Starting phenix.real_space_refine on Sat May 17 14:07:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hze_52523/05_2025/9hze_52523.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hze_52523/05_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_52523/05_2025/9hze_52523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hze_52523/05_2025/9hze_52523.map" model { file = "/net/cci-nas-00/data/ceres_data/9hze_52523/05_2025/9hze_52523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hze_52523/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 3.64, 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: 3.24 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: 2.00 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: 4.03 Time building geometry restraints manager: 3.88 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 27.930 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.610 ------------------------------------------------------------------------------- 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 : 1.546 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: 0.2054 time to fit residues: 49.9330 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 : 1.796 ------------------------------------------------------------------------------- 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 = 77959.710| |-----------------------------------------------------------------------------| 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 : 1.697 Fit side-chains REVERT: D 37 ASP cc_start: 0.9132 (p0) cc_final: 0.8831 (p0) REVERT: F 8 MET cc_start: 0.9384 (mtm) cc_final: 0.9152 (mtt) REVERT: F 87 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9178 (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: 0.9155 (p0) cc_final: 0.8876 (p0) REVERT: M 37 ASP cc_start: 0.9068 (p0) cc_final: 0.8291 (p0) REVERT: N 87 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9113 (mm) REVERT: P 35 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8874 (mt) REVERT: P 87 ILE cc_start: 0.9533 (OUTLIER) cc_final: 0.9323 (mm) REVERT: Q 87 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9283 (mm) REVERT: R 35 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9006 (mt) REVERT: T 37 ASP cc_start: 0.9018 (p0) cc_final: 0.8553 (p0) REVERT: U 5 GLN cc_start: 0.9418 (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: 0.9257 (mtm) cc_final: 0.8899 (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: 0.1932 time to fit residues: 57.8868 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 : 1.669 ------------------------------------------------------------------------------- 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: 0.6980 chunk 171 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.2728 r_free = 0.2728 target = 0.032047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.025709 restraints weight = 75941.937| |-----------------------------------------------------------------------------| r_work (start): 0.2494 rms_B_bonded: 3.68 r_work: 0.2388 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.1954 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 3.109 22680 Z= 0.211 Chirality : 0.045 0.156 2832 Planarity : 0.004 0.031 2904 Dihedral : 3.475 10.734 2376 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.20 % Allowed : 18.69 % 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: 0.36 (0.18), residues: 2232 helix: None (None), residues: 0 sheet: 0.62 (0.17), residues: 888 loop : 0.06 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE K 93 TYR 0.006 0.001 TYR P 54 ARG 0.001 0.000 ARG T 12 Details of bonding type rmsd hydrogen bonds : bond 0.02354 ( 384) hydrogen bonds : angle 4.63602 ( 936) covalent geometry : bond 0.00264 (16512) covalent geometry : angle 0.40995 (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 142 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 1.818 Fit side-chains REVERT: D 37 ASP cc_start: 0.9140 (p0) cc_final: 0.8791 (p0) REVERT: G 37 ASP cc_start: 0.9144 (p0) cc_final: 0.8513 (p0) REVERT: I 37 ASP cc_start: 0.9170 (p0) cc_final: 0.8943 (p0) REVERT: J 37 ASP cc_start: 0.9121 (p0) cc_final: 0.8894 (p0) REVERT: M 37 ASP cc_start: 0.9030 (p0) cc_final: 0.8281 (p0) REVERT: P 35 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8828 (mt) REVERT: Q 87 ILE cc_start: 0.9603 (OUTLIER) cc_final: 0.9340 (mm) REVERT: T 37 ASP cc_start: 0.8982 (p0) cc_final: 0.8568 (p0) REVERT: U 5 GLN cc_start: 0.9389 (mt0) cc_final: 0.9180 (mt0) REVERT: U 37 ASP cc_start: 0.9246 (p0) cc_final: 0.8753 (p0) REVERT: Y 92 GLU cc_start: 0.8895 (tt0) cc_final: 0.8490 (tt0) outliers start: 37 outliers final: 21 residues processed: 137 average time/residue: 0.2005 time to fit residues: 46.8949 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 : 1.577 ------------------------------------------------------------------------------- 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: 4.9990 chunk 135 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 167 optimal weight: 0.0980 chunk 38 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 26 optimal weight: 0.0170 overall best weight: 0.5620 ------------------------------------------------------------------------------- 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 = 0.2750 r_free = 0.2750 target = 0.032632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.026282 restraints weight = 74983.983| |-----------------------------------------------------------------------------| r_work (start): 0.2518 rms_B_bonded: 3.77 r_work: 0.2408 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 16512 Z= 0.077 Angle : 0.394 4.594 22680 Z= 0.200 Chirality : 0.045 0.152 2832 Planarity : 0.004 0.031 2904 Dihedral : 3.172 9.951 2376 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Rotamer: Outliers : 1.43 % Allowed : 20.30 % 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: 0.56 (0.18), residues: 2232 helix: None (None), residues: 0 sheet: 0.84 (0.17), residues: 888 loop : 0.12 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.000 PHE D 7 TYR 0.006 0.001 TYR F 50 ARG 0.001 0.000 ARG S 11 Details of bonding type rmsd hydrogen bonds : bond 0.02223 ( 384) hydrogen bonds : angle 4.43474 ( 936) covalent geometry : bond 0.00172 (16512) covalent geometry : angle 0.39354 (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: 24 poor density : 111 time to evaluate : 1.675 Fit side-chains REVERT: D 37 ASP cc_start: 0.9168 (p0) cc_final: 0.8896 (p0) REVERT: G 37 ASP cc_start: 0.9225 (p0) cc_final: 0.8877 (p0) REVERT: I 35 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8913 (mt) REVERT: I 37 ASP cc_start: 0.9212 (p0) cc_final: 0.8992 (p0) REVERT: J 37 ASP cc_start: 0.9141 (p0) cc_final: 0.8922 (p0) REVERT: K 8 MET cc_start: 0.9248 (ttm) cc_final: 0.8663 (mmm) REVERT: M 37 ASP cc_start: 0.9086 (p0) cc_final: 0.8382 (p0) REVERT: P 37 ASP cc_start: 0.9259 (p0) cc_final: 0.8887 (p0) REVERT: T 37 ASP cc_start: 0.9089 (p0) cc_final: 0.8766 (p0) REVERT: U 5 GLN cc_start: 0.9437 (mt0) cc_final: 0.9234 (mt0) REVERT: U 37 ASP cc_start: 0.9280 (p0) cc_final: 0.8801 (p0) REVERT: Y 92 GLU cc_start: 0.8946 (tt0) cc_final: 0.8566 (tt0) outliers start: 24 outliers final: 16 residues processed: 130 average time/residue: 0.2038 time to fit residues: 45.1547 Evaluate side-chains 121 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 I residue 35 LEU Chi-restraints excluded: chain J residue 35 LEU Chi-restraints excluded: chain M residue 63 VAL 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 V 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: 0.0980 chunk 206 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- 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 = 0.2691 r_free = 0.2691 target = 0.030951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.024772 restraints weight = 78389.631| |-----------------------------------------------------------------------------| r_work (start): 0.2467 rms_B_bonded: 3.67 r_work: 0.2364 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16512 Z= 0.236 Angle : 0.469 4.947 22680 Z= 0.234 Chirality : 0.046 0.164 2832 Planarity : 0.004 0.030 2904 Dihedral : 3.824 12.098 2376 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 1.55 % Allowed : 20.42 % 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: 0.74 (0.18), residues: 2232 helix: None (None), residues: 0 sheet: 0.94 (0.17), residues: 888 loop : 0.26 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE K 13 TYR 0.013 0.001 TYR P 54 ARG 0.002 0.000 ARG E 12 Details of bonding type rmsd hydrogen bonds : bond 0.02563 ( 384) hydrogen bonds : angle 4.56770 ( 936) covalent geometry : bond 0.00542 (16512) covalent geometry : angle 0.46940 (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 121 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 1.602 Fit side-chains REVERT: C 37 ASP cc_start: 0.9109 (p0) cc_final: 0.8656 (p0) REVERT: D 37 ASP cc_start: 0.9220 (p0) cc_final: 0.8934 (p0) REVERT: G 37 ASP cc_start: 0.9188 (p0) cc_final: 0.8617 (p0) REVERT: I 37 ASP cc_start: 0.9283 (p0) cc_final: 0.9081 (p0) REVERT: K 37 ASP cc_start: 0.9144 (p0) cc_final: 0.8757 (p0) REVERT: M 37 ASP cc_start: 0.9163 (p0) cc_final: 0.8546 (p0) REVERT: N 37 ASP cc_start: 0.9198 (p0) cc_final: 0.8778 (p0) REVERT: P 35 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8912 (mt) REVERT: P 37 ASP cc_start: 0.9290 (p0) cc_final: 0.8897 (p0) REVERT: Q 37 ASP cc_start: 0.9274 (p0) cc_final: 0.8835 (p0) REVERT: R 37 ASP cc_start: 0.9154 (p0) cc_final: 0.8831 (p0) REVERT: T 37 ASP cc_start: 0.9163 (p0) cc_final: 0.8778 (p0) REVERT: U 37 ASP cc_start: 0.9308 (p0) cc_final: 0.8869 (p0) REVERT: V 8 MET cc_start: 0.9407 (mtp) cc_final: 0.9126 (mtm) REVERT: V 37 ASP cc_start: 0.9153 (p0) cc_final: 0.8491 (p0) REVERT: Y 37 ASP cc_start: 0.9312 (p0) cc_final: 0.8659 (p0) outliers start: 26 outliers final: 21 residues processed: 116 average time/residue: 0.1990 time to fit residues: 39.3608 Evaluate side-chains 109 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 83 LEU 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 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 83 LEU 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 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 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: 1.9990 chunk 64 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 chunk 121 optimal weight: 0.4980 chunk 95 optimal weight: 0.0270 chunk 176 optimal weight: 0.3980 chunk 161 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- 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 = 0.2734 r_free = 0.2734 target = 0.032226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.025894 restraints weight = 76418.663| |-----------------------------------------------------------------------------| r_work (start): 0.2507 rms_B_bonded: 3.72 r_work: 0.2401 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16512 Z= 0.091 Angle : 0.399 5.456 22680 Z= 0.201 Chirality : 0.045 0.156 2832 Planarity : 0.003 0.030 2904 Dihedral : 3.315 10.493 2376 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 1.79 % Allowed : 20.36 % Favored : 77.86 % 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: 0.64 (0.19), residues: 2232 helix: None (None), residues: 0 sheet: 0.85 (0.18), residues: 936 loop : 0.19 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.000 PHE D 93 TYR 0.005 0.001 TYR G 50 ARG 0.001 0.000 ARG C 12 Details of bonding type rmsd hydrogen bonds : bond 0.02242 ( 384) hydrogen bonds : angle 4.40417 ( 936) covalent geometry : bond 0.00208 (16512) covalent geometry : angle 0.39937 (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 121 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 1.663 Fit side-chains REVERT: C 37 ASP cc_start: 0.9123 (p0) cc_final: 0.8686 (p0) REVERT: D 37 ASP cc_start: 0.9217 (p0) cc_final: 0.8970 (p0) REVERT: G 37 ASP cc_start: 0.9175 (p0) cc_final: 0.8884 (p0) REVERT: I 35 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9018 (mt) REVERT: K 37 ASP cc_start: 0.9149 (p0) cc_final: 0.8862 (p0) REVERT: M 37 ASP cc_start: 0.9257 (p0) cc_final: 0.8698 (p0) REVERT: N 37 ASP cc_start: 0.9224 (p0) cc_final: 0.8860 (p0) REVERT: P 35 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8820 (mt) REVERT: P 37 ASP cc_start: 0.9328 (p0) cc_final: 0.8927 (p0) REVERT: Q 37 ASP cc_start: 0.9271 (p0) cc_final: 0.8862 (p0) REVERT: R 37 ASP cc_start: 0.9174 (p0) cc_final: 0.8860 (p0) REVERT: T 37 ASP cc_start: 0.9185 (p0) cc_final: 0.8942 (p0) REVERT: U 37 ASP cc_start: 0.9279 (p0) cc_final: 0.8736 (p0) REVERT: V 37 ASP cc_start: 0.9086 (p0) cc_final: 0.8502 (p0) REVERT: Y 37 ASP cc_start: 0.9241 (p0) cc_final: 0.8749 (p0) outliers start: 30 outliers final: 22 residues processed: 114 average time/residue: 0.1990 time to fit residues: 38.8882 Evaluate side-chains 112 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain G residue 5 GLN Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain I residue 35 LEU 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 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 V 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 151 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 153 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.2701 r_free = 0.2701 target = 0.031202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.025039 restraints weight = 77157.252| |-----------------------------------------------------------------------------| r_work (start): 0.2471 rms_B_bonded: 3.62 r_work: 0.2366 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16512 Z= 0.196 Angle : 0.446 6.698 22680 Z= 0.221 Chirality : 0.045 0.157 2832 Planarity : 0.003 0.030 2904 Dihedral : 3.630 11.756 2376 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 1.67 % Allowed : 20.30 % 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: 1.18 (0.19), residues: 2232 helix: None (None), residues: 0 sheet: 1.21 (0.18), residues: 888 loop : 0.60 (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 0.002 0.000 ARG H 11 Details of bonding type rmsd hydrogen bonds : bond 0.02374 ( 384) hydrogen bonds : angle 4.49357 ( 936) covalent geometry : bond 0.00449 (16512) covalent geometry : angle 0.44639 (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 113 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 1.537 Fit side-chains REVERT: C 37 ASP cc_start: 0.9237 (p0) cc_final: 0.8805 (p0) REVERT: D 37 ASP cc_start: 0.9300 (p0) cc_final: 0.9058 (p0) REVERT: G 37 ASP cc_start: 0.9229 (p0) cc_final: 0.8638 (p0) REVERT: I 35 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9113 (mt) REVERT: K 37 ASP cc_start: 0.9178 (p0) cc_final: 0.8909 (p0) REVERT: M 8 MET cc_start: 0.9283 (mtp) cc_final: 0.8953 (tpp) REVERT: N 37 ASP cc_start: 0.9237 (p0) cc_final: 0.8927 (p0) REVERT: P 35 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8950 (mt) REVERT: P 37 ASP cc_start: 0.9336 (p0) cc_final: 0.8937 (p0) REVERT: Q 37 ASP cc_start: 0.9276 (p0) cc_final: 0.8901 (p0) REVERT: R 8 MET cc_start: 0.9337 (ttm) cc_final: 0.9004 (ttm) REVERT: R 37 ASP cc_start: 0.9167 (p0) cc_final: 0.8868 (p0) REVERT: T 37 ASP cc_start: 0.9262 (p0) cc_final: 0.9010 (p0) REVERT: U 37 ASP cc_start: 0.9303 (p0) cc_final: 0.8822 (p0) REVERT: V 37 ASP cc_start: 0.9229 (p0) cc_final: 0.8655 (p0) REVERT: V 84 ASP cc_start: 0.9016 (t70) cc_final: 0.8579 (t0) REVERT: X 35 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9086 (mt) REVERT: Y 37 ASP cc_start: 0.9280 (p0) cc_final: 0.8828 (p0) outliers start: 28 outliers final: 21 residues processed: 111 average time/residue: 0.1984 time to fit residues: 37.5978 Evaluate side-chains 106 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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 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 63 VAL 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 R residue 91 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 35 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 60 optimal weight: 5.9990 chunk 38 optimal weight: 0.3980 chunk 170 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 160 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 59 optimal weight: 0.4980 chunk 113 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.2738 r_free = 0.2738 target = 0.032274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.026041 restraints weight = 75827.961| |-----------------------------------------------------------------------------| r_work (start): 0.2525 rms_B_bonded: 3.69 r_work: 0.2420 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16512 Z= 0.085 Angle : 0.402 5.353 22680 Z= 0.200 Chirality : 0.044 0.153 2832 Planarity : 0.003 0.030 2904 Dihedral : 3.226 10.503 2376 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.25 % Allowed : 20.36 % 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 (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: 0.99 (0.19), residues: 2232 helix: None (None), residues: 0 sheet: 1.03 (0.18), residues: 936 loop : 0.49 (0.19), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.000 PHE K 93 TYR 0.005 0.001 TYR G 50 ARG 0.001 0.000 ARG C 11 Details of bonding type rmsd hydrogen bonds : bond 0.02151 ( 384) hydrogen bonds : angle 4.34004 ( 936) covalent geometry : bond 0.00190 (16512) covalent geometry : angle 0.40230 (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 120 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 1.936 Fit side-chains REVERT: C 37 ASP cc_start: 0.9181 (p0) cc_final: 0.8849 (p0) REVERT: D 37 ASP cc_start: 0.9288 (p0) cc_final: 0.9040 (p0) REVERT: G 37 ASP cc_start: 0.9249 (p0) cc_final: 0.8944 (p0) REVERT: I 35 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9007 (mt) REVERT: K 37 ASP cc_start: 0.9217 (p0) cc_final: 0.8984 (p0) REVERT: N 37 ASP cc_start: 0.9223 (p0) cc_final: 0.8775 (p0) REVERT: P 37 ASP cc_start: 0.9320 (p0) cc_final: 0.8932 (p0) REVERT: Q 37 ASP cc_start: 0.9276 (p0) cc_final: 0.8880 (p0) REVERT: R 37 ASP cc_start: 0.9207 (p0) cc_final: 0.8948 (p0) REVERT: T 37 ASP cc_start: 0.9207 (p0) cc_final: 0.8973 (p0) REVERT: U 37 ASP cc_start: 0.9274 (p0) cc_final: 0.8798 (p0) REVERT: V 37 ASP cc_start: 0.9122 (p0) cc_final: 0.8579 (p0) REVERT: V 84 ASP cc_start: 0.8966 (t70) cc_final: 0.8505 (t0) REVERT: Y 37 ASP cc_start: 0.9279 (p0) cc_final: 0.8839 (p0) REVERT: Y 92 GLU cc_start: 0.8888 (tt0) cc_final: 0.8482 (tt0) outliers start: 21 outliers final: 14 residues processed: 117 average time/residue: 0.2082 time to fit residues: 41.5491 Evaluate side-chains 104 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 63 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain Q residue 35 LEU Chi-restraints excluded: chain Q residue 63 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 175 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 113 optimal weight: 0.0270 chunk 210 optimal weight: 0.0980 chunk 125 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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 = 0.2739 r_free = 0.2739 target = 0.032312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.026050 restraints weight = 75902.221| |-----------------------------------------------------------------------------| r_work (start): 0.2508 rms_B_bonded: 3.71 r_work: 0.2401 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 16512 Z= 0.087 Angle : 0.398 6.696 22680 Z= 0.197 Chirality : 0.045 0.152 2832 Planarity : 0.003 0.030 2904 Dihedral : 3.137 10.497 2376 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.07 % Allowed : 20.77 % Favored : 78.15 % 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: 1.17 (0.19), residues: 2232 helix: None (None), residues: 0 sheet: 1.14 (0.18), residues: 936 loop : 0.62 (0.19), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.000 PHE D 93 TYR 0.006 0.001 TYR G 50 ARG 0.001 0.000 ARG P 11 Details of bonding type rmsd hydrogen bonds : bond 0.02127 ( 384) hydrogen bonds : angle 4.31388 ( 936) covalent geometry : bond 0.00198 (16512) covalent geometry : angle 0.39771 (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 110 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 1.595 Fit side-chains REVERT: C 37 ASP cc_start: 0.9181 (p0) cc_final: 0.8831 (p0) REVERT: D 37 ASP cc_start: 0.9293 (p0) cc_final: 0.9032 (p0) REVERT: G 37 ASP cc_start: 0.9263 (p0) cc_final: 0.8955 (p0) REVERT: K 37 ASP cc_start: 0.9236 (p0) cc_final: 0.9000 (p0) REVERT: N 37 ASP cc_start: 0.9237 (p0) cc_final: 0.8783 (p0) REVERT: P 37 ASP cc_start: 0.9325 (p0) cc_final: 0.8917 (p0) REVERT: Q 37 ASP cc_start: 0.9285 (p0) cc_final: 0.8899 (p0) REVERT: R 37 ASP cc_start: 0.9215 (p0) cc_final: 0.8988 (p0) REVERT: T 37 ASP cc_start: 0.9342 (p0) cc_final: 0.9060 (p0) REVERT: U 37 ASP cc_start: 0.9283 (p0) cc_final: 0.8817 (p0) REVERT: V 37 ASP cc_start: 0.9126 (p0) cc_final: 0.8602 (p0) REVERT: V 84 ASP cc_start: 0.8952 (t70) cc_final: 0.8501 (t0) REVERT: Y 37 ASP cc_start: 0.9293 (p0) cc_final: 0.8886 (p0) outliers start: 18 outliers final: 12 residues processed: 108 average time/residue: 0.2057 time to fit residues: 37.8937 Evaluate side-chains 103 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 M residue 63 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain Q residue 63 VAL 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 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: 0.2980 chunk 205 optimal weight: 4.9990 chunk 58 optimal weight: 0.0370 chunk 94 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 131 optimal weight: 0.2980 chunk 195 optimal weight: 2.9990 overall best weight: 0.4460 ------------------------------------------------------------------------------- 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 = 0.2766 r_free = 0.2766 target = 0.033002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.026737 restraints weight = 76264.064| |-----------------------------------------------------------------------------| r_work (start): 0.2538 rms_B_bonded: 3.75 r_work: 0.2429 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.2573 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= 0.068 Angle : 0.388 5.930 22680 Z= 0.192 Chirality : 0.045 0.148 2832 Planarity : 0.003 0.030 2904 Dihedral : 2.936 10.699 2376 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.83 % Allowed : 20.77 % 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 (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: 1.40 (0.19), residues: 2232 helix: None (None), residues: 0 sheet: 1.31 (0.18), residues: 936 loop : 0.77 (0.19), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE S 93 TYR 0.006 0.001 TYR G 50 ARG 0.001 0.000 ARG E 11 Details of bonding type rmsd hydrogen bonds : bond 0.02083 ( 384) hydrogen bonds : angle 4.19238 ( 936) covalent geometry : bond 0.00155 (16512) covalent geometry : angle 0.38765 (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 116 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 1.571 Fit side-chains REVERT: C 37 ASP cc_start: 0.9210 (p0) cc_final: 0.8851 (p0) REVERT: D 37 ASP cc_start: 0.9279 (p0) cc_final: 0.9025 (p0) REVERT: G 37 ASP cc_start: 0.9233 (p0) cc_final: 0.8919 (p0) REVERT: K 37 ASP cc_start: 0.9227 (p0) cc_final: 0.9005 (p0) REVERT: N 37 ASP cc_start: 0.9211 (p0) cc_final: 0.8774 (p0) REVERT: P 37 ASP cc_start: 0.9333 (p0) cc_final: 0.8970 (p0) REVERT: Q 37 ASP cc_start: 0.9296 (p0) cc_final: 0.8915 (p0) REVERT: T 37 ASP cc_start: 0.9343 (p0) cc_final: 0.9073 (p0) REVERT: U 37 ASP cc_start: 0.9242 (p0) cc_final: 0.8775 (p0) REVERT: V 37 ASP cc_start: 0.9220 (p0) cc_final: 0.8699 (p0) REVERT: V 84 ASP cc_start: 0.8987 (t70) cc_final: 0.8521 (t0) REVERT: Y 37 ASP cc_start: 0.9292 (p0) cc_final: 0.8927 (p0) outliers start: 14 outliers final: 12 residues processed: 115 average time/residue: 0.2023 time to fit residues: 39.5773 Evaluate side-chains 109 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 M residue 63 VAL Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain Q residue 63 VAL 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 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 193 optimal weight: 6.9990 chunk 195 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 173 optimal weight: 0.4980 chunk 164 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.2716 r_free = 0.2716 target = 0.031604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.025509 restraints weight = 76685.062| |-----------------------------------------------------------------------------| r_work (start): 0.2493 rms_B_bonded: 3.56 r_work: 0.2393 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16512 Z= 0.156 Angle : 0.429 7.292 22680 Z= 0.210 Chirality : 0.045 0.152 2832 Planarity : 0.003 0.030 2904 Dihedral : 3.381 11.165 2376 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Rotamer: Outliers : 0.77 % Allowed : 21.19 % 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: 1.88 (0.19), residues: 2232 helix: None (None), residues: 0 sheet: 1.67 (0.18), residues: 888 loop : 1.10 (0.19), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE S 93 TYR 0.009 0.001 TYR P 54 ARG 0.002 0.000 ARG N 11 Details of bonding type rmsd hydrogen bonds : bond 0.02245 ( 384) hydrogen bonds : angle 4.41073 ( 936) covalent geometry : bond 0.00357 (16512) covalent geometry : angle 0.42937 (22680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5107.06 seconds wall clock time: 89 minutes 59.64 seconds (5399.64 seconds total)