (p0) cc_final: 0.8827 (p0) REVERT: P 37 ASP cc_start: 0.9346 (p0) cc_final: 0.8968 (p0) REVERT: Q 37 ASP cc_start: 0.9307 (p0) cc_final: 0.8914 (p0) REVERT: R 37 ASP cc_start: 0.9178 (p0) cc_final: 0.8892 (p0) REVERT: U 37 ASP cc_start: 0.9294 (p0) cc_final: 0.8840 (p0) REVERT: V 37 ASP cc_start: 0.9134 (p0) cc_final: 0.8579 (p0) REVERT: V 84 ASP cc_start: 0.8964 (t70) cc_final: 0.8538 (t0) REVERT: Y 37 ASP cc_start: 0.9265 (p0) cc_final: 0.8745 (p0) outliers start: 24 outliers final: 20 residues processed: 117 average time/residue: 0.2028 time to fit residues: 40.5796 Evaluate side-chains 107 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 1.819 ------------------------------------------------------------------------------- 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 77 ILE Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain P residue 8 MET Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 66 SER Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 77 ILE 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 Y residue 63 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 175 optimal weight: 2.9990 chunk 171 optimal weight: 0.0010 chunk 66 optimal weight: 0.0470 chunk 83 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 210 optimal weight: 4.9990 chunk 125 optimal weight: 0.0060 chunk 126 optimal weight: 7.9990 chunk 15 optimal weight: 0.0770 chunk 31 optimal weight: 0.9990 overall best weight: 0.2260 ------------------------------------------------------------------------------- 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 = 0.2775 r_free = 0.2775 target = 0.033255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.027046 restraints weight = 75584.501| |-----------------------------------------------------------------------------| r_work (start): 0.2548 rms_B_bonded: 3.64 r_work: 0.2442 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.023 16512 Z= 0.065 Angle : 0.397 5.102 22680 Z= 0.197 Chirality : 0.045 0.150 2832 Planarity : 0.003 0.029 2904 Dihedral : 2.941 10.494 2376 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.89 % Allowed : 20.83 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.19), residues: 2232 helix: None (None), residues: 0 sheet: 1.28 (0.18), residues: 936 loop : 0.60 (0.19), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE K 93 TYR 0.007 0.001 TYR G 50 ARG 0.001 0.000 ARG N 11 Details of bonding type rmsd hydrogen bonds : bond 0.02123 ( 384) hydrogen bonds : angle 4.23538 ( 936) covalent geometry : bond 0.00145 (16512) covalent geometry : angle 0.39717 (22680) *********************** 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 120 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 1.841 Fit side-chains REVERT: C 37 ASP cc_start: 0.9206 (p0) cc_final: 0.8856 (p0) REVERT: D 37 ASP cc_start: 0.9235 (p0) cc_final: 0.8970 (p0) REVERT: G 37 ASP cc_start: 0.9216 (p0) cc_final: 0.8884 (p0) REVERT: I 8 MET cc_start: 0.9154 (mtp) cc_final: 0.8850 (mtp) REVERT: K 8 MET cc_start: 0.9162 (mmm) cc_final: 0.8962 (mmm) REVERT: K 37 ASP cc_start: 0.9218 (p0) cc_final: 0.8980 (p0) REVERT: N 37 ASP cc_start: 0.9162 (p0) cc_final: 0.8735 (p0) REVERT: P 37 ASP cc_start: 0.9303 (p0) cc_final: 0.8913 (p0) REVERT: Q 37 ASP cc_start: 0.9254 (p0) cc_final: 0.8857 (p0) REVERT: R 37 ASP cc_start: 0.9190 (p0) cc_final: 0.8943 (p0) REVERT: S 37 ASP cc_start: 0.9197 (p0) cc_final: 0.8994 (p0) REVERT: U 37 ASP cc_start: 0.9231 (p0) cc_final: 0.8756 (p0) REVERT: V 37 ASP cc_start: 0.9094 (p0) cc_final: 0.8551 (p0) REVERT: V 84 ASP cc_start: 0.8996 (t70) cc_final: 0.8602 (t0) REVERT: Y 37 ASP cc_start: 0.9257 (p0) cc_final: 0.8878 (p0) outliers start: 15 outliers final: 10 residues processed: 117 average time/residue: 0.2127 time to fit residues: 42.8345 Evaluate side-chains 106 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 77 ILE Chi-restraints excluded: chain V residue 63 VAL Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain Y residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 38 optimal weight: 0.5980 chunk 203 optimal weight: 0.9980 chunk 205 optimal weight: 0.4980 chunk 58 optimal weight: 0.0070 chunk 94 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 196 optimal weight: 0.0980 chunk 131 optimal weight: 0.2980 chunk 195 optimal weight: 3.9990 overall best weight: 0.2998 ------------------------------------------------------------------------------- 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 = 0.2787 r_free = 0.2787 target = 0.033532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.027366 restraints weight = 76195.555| |-----------------------------------------------------------------------------| r_work (start): 0.2562 rms_B_bonded: 3.64 r_work: 0.2455 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.022 16512 Z= 0.063 Angle : 0.391 5.134 22680 Z= 0.192 Chirality : 0.045 0.152 2832 Planarity : 0.003 0.030 2904 Dihedral : 2.856 10.920 2376 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.60 % Allowed : 21.13 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.19), residues: 2232 helix: None (None), residues: 0 sheet: 1.46 (0.18), residues: 936 loop : 0.74 (0.19), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE J 93 TYR 0.008 0.001 TYR G 50 ARG 0.002 0.000 ARG O 11 Details of bonding type rmsd hydrogen bonds : bond 0.02085 ( 384) hydrogen bonds : angle 4.21596 ( 936) covalent geometry : bond 0.00144 (16512) covalent geometry : angle 0.39074 (22680) ********************** 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 108 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 1.857 Fit side-chains REVERT: C 37 ASP cc_start: 0.9182 (p0) cc_final: 0.8829 (p0) REVERT: D 8 MET cc_start: 0.8591 (mtt) cc_final: 0.8345 (mtt) REVERT: D 37 ASP cc_start: 0.9217 (p0) cc_final: 0.8599 (p0) REVERT: G 8 MET cc_start: 0.8047 (mmt) cc_final: 0.7553 (mmt) REVERT: G 37 ASP cc_start: 0.9197 (p0) cc_final: 0.8855 (p0) REVERT: I 8 MET cc_start: 0.9174 (mtp) cc_final: 0.8928 (mtp) REVERT: I 37 ASP cc_start: 0.9285 (p0) cc_final: 0.9058 (p0) REVERT: K 37 ASP cc_start: 0.9199 (p0) cc_final: 0.8956 (p0) REVERT: N 37 ASP cc_start: 0.9184 (p0) cc_final: 0.8728 (p0) REVERT: Q 37 ASP cc_start: 0.9244 (p0) cc_final: 0.8821 (p0) REVERT: R 37 ASP cc_start: 0.9171 (p0) cc_final: 0.8956 (p0) REVERT: S 37 ASP cc_start: 0.9188 (p0) cc_final: 0.8973 (p0) REVERT: U 8 MET cc_start: 0.8823 (mmm) cc_final: 0.8555 (mmt) REVERT: U 37 ASP cc_start: 0.9193 (p0) cc_final: 0.8702 (p0) REVERT: V 37 ASP cc_start: 0.9207 (p0) cc_final: 0.8662 (p0) REVERT: V 84 ASP cc_start: 0.9003 (t70) cc_final: 0.8600 (t0) REVERT: Y 37 ASP cc_start: 0.9238 (p0) cc_final: 0.8889 (p0) outliers start: 10 outliers final: 7 residues processed: 108 average time/residue: 0.2077 time to fit residues: 38.2778 Evaluate side-chains 101 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain X residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 193 optimal weight: 5.9990 chunk 195 optimal weight: 0.1980 chunk 182 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 205 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 173 optimal weight: 0.3980 chunk 164 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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 = 0.2768 r_free = 0.2768 target = 0.032982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.026891 restraints weight = 75975.096| |-----------------------------------------------------------------------------| r_work (start): 0.2553 rms_B_bonded: 3.58 r_work: 0.2449 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 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 0.022 16512 Z= 0.080 Angle : 0.396 5.979 22680 Z= 0.194 Chirality : 0.045 0.149 2832 Planarity : 0.003 0.029 2904 Dihedral : 2.916 10.560 2376 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.60 % Allowed : 21.19 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.19), residues: 2232 helix: None (None), residues: 0 sheet: 1.55 (0.18), residues: 936 loop : 0.92 (0.19), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.000 PHE J 93 TYR 0.007 0.001 TYR G 50 ARG 0.001 0.000 ARG X 11 Details of bonding type rmsd hydrogen bonds : bond 0.02115 ( 384) hydrogen bonds : angle 4.22238 ( 936) covalent geometry : bond 0.00181 (16512) covalent geometry : angle 0.39611 (22680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5298.98 seconds wall clock time: 92 minutes 20.86 seconds (5540.86 seconds total)