Starting phenix.real_space_refine on Tue Aug 26 10:31:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8et1_28583/08_2025/8et1_28583.cif Found real_map, /net/cci-nas-00/data/ceres_data/8et1_28583/08_2025/8et1_28583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8et1_28583/08_2025/8et1_28583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8et1_28583/08_2025/8et1_28583.map" model { file = "/net/cci-nas-00/data/ceres_data/8et1_28583/08_2025/8et1_28583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8et1_28583/08_2025/8et1_28583.cif" } resolution = 4.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.031 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 144 5.16 5 C 22752 2.51 5 N 6432 2.21 5 O 6648 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35976 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1499 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 3 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Time building chain proxies: 3.14, per 1000 atoms: 0.09 Number of scatterers: 35976 At special positions: 0 Unit cell: (270.58, 270.58, 53.12, 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 144 16.00 O 6648 8.00 N 6432 7.00 C 22752 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: 3.11 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8304 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 96 sheets defined 18.1% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 Processing helix chain 'A' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'B' and resid 4 through 17 Processing helix chain 'B' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA B 131 " --> pdb=" O GLN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 152 Processing helix chain 'C' and resid 4 through 17 Processing helix chain 'C' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 152 Processing helix chain 'D' and resid 4 through 17 Processing helix chain 'D' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 152 Processing helix chain 'E' and resid 4 through 17 Processing helix chain 'E' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA E 131 " --> pdb=" O GLN E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 152 Processing helix chain 'F' and resid 4 through 17 Processing helix chain 'F' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA F 131 " --> pdb=" O GLN F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 152 Processing helix chain 'G' and resid 4 through 17 Processing helix chain 'G' and resid 127 through 136 removed outlier: 3.669A pdb=" N ALA G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 152 Processing helix chain 'H' and resid 4 through 17 Processing helix chain 'H' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA H 131 " --> pdb=" O GLN H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 152 Processing helix chain 'I' and resid 4 through 17 Processing helix chain 'I' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA I 131 " --> pdb=" O GLN I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 152 Processing helix chain 'J' and resid 4 through 17 Processing helix chain 'J' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA J 131 " --> pdb=" O GLN J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 152 Processing helix chain 'K' and resid 4 through 17 Processing helix chain 'K' and resid 127 through 136 removed outlier: 3.667A pdb=" N ALA K 131 " --> pdb=" O GLN K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 152 Processing helix chain 'L' and resid 4 through 17 Processing helix chain 'L' and resid 127 through 136 removed outlier: 3.667A pdb=" N ALA L 131 " --> pdb=" O GLN L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 152 Processing helix chain 'M' and resid 4 through 17 Processing helix chain 'M' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA M 131 " --> pdb=" O GLN M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 152 Processing helix chain 'N' and resid 4 through 17 Processing helix chain 'N' and resid 127 through 136 removed outlier: 3.669A pdb=" N ALA N 131 " --> pdb=" O GLN N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 152 Processing helix chain 'O' and resid 4 through 17 Processing helix chain 'O' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA O 131 " --> pdb=" O GLN O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 144 through 152 Processing helix chain 'P' and resid 4 through 17 Processing helix chain 'P' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA P 131 " --> pdb=" O GLN P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 144 through 152 Processing helix chain 'Q' and resid 4 through 17 Processing helix chain 'Q' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA Q 131 " --> pdb=" O GLN Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 152 Processing helix chain 'R' and resid 4 through 17 Processing helix chain 'R' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA R 131 " --> pdb=" O GLN R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 152 Processing helix chain 'S' and resid 4 through 17 Processing helix chain 'S' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA S 131 " --> pdb=" O GLN S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 144 through 152 Processing helix chain 'T' and resid 4 through 17 Processing helix chain 'T' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA T 131 " --> pdb=" O GLN T 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 144 through 152 Processing helix chain 'U' and resid 4 through 17 Processing helix chain 'U' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA U 131 " --> pdb=" O GLN U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 144 through 152 Processing helix chain 'V' and resid 4 through 17 Processing helix chain 'V' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA V 131 " --> pdb=" O GLN V 127 " (cutoff:3.500A) Processing helix chain 'V' and resid 144 through 152 Processing helix chain 'W' and resid 4 through 17 Processing helix chain 'W' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA W 131 " --> pdb=" O GLN W 127 " (cutoff:3.500A) Processing helix chain 'W' and resid 144 through 152 Processing helix chain 'X' and resid 4 through 17 Processing helix chain 'X' and resid 127 through 136 removed outlier: 3.668A pdb=" N ALA X 131 " --> pdb=" O GLN X 127 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 152 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 90 Processing sheet with id=AA4, first strand: chain 'A' and resid 211 through 213 Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 90 Processing sheet with id=AA8, first strand: chain 'B' and resid 211 through 213 Processing sheet with id=AA9, first strand: chain 'C' and resid 23 through 24 Processing sheet with id=AB1, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'C' and resid 84 through 90 Processing sheet with id=AB3, first strand: chain 'C' and resid 211 through 213 Processing sheet with id=AB4, first strand: chain 'D' and resid 23 through 24 Processing sheet with id=AB5, first strand: chain 'D' and resid 43 through 44 Processing sheet with id=AB6, first strand: chain 'D' and resid 84 through 90 Processing sheet with id=AB7, first strand: chain 'D' and resid 211 through 213 Processing sheet with id=AB8, first strand: chain 'E' and resid 23 through 24 Processing sheet with id=AB9, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AC1, first strand: chain 'E' and resid 84 through 90 Processing sheet with id=AC2, first strand: chain 'E' and resid 211 through 213 Processing sheet with id=AC3, first strand: chain 'F' and resid 23 through 24 Processing sheet with id=AC4, first strand: chain 'F' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'F' and resid 84 through 90 Processing sheet with id=AC6, first strand: chain 'F' and resid 211 through 213 Processing sheet with id=AC7, first strand: chain 'G' and resid 23 through 24 Processing sheet with id=AC8, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'G' and resid 84 through 90 Processing sheet with id=AD1, first strand: chain 'G' and resid 211 through 213 Processing sheet with id=AD2, first strand: chain 'H' and resid 23 through 24 Processing sheet with id=AD3, first strand: chain 'H' and resid 43 through 44 Processing sheet with id=AD4, first strand: chain 'H' and resid 84 through 90 Processing sheet with id=AD5, first strand: chain 'H' and resid 211 through 213 Processing sheet with id=AD6, first strand: chain 'I' and resid 23 through 24 Processing sheet with id=AD7, first strand: chain 'I' and resid 43 through 44 Processing sheet with id=AD8, first strand: chain 'I' and resid 84 through 90 Processing sheet with id=AD9, first strand: chain 'I' and resid 211 through 213 Processing sheet with id=AE1, first strand: chain 'J' and resid 23 through 24 Processing sheet with id=AE2, first strand: chain 'J' and resid 43 through 44 Processing sheet with id=AE3, first strand: chain 'J' and resid 84 through 90 Processing sheet with id=AE4, first strand: chain 'J' and resid 211 through 213 Processing sheet with id=AE5, first strand: chain 'K' and resid 23 through 24 Processing sheet with id=AE6, first strand: chain 'K' and resid 43 through 44 Processing sheet with id=AE7, first strand: chain 'K' and resid 84 through 90 Processing sheet with id=AE8, first strand: chain 'K' and resid 211 through 213 Processing sheet with id=AE9, first strand: chain 'L' and resid 23 through 24 Processing sheet with id=AF1, first strand: chain 'L' and resid 43 through 44 Processing sheet with id=AF2, first strand: chain 'L' and resid 84 through 90 Processing sheet with id=AF3, first strand: chain 'L' and resid 211 through 213 Processing sheet with id=AF4, first strand: chain 'M' and resid 23 through 24 Processing sheet with id=AF5, first strand: chain 'M' and resid 43 through 44 Processing sheet with id=AF6, first strand: chain 'M' and resid 84 through 90 Processing sheet with id=AF7, first strand: chain 'M' and resid 211 through 213 Processing sheet with id=AF8, first strand: chain 'N' and resid 23 through 24 Processing sheet with id=AF9, first strand: chain 'N' and resid 43 through 44 Processing sheet with id=AG1, first strand: chain 'N' and resid 84 through 90 Processing sheet with id=AG2, first strand: chain 'N' and resid 211 through 213 Processing sheet with id=AG3, first strand: chain 'O' and resid 23 through 24 Processing sheet with id=AG4, first strand: chain 'O' and resid 43 through 44 Processing sheet with id=AG5, first strand: chain 'O' and resid 84 through 90 Processing sheet with id=AG6, first strand: chain 'O' and resid 211 through 213 Processing sheet with id=AG7, first strand: chain 'P' and resid 23 through 24 Processing sheet with id=AG8, first strand: chain 'P' and resid 43 through 44 Processing sheet with id=AG9, first strand: chain 'P' and resid 84 through 90 Processing sheet with id=AH1, first strand: chain 'P' and resid 211 through 213 Processing sheet with id=AH2, first strand: chain 'Q' and resid 23 through 24 Processing sheet with id=AH3, first strand: chain 'Q' and resid 43 through 44 Processing sheet with id=AH4, first strand: chain 'Q' and resid 84 through 90 Processing sheet with id=AH5, first strand: chain 'Q' and resid 211 through 213 Processing sheet with id=AH6, first strand: chain 'R' and resid 23 through 24 Processing sheet with id=AH7, first strand: chain 'R' and resid 43 through 44 Processing sheet with id=AH8, first strand: chain 'R' and resid 84 through 90 Processing sheet with id=AH9, first strand: chain 'R' and resid 211 through 213 Processing sheet with id=AI1, first strand: chain 'S' and resid 23 through 24 Processing sheet with id=AI2, first strand: chain 'S' and resid 43 through 44 Processing sheet with id=AI3, first strand: chain 'S' and resid 84 through 90 Processing sheet with id=AI4, first strand: chain 'S' and resid 211 through 213 Processing sheet with id=AI5, first strand: chain 'T' and resid 23 through 24 Processing sheet with id=AI6, first strand: chain 'T' and resid 43 through 44 Processing sheet with id=AI7, first strand: chain 'T' and resid 84 through 90 Processing sheet with id=AI8, first strand: chain 'T' and resid 211 through 213 Processing sheet with id=AI9, first strand: chain 'U' and resid 23 through 24 Processing sheet with id=AJ1, first strand: chain 'U' and resid 43 through 44 Processing sheet with id=AJ2, first strand: chain 'U' and resid 84 through 90 Processing sheet with id=AJ3, first strand: chain 'U' and resid 211 through 213 Processing sheet with id=AJ4, first strand: chain 'V' and resid 23 through 24 Processing sheet with id=AJ5, first strand: chain 'V' and resid 43 through 44 Processing sheet with id=AJ6, first strand: chain 'V' and resid 84 through 90 Processing sheet with id=AJ7, first strand: chain 'V' and resid 211 through 213 Processing sheet with id=AJ8, first strand: chain 'W' and resid 23 through 24 Processing sheet with id=AJ9, first strand: chain 'W' and resid 43 through 44 Processing sheet with id=AK1, first strand: chain 'W' and resid 84 through 90 Processing sheet with id=AK2, first strand: chain 'W' and resid 211 through 213 Processing sheet with id=AK3, first strand: chain 'X' and resid 23 through 24 Processing sheet with id=AK4, first strand: chain 'X' and resid 43 through 44 Processing sheet with id=AK5, first strand: chain 'X' and resid 84 through 90 Processing sheet with id=AK6, first strand: chain 'X' and resid 211 through 213 912 hydrogen bonds defined for protein. 2232 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: 4.72 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11952 1.34 - 1.46: 6129 1.46 - 1.57: 18207 1.57 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 36528 Sorted by residual: bond pdb=" SD MET J 16 " pdb=" CE MET J 16 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.78e+00 bond pdb=" SD MET S 16 " pdb=" CE MET S 16 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.75e+00 bond pdb=" SD MET Q 16 " pdb=" CE MET Q 16 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.75e+00 bond pdb=" SD MET C 16 " pdb=" CE MET C 16 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.75e+00 bond pdb=" SD MET W 16 " pdb=" CE MET W 16 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.75e+00 ... (remaining 36523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 45709 1.50 - 2.99: 2667 2.99 - 4.49: 416 4.49 - 5.98: 96 5.98 - 7.48: 72 Bond angle restraints: 48960 Sorted by residual: angle pdb=" CA MET S 16 " pdb=" CB MET S 16 " pdb=" CG MET S 16 " ideal model delta sigma weight residual 114.10 120.40 -6.30 2.00e+00 2.50e-01 9.93e+00 angle pdb=" CA MET V 16 " pdb=" CB MET V 16 " pdb=" CG MET V 16 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.86e+00 angle pdb=" CA MET O 16 " pdb=" CB MET O 16 " pdb=" CG MET O 16 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.86e+00 angle pdb=" CA MET H 16 " pdb=" CB MET H 16 " pdb=" CG MET H 16 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.85e+00 angle pdb=" CA MET R 16 " pdb=" CB MET R 16 " pdb=" CG MET R 16 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.85e+00 ... (remaining 48955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 19361 15.49 - 30.97: 2071 30.97 - 46.46: 696 46.46 - 61.95: 96 61.95 - 77.44: 48 Dihedral angle restraints: 22272 sinusoidal: 9600 harmonic: 12672 Sorted by residual: dihedral pdb=" CA MET P 16 " pdb=" C MET P 16 " pdb=" N ASP P 17 " pdb=" CA ASP P 17 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA MET J 16 " pdb=" C MET J 16 " pdb=" N ASP J 17 " pdb=" CA ASP J 17 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA MET W 16 " pdb=" C MET W 16 " pdb=" N ASP W 17 " pdb=" CA ASP W 17 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 22269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3238 0.033 - 0.065: 1525 0.065 - 0.098: 420 0.098 - 0.130: 222 0.130 - 0.163: 91 Chirality restraints: 5496 Sorted by residual: chirality pdb=" CA ASN R 154 " pdb=" N ASN R 154 " pdb=" C ASN R 154 " pdb=" CB ASN R 154 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CA ASN J 154 " pdb=" N ASN J 154 " pdb=" C ASN J 154 " pdb=" CB ASN J 154 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA ASN F 154 " pdb=" N ASN F 154 " pdb=" C ASN F 154 " pdb=" CB ASN F 154 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 5493 not shown) Planarity restraints: 6240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE U 214 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO U 215 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO U 215 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO U 215 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE I 214 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO I 215 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO I 215 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 215 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE P 214 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PRO P 215 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO P 215 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO P 215 " 0.029 5.00e-02 4.00e+02 ... (remaining 6237 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2259 2.72 - 3.27: 38320 3.27 - 3.81: 60291 3.81 - 4.36: 68571 4.36 - 4.90: 111979 Nonbonded interactions: 281420 Sorted by model distance: nonbonded pdb=" O GLY F 66 " pdb=" OH TYR F 129 " model vdw 2.180 3.040 nonbonded pdb=" O GLY I 66 " pdb=" OH TYR I 129 " model vdw 2.180 3.040 nonbonded pdb=" O GLY T 66 " pdb=" OH TYR T 129 " model vdw 2.180 3.040 nonbonded pdb=" O GLY O 66 " pdb=" OH TYR O 129 " model vdw 2.180 3.040 nonbonded pdb=" O GLY L 66 " pdb=" OH TYR L 129 " model vdw 2.181 3.040 ... (remaining 281415 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.040 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 23.910 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 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 : 0.003 0.033 36528 Z= 0.168 Angle : 0.818 7.476 48960 Z= 0.471 Chirality : 0.046 0.163 5496 Planarity : 0.005 0.052 6240 Dihedral : 15.011 77.436 13968 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 29.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.55 (0.12), residues: 4176 helix: 0.33 (0.20), residues: 744 sheet: -1.61 (0.19), residues: 888 loop : -3.73 (0.10), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 208 TYR 0.007 0.002 TYR G 156 PHE 0.015 0.001 PHE J 5 TRP 0.001 0.000 TRP S 69 HIS 0.012 0.003 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00317 (36528) covalent geometry : angle 0.81765 (48960) hydrogen bonds : bond 0.15587 ( 912) hydrogen bonds : angle 9.27518 ( 2232) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 THR cc_start: 0.7391 (p) cc_final: 0.7178 (p) REVERT: E 164 THR cc_start: 0.7586 (p) cc_final: 0.7356 (p) REVERT: G 164 THR cc_start: 0.7384 (p) cc_final: 0.7162 (p) REVERT: H 17 ASP cc_start: 0.7390 (p0) cc_final: 0.6713 (p0) REVERT: J 17 ASP cc_start: 0.7146 (p0) cc_final: 0.6540 (p0) REVERT: J 164 THR cc_start: 0.7653 (p) cc_final: 0.7414 (p) REVERT: K 164 THR cc_start: 0.6781 (p) cc_final: 0.6489 (p) REVERT: L 17 ASP cc_start: 0.7215 (p0) cc_final: 0.6969 (p0) REVERT: N 37 PHE cc_start: 0.8555 (m-80) cc_final: 0.8346 (m-80) REVERT: P 164 THR cc_start: 0.6754 (p) cc_final: 0.6508 (p) REVERT: V 164 THR cc_start: 0.7282 (p) cc_final: 0.7070 (p) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.2381 time to fit residues: 119.3785 Evaluate side-chains 195 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0060 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 8.9990 chunk 155 optimal weight: 7.9990 overall best weight: 3.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN A 211 GLN ** B 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN B 211 GLN ** C 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 ASN C 211 GLN ** D 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN D 211 GLN ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 ASN E 211 GLN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN F 211 GLN G 51 HIS ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 ASN G 211 GLN ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 202 ASN H 211 GLN I 51 HIS ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 202 ASN I 211 GLN ** J 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 ASN J 211 GLN ** K 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 202 ASN K 211 GLN ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 202 ASN L 211 GLN ** M 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 202 ASN M 211 GLN ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 202 ASN N 211 GLN O 51 HIS ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 202 ASN O 211 GLN ** P 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 202 ASN P 211 GLN ** Q 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 202 ASN Q 211 GLN ** R 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN R 211 GLN ** S 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 202 ASN S 211 GLN ** T 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 202 ASN T 211 GLN U 51 HIS ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 202 ASN U 211 GLN ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 202 ASN V 211 GLN ** W 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 202 ASN W 211 GLN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 202 ASN X 211 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.090504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.080424 restraints weight = 273725.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.081820 restraints weight = 206161.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.082866 restraints weight = 162441.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.083658 restraints weight = 132815.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.084266 restraints weight = 111993.420| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 36528 Z= 0.187 Angle : 0.756 8.898 48960 Z= 0.414 Chirality : 0.047 0.181 5496 Planarity : 0.006 0.049 6240 Dihedral : 6.761 21.307 4752 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 26.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.78 (0.11), residues: 4176 helix: -0.14 (0.18), residues: 768 sheet: 0.27 (0.23), residues: 552 loop : -4.14 (0.08), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 33 TYR 0.018 0.002 TYR C 52 PHE 0.022 0.002 PHE D 5 TRP 0.004 0.001 TRP G 69 HIS 0.011 0.002 HIS L 38 Details of bonding type rmsd covalent geometry : bond 0.00406 (36528) covalent geometry : angle 0.75559 (48960) hydrogen bonds : bond 0.04116 ( 912) hydrogen bonds : angle 6.79484 ( 2232) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8792 (mmp) cc_final: 0.8373 (mmm) REVERT: A 26 ARG cc_start: 0.5855 (tpt90) cc_final: 0.5185 (tpt90) REVERT: B 164 THR cc_start: 0.7058 (p) cc_final: 0.6800 (p) REVERT: D 22 MET cc_start: 0.8697 (mmp) cc_final: 0.8378 (mmm) REVERT: G 26 ARG cc_start: 0.6168 (tpt90) cc_final: 0.5362 (tpt90) REVERT: G 37 PHE cc_start: 0.8370 (m-80) cc_final: 0.8153 (m-80) REVERT: H 37 PHE cc_start: 0.8342 (m-80) cc_final: 0.7964 (m-80) REVERT: I 37 PHE cc_start: 0.8421 (m-80) cc_final: 0.8009 (m-80) REVERT: J 37 PHE cc_start: 0.8280 (m-80) cc_final: 0.8015 (m-80) REVERT: K 164 THR cc_start: 0.6455 (p) cc_final: 0.6159 (p) REVERT: L 22 MET cc_start: 0.8985 (mmp) cc_final: 0.8593 (mmp) REVERT: M 37 PHE cc_start: 0.8136 (m-80) cc_final: 0.7929 (m-80) REVERT: O 37 PHE cc_start: 0.8020 (m-80) cc_final: 0.7763 (m-80) REVERT: Q 164 THR cc_start: 0.6873 (p) cc_final: 0.6571 (p) REVERT: R 22 MET cc_start: 0.9024 (mmp) cc_final: 0.8758 (mmm) REVERT: S 85 GLN cc_start: 0.8206 (pp30) cc_final: 0.7973 (pp30) REVERT: U 85 GLN cc_start: 0.8511 (pp30) cc_final: 0.8294 (pp30) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.2122 time to fit residues: 84.7705 Evaluate side-chains 181 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 55 optimal weight: 2.9990 chunk 383 optimal weight: 20.0000 chunk 304 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 83 optimal weight: 0.3980 chunk 259 optimal weight: 6.9990 chunk 423 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 338 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 HIS B 154 ASN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS C 154 ASN ** D 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 ASN ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 HIS ** H 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 154 ASN ** K 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 ASN ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 ASN ** M 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 HIS N 154 ASN ** O 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 ASN ** Q 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 ASN ** S 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 154 ASN T 51 HIS T 154 ASN ** U 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 154 ASN ** W 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 154 ASN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 154 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.090519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.080413 restraints weight = 271931.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.081833 restraints weight = 205877.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.082902 restraints weight = 162506.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.083728 restraints weight = 132911.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.084359 restraints weight = 111803.028| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 36528 Z= 0.174 Angle : 0.741 9.537 48960 Z= 0.406 Chirality : 0.048 0.199 5496 Planarity : 0.006 0.049 6240 Dihedral : 6.957 20.862 4752 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 26.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 0.60 % Allowed : 5.51 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.89 (0.11), residues: 4176 helix: -0.48 (0.19), residues: 768 sheet: -0.13 (0.22), residues: 552 loop : -4.05 (0.08), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 208 TYR 0.015 0.002 TYR I 52 PHE 0.019 0.002 PHE V 5 TRP 0.004 0.001 TRP E 69 HIS 0.009 0.002 HIS L 38 Details of bonding type rmsd covalent geometry : bond 0.00380 (36528) covalent geometry : angle 0.74147 (48960) hydrogen bonds : bond 0.04291 ( 912) hydrogen bonds : angle 6.81161 ( 2232) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 251 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8943 (mmp) cc_final: 0.8743 (mmm) REVERT: E 37 PHE cc_start: 0.8871 (m-80) cc_final: 0.8665 (m-80) REVERT: F 37 PHE cc_start: 0.8091 (m-80) cc_final: 0.7868 (m-80) REVERT: J 37 PHE cc_start: 0.8128 (m-80) cc_final: 0.7889 (m-80) REVERT: P 220 MET cc_start: 0.0385 (mmm) cc_final: 0.0162 (mmt) REVERT: Q 164 THR cc_start: 0.6924 (p) cc_final: 0.6631 (p) REVERT: R 219 THR cc_start: 0.6633 (p) cc_final: 0.6298 (t) REVERT: U 37 PHE cc_start: 0.8060 (m-80) cc_final: 0.7790 (m-80) REVERT: X 37 PHE cc_start: 0.8081 (m-80) cc_final: 0.7878 (m-80) outliers start: 24 outliers final: 0 residues processed: 275 average time/residue: 0.2012 time to fit residues: 88.5974 Evaluate side-chains 174 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 213 optimal weight: 4.9990 chunk 315 optimal weight: 10.0000 chunk 421 optimal weight: 0.8980 chunk 346 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 chunk 277 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 428 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN B 154 ASN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** D 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 ASN G 154 ASN H 154 ASN ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 ASN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 154 ASN ** K 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 ASN ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 ASN ** M 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 ASN N 154 ASN ** O 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 154 ASN ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 ASN ** Q 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 154 ASN ** R 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 ASN ** S 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 154 ASN T 154 ASN ** U 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 154 ASN ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 154 ASN ** W 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 154 ASN ** X 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 154 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.090013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.079943 restraints weight = 268071.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.081346 restraints weight = 203910.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.082403 restraints weight = 161649.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.083207 restraints weight = 132637.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.083826 restraints weight = 111936.850| |-----------------------------------------------------------------------------| r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6086 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 36528 Z= 0.168 Angle : 0.741 9.103 48960 Z= 0.405 Chirality : 0.048 0.188 5496 Planarity : 0.006 0.051 6240 Dihedral : 6.881 20.850 4752 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 26.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Rotamer: Outliers : 0.60 % Allowed : 3.72 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.84 (0.11), residues: 4176 helix: -0.27 (0.19), residues: 768 sheet: -0.32 (0.21), residues: 552 loop : -4.03 (0.09), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 195 TYR 0.012 0.002 TYR V 52 PHE 0.019 0.002 PHE V 5 TRP 0.004 0.001 TRP W 69 HIS 0.010 0.002 HIS R 51 Details of bonding type rmsd covalent geometry : bond 0.00364 (36528) covalent geometry : angle 0.74108 (48960) hydrogen bonds : bond 0.04140 ( 912) hydrogen bonds : angle 6.78395 ( 2232) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 251 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6239 (tpt90) cc_final: 0.5569 (tpt90) REVERT: A 85 GLN cc_start: 0.8148 (pp30) cc_final: 0.7924 (pp30) REVERT: B 219 THR cc_start: 0.6359 (p) cc_final: 0.5852 (t) REVERT: E 26 ARG cc_start: 0.5778 (tpt170) cc_final: 0.5378 (tpt90) REVERT: F 37 PHE cc_start: 0.8040 (m-80) cc_final: 0.7828 (m-80) REVERT: F 219 THR cc_start: 0.6784 (p) cc_final: 0.6508 (t) REVERT: L 26 ARG cc_start: 0.6437 (tpt90) cc_final: 0.6052 (tpt90) REVERT: M 22 MET cc_start: 0.8576 (mmm) cc_final: 0.7961 (mmm) REVERT: N 26 ARG cc_start: 0.5772 (tpt90) cc_final: 0.5367 (tpt90) REVERT: O 37 PHE cc_start: 0.8080 (m-80) cc_final: 0.7773 (m-80) REVERT: P 220 MET cc_start: 0.0425 (mmm) cc_final: 0.0159 (mmt) REVERT: Q 164 THR cc_start: 0.7110 (p) cc_final: 0.6843 (p) REVERT: R 219 THR cc_start: 0.6571 (p) cc_final: 0.6223 (t) REVERT: S 85 GLN cc_start: 0.8378 (pp30) cc_final: 0.8050 (pp30) REVERT: T 219 THR cc_start: 0.6403 (p) cc_final: 0.6006 (t) REVERT: U 37 PHE cc_start: 0.8095 (m-80) cc_final: 0.7852 (m-80) REVERT: X 219 THR cc_start: 0.6778 (p) cc_final: 0.6407 (t) outliers start: 24 outliers final: 0 residues processed: 275 average time/residue: 0.1989 time to fit residues: 87.2567 Evaluate side-chains 176 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 315 optimal weight: 5.9990 chunk 348 optimal weight: 8.9990 chunk 346 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 362 optimal weight: 0.0870 chunk 230 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 380 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 150 optimal weight: 0.5980 chunk 403 optimal weight: 3.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 HIS ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 154 ASN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 ASN ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 ASN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 ASN L 51 HIS L 154 ASN ** M 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 HIS M 154 ASN ** N 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 154 ASN ** O 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 154 ASN ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 ASN ** Q 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 154 ASN ** R 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 HIS R 154 ASN ** S 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 51 HIS S 154 ASN ** T 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 154 ASN ** U 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 154 ASN ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 154 ASN ** W 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 154 ASN ** X 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 154 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.092979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.082769 restraints weight = 263117.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.084224 restraints weight = 199167.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.085305 restraints weight = 157336.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.086144 restraints weight = 128967.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.086800 restraints weight = 108625.307| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36528 Z= 0.124 Angle : 0.671 7.869 48960 Z= 0.367 Chirality : 0.047 0.180 5496 Planarity : 0.006 0.052 6240 Dihedral : 6.328 20.368 4752 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.62 % Allowed : 4.79 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.50 (0.12), residues: 4176 helix: 0.27 (0.20), residues: 768 sheet: -1.44 (0.17), residues: 840 loop : -3.72 (0.10), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 26 TYR 0.009 0.001 TYR L 52 PHE 0.012 0.001 PHE W 5 TRP 0.002 0.001 TRP M 69 HIS 0.008 0.002 HIS Q 51 Details of bonding type rmsd covalent geometry : bond 0.00262 (36528) covalent geometry : angle 0.67058 (48960) hydrogen bonds : bond 0.03451 ( 912) hydrogen bonds : angle 6.62422 ( 2232) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 303 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6253 (tpt90) cc_final: 0.6003 (tpt90) REVERT: A 164 THR cc_start: 0.7505 (p) cc_final: 0.7292 (p) REVERT: D 164 THR cc_start: 0.7056 (p) cc_final: 0.6770 (p) REVERT: E 26 ARG cc_start: 0.5664 (tpt170) cc_final: 0.5332 (tpt90) REVERT: E 37 PHE cc_start: 0.8658 (m-80) cc_final: 0.8429 (m-80) REVERT: E 164 THR cc_start: 0.7501 (p) cc_final: 0.7279 (p) REVERT: F 37 PHE cc_start: 0.7913 (m-80) cc_final: 0.7710 (m-80) REVERT: G 164 THR cc_start: 0.7480 (p) cc_final: 0.7261 (p) REVERT: I 164 THR cc_start: 0.7052 (p) cc_final: 0.6751 (p) REVERT: J 164 THR cc_start: 0.7399 (p) cc_final: 0.7149 (p) REVERT: L 26 ARG cc_start: 0.6245 (tpt90) cc_final: 0.5892 (tpt90) REVERT: M 85 GLN cc_start: 0.8038 (pp30) cc_final: 0.7830 (pp30) REVERT: N 164 THR cc_start: 0.6901 (p) cc_final: 0.6646 (p) REVERT: N 219 THR cc_start: 0.6752 (p) cc_final: 0.6441 (t) REVERT: O 164 THR cc_start: 0.6803 (p) cc_final: 0.6498 (p) REVERT: O 219 THR cc_start: 0.5841 (p) cc_final: 0.5472 (t) REVERT: P 164 THR cc_start: 0.6990 (p) cc_final: 0.6715 (p) REVERT: P 220 MET cc_start: 0.0510 (mmm) cc_final: 0.0287 (mmt) REVERT: Q 26 ARG cc_start: 0.5398 (tpt90) cc_final: 0.5163 (tpt90) REVERT: Q 37 PHE cc_start: 0.8305 (m-80) cc_final: 0.8094 (m-80) REVERT: Q 164 THR cc_start: 0.7307 (p) cc_final: 0.7028 (p) REVERT: R 219 THR cc_start: 0.6355 (p) cc_final: 0.5995 (t) REVERT: S 22 MET cc_start: 0.8293 (mmm) cc_final: 0.7760 (mmm) REVERT: S 26 ARG cc_start: 0.5687 (tpt170) cc_final: 0.5406 (tpt90) REVERT: S 164 THR cc_start: 0.6969 (p) cc_final: 0.6709 (p) REVERT: S 220 MET cc_start: 0.1043 (mmm) cc_final: 0.0598 (mmt) REVERT: T 219 THR cc_start: 0.6215 (p) cc_final: 0.5802 (t) REVERT: V 164 THR cc_start: 0.7291 (p) cc_final: 0.7029 (p) REVERT: W 164 THR cc_start: 0.7319 (p) cc_final: 0.7072 (p) REVERT: X 219 THR cc_start: 0.6527 (p) cc_final: 0.6150 (t) outliers start: 25 outliers final: 1 residues processed: 328 average time/residue: 0.2400 time to fit residues: 126.2884 Evaluate side-chains 190 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 248 optimal weight: 0.6980 chunk 253 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 303 optimal weight: 10.0000 chunk 152 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 288 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS A 154 ASN B 154 ASN C 154 ASN D 51 HIS D 154 ASN E 154 ASN F 51 HIS F 154 ASN G 154 ASN H 154 ASN ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 ASN J 51 HIS J 154 ASN K 51 HIS K 154 ASN L 154 ASN ** M 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 ASN N 154 ASN O 154 ASN P 51 HIS P 154 ASN Q 51 HIS Q 154 ASN R 154 ASN S 154 ASN T 154 ASN U 154 ASN V 51 HIS V 154 ASN W 51 HIS W 154 ASN X 51 HIS X 154 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.089640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.079598 restraints weight = 268584.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.080969 restraints weight = 205196.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.082015 restraints weight = 163574.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.082824 restraints weight = 134747.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.083446 restraints weight = 113890.207| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 36528 Z= 0.180 Angle : 0.728 8.606 48960 Z= 0.401 Chirality : 0.047 0.180 5496 Planarity : 0.006 0.077 6240 Dihedral : 6.828 21.352 4752 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 28.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.29 % Favored : 86.71 % Rotamer: Outliers : 0.60 % Allowed : 4.42 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.74 (0.11), residues: 4176 helix: -0.25 (0.19), residues: 768 sheet: -1.58 (0.17), residues: 840 loop : -3.78 (0.10), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 26 TYR 0.012 0.002 TYR R 52 PHE 0.019 0.002 PHE A 5 TRP 0.005 0.002 TRP H 69 HIS 0.007 0.002 HIS Q 51 Details of bonding type rmsd covalent geometry : bond 0.00389 (36528) covalent geometry : angle 0.72825 (48960) hydrogen bonds : bond 0.04441 ( 912) hydrogen bonds : angle 6.66521 ( 2232) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 257 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6452 (tpt90) cc_final: 0.6189 (tpt90) REVERT: L 22 MET cc_start: 0.8613 (mmm) cc_final: 0.8288 (mmm) REVERT: L 219 THR cc_start: 0.5514 (p) cc_final: 0.5250 (t) REVERT: N 26 ARG cc_start: 0.5843 (tpt90) cc_final: 0.5490 (tpt90) REVERT: O 37 PHE cc_start: 0.7897 (m-80) cc_final: 0.7548 (m-80) REVERT: P 220 MET cc_start: 0.0428 (mmm) cc_final: 0.0174 (mmt) REVERT: Q 37 PHE cc_start: 0.8428 (m-80) cc_final: 0.8204 (m-80) REVERT: Q 164 THR cc_start: 0.6978 (p) cc_final: 0.6704 (p) REVERT: R 219 THR cc_start: 0.6671 (p) cc_final: 0.6341 (t) REVERT: T 219 THR cc_start: 0.6465 (p) cc_final: 0.6025 (t) REVERT: U 37 PHE cc_start: 0.8030 (m-80) cc_final: 0.7740 (m-80) REVERT: X 164 THR cc_start: 0.7347 (p) cc_final: 0.7089 (p) REVERT: X 219 THR cc_start: 0.6466 (p) cc_final: 0.6112 (t) outliers start: 24 outliers final: 0 residues processed: 281 average time/residue: 0.2454 time to fit residues: 110.0509 Evaluate side-chains 168 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 177 optimal weight: 6.9990 chunk 146 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 0.1980 chunk 235 optimal weight: 5.9990 chunk 352 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 343 optimal weight: 5.9990 chunk 408 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 chunk 249 optimal weight: 7.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 154 ASN C 154 ASN D 154 ASN E 154 ASN F 154 ASN G 154 ASN H 154 ASN I 154 ASN K 154 ASN M 127 GLN M 154 ASN N 154 ASN O 154 ASN P 154 ASN Q 154 ASN R 154 ASN S 154 ASN T 154 ASN U 154 ASN V 154 ASN W 154 ASN X 154 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.088248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.078090 restraints weight = 269898.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.079517 restraints weight = 204213.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.080587 restraints weight = 161148.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.081400 restraints weight = 132069.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.082023 restraints weight = 111371.705| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 36528 Z= 0.194 Angle : 0.775 10.160 48960 Z= 0.427 Chirality : 0.049 0.199 5496 Planarity : 0.007 0.053 6240 Dihedral : 7.278 26.626 4752 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 30.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.10 % Favored : 85.90 % Rotamer: Outliers : 0.55 % Allowed : 2.12 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.74 (0.12), residues: 4176 helix: -0.40 (0.19), residues: 768 sheet: -1.35 (0.20), residues: 648 loop : -3.68 (0.10), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 26 TYR 0.016 0.003 TYR Q 52 PHE 0.029 0.002 PHE B 5 TRP 0.007 0.002 TRP H 69 HIS 0.006 0.002 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00418 (36528) covalent geometry : angle 0.77522 (48960) hydrogen bonds : bond 0.04723 ( 912) hydrogen bonds : angle 6.95232 ( 2232) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 251 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 37 PHE cc_start: 0.8646 (m-80) cc_final: 0.8084 (m-80) REVERT: L 219 THR cc_start: 0.6416 (p) cc_final: 0.6172 (t) REVERT: P 220 MET cc_start: 0.0480 (mmm) cc_final: 0.0175 (mmt) REVERT: Q 37 PHE cc_start: 0.8472 (m-80) cc_final: 0.8091 (m-10) REVERT: S 26 ARG cc_start: 0.5816 (tpt90) cc_final: 0.5233 (tpt90) REVERT: T 219 THR cc_start: 0.6625 (p) cc_final: 0.6168 (t) REVERT: U 37 PHE cc_start: 0.8226 (m-80) cc_final: 0.7966 (m-80) outliers start: 22 outliers final: 0 residues processed: 273 average time/residue: 0.2427 time to fit residues: 106.6731 Evaluate side-chains 161 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 416 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 292 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 336 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 402 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 284 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 154 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 ASN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN C 154 ASN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN ** E 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 ASN ** G 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 154 ASN H 154 ASN ** I 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 154 ASN ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 154 ASN ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 154 ASN L 154 ASN ** M 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 ASN N 154 ASN ** O 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 154 ASN P 154 ASN ** Q 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 135 ASN ** Q 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 ASN S 154 ASN T 154 ASN ** U 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 154 ASN ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 154 ASN ** W 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 154 ASN ** X 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 154 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.091274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.081119 restraints weight = 264338.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.082562 restraints weight = 199130.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.083666 restraints weight = 157358.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.084499 restraints weight = 128582.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.085142 restraints weight = 108253.649| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 36528 Z= 0.141 Angle : 0.710 10.798 48960 Z= 0.390 Chirality : 0.048 0.182 5496 Planarity : 0.006 0.061 6240 Dihedral : 6.809 24.899 4752 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.45 % Favored : 87.55 % Rotamer: Outliers : 0.55 % Allowed : 1.22 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.47 (0.12), residues: 4176 helix: -0.08 (0.20), residues: 768 sheet: -1.14 (0.20), residues: 648 loop : -3.54 (0.10), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 208 TYR 0.013 0.002 TYR P 52 PHE 0.016 0.001 PHE W 5 TRP 0.004 0.001 TRP H 69 HIS 0.006 0.001 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00299 (36528) covalent geometry : angle 0.70974 (48960) hydrogen bonds : bond 0.03909 ( 912) hydrogen bonds : angle 6.77825 ( 2232) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 296 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 THR cc_start: 0.6562 (p) cc_final: 0.6263 (p) REVERT: D 22 MET cc_start: 0.8209 (mmm) cc_final: 0.7433 (mmm) REVERT: D 164 THR cc_start: 0.7372 (p) cc_final: 0.7080 (p) REVERT: E 164 THR cc_start: 0.7575 (p) cc_final: 0.7346 (p) REVERT: G 164 THR cc_start: 0.6685 (p) cc_final: 0.6345 (p) REVERT: J 164 THR cc_start: 0.7218 (p) cc_final: 0.6913 (p) REVERT: K 37 PHE cc_start: 0.8566 (m-80) cc_final: 0.8082 (m-10) REVERT: L 26 ARG cc_start: 0.6240 (tpt170) cc_final: 0.5827 (tpt90) REVERT: L 219 THR cc_start: 0.6303 (p) cc_final: 0.6050 (t) REVERT: M 22 MET cc_start: 0.8331 (mmm) cc_final: 0.7407 (mmm) REVERT: P 164 THR cc_start: 0.7082 (p) cc_final: 0.6782 (p) REVERT: P 220 MET cc_start: 0.0773 (mmm) cc_final: 0.0503 (mmt) REVERT: Q 37 PHE cc_start: 0.8556 (m-80) cc_final: 0.8333 (m-80) REVERT: R 22 MET cc_start: 0.8775 (mmm) cc_final: 0.8393 (mmm) REVERT: S 22 MET cc_start: 0.8332 (mmm) cc_final: 0.7322 (mmm) REVERT: S 26 ARG cc_start: 0.5489 (tpt90) cc_final: 0.4759 (tpt90) REVERT: S 164 THR cc_start: 0.7101 (p) cc_final: 0.6838 (p) REVERT: T 219 THR cc_start: 0.6417 (p) cc_final: 0.5954 (t) REVERT: U 37 PHE cc_start: 0.8026 (m-80) cc_final: 0.7703 (m-80) REVERT: V 164 THR cc_start: 0.7012 (p) cc_final: 0.6728 (p) REVERT: W 37 PHE cc_start: 0.8493 (m-80) cc_final: 0.8266 (m-80) REVERT: X 219 THR cc_start: 0.6465 (p) cc_final: 0.6072 (t) outliers start: 22 outliers final: 0 residues processed: 318 average time/residue: 0.2301 time to fit residues: 117.4029 Evaluate side-chains 173 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 314 optimal weight: 6.9990 chunk 212 optimal weight: 6.9990 chunk 421 optimal weight: 7.9990 chunk 149 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 chunk 294 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 342 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 154 ASN C 154 ASN D 154 ASN E 154 ASN F 154 ASN G 154 ASN H 154 ASN I 154 ASN J 154 ASN K 154 ASN M 154 ASN N 154 ASN N 202 ASN O 154 ASN P 154 ASN Q 154 ASN R 154 ASN S 154 ASN T 154 ASN T 202 ASN U 154 ASN V 154 ASN W 154 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.085599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.075517 restraints weight = 270942.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.076897 restraints weight = 205523.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.077938 restraints weight = 162386.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.078737 restraints weight = 133108.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.079348 restraints weight = 112366.862| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 36528 Z= 0.258 Angle : 0.904 13.522 48960 Z= 0.494 Chirality : 0.052 0.234 5496 Planarity : 0.008 0.099 6240 Dihedral : 7.852 27.215 4752 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 36.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.38 % Favored : 83.62 % Rotamer: Outliers : 0.55 % Allowed : 1.50 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.26 (0.11), residues: 4176 helix: -1.07 (0.17), residues: 768 sheet: -2.21 (0.30), residues: 288 loop : -3.70 (0.09), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 26 TYR 0.031 0.003 TYR K 52 PHE 0.036 0.003 PHE R 5 TRP 0.012 0.003 TRP H 69 HIS 0.007 0.003 HIS R 51 Details of bonding type rmsd covalent geometry : bond 0.00562 (36528) covalent geometry : angle 0.90419 (48960) hydrogen bonds : bond 0.05585 ( 912) hydrogen bonds : angle 7.12429 ( 2232) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8546 (mmm) cc_final: 0.7721 (mmm) REVERT: A 26 ARG cc_start: 0.5498 (tpt90) cc_final: 0.4920 (tpt90) REVERT: D 22 MET cc_start: 0.8321 (mmm) cc_final: 0.7784 (mmm) REVERT: G 22 MET cc_start: 0.8716 (mmm) cc_final: 0.7905 (mmm) REVERT: M 22 MET cc_start: 0.8767 (mmm) cc_final: 0.8020 (mmm) REVERT: P 220 MET cc_start: 0.0714 (mmm) cc_final: 0.0413 (mmt) REVERT: R 22 MET cc_start: 0.8566 (mmm) cc_final: 0.8146 (mmm) REVERT: S 22 MET cc_start: 0.8785 (mmm) cc_final: 0.8025 (mmm) REVERT: S 26 ARG cc_start: 0.6498 (tpt90) cc_final: 0.5853 (tpt90) REVERT: W 37 PHE cc_start: 0.8472 (m-80) cc_final: 0.7999 (m-10) outliers start: 22 outliers final: 0 residues processed: 250 average time/residue: 0.2588 time to fit residues: 103.0308 Evaluate side-chains 163 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 53 optimal weight: 7.9990 chunk 177 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 412 optimal weight: 9.9990 chunk 17 optimal weight: 30.0000 chunk 67 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 385 optimal weight: 2.9990 chunk 221 optimal weight: 20.0000 chunk 351 optimal weight: 5.9990 chunk 214 optimal weight: 0.3980 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 154 ASN B 202 ASN C 154 ASN D 154 ASN E 154 ASN F 154 ASN F 202 ASN G 154 ASN H 154 ASN I 154 ASN J 154 ASN K 154 ASN L 154 ASN M 154 ASN N 154 ASN O 154 ASN P 154 ASN Q 154 ASN R 154 ASN S 154 ASN T 154 ASN U 154 ASN V 154 ASN W 154 ASN X 154 ASN X 202 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.088070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.077922 restraints weight = 267730.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.079336 restraints weight = 202341.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.080407 restraints weight = 159714.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.081235 restraints weight = 130565.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.081866 restraints weight = 109874.379| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 36528 Z= 0.181 Angle : 0.792 11.547 48960 Z= 0.435 Chirality : 0.050 0.248 5496 Planarity : 0.007 0.061 6240 Dihedral : 7.493 26.907 4752 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 29.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.03 % Favored : 85.97 % Rotamer: Outliers : 0.60 % Allowed : 0.57 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.83 (0.12), residues: 4176 helix: -0.67 (0.19), residues: 768 sheet: -1.22 (0.20), residues: 648 loop : -3.73 (0.10), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 26 TYR 0.015 0.002 TYR R 52 PHE 0.023 0.002 PHE Q 5 TRP 0.008 0.002 TRP B 69 HIS 0.005 0.002 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00393 (36528) covalent geometry : angle 0.79171 (48960) hydrogen bonds : bond 0.04582 ( 912) hydrogen bonds : angle 6.98737 ( 2232) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 251 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8149 (mmm) cc_final: 0.7297 (mmm) REVERT: D 22 MET cc_start: 0.8322 (mmm) cc_final: 0.7784 (mmm) REVERT: F 22 MET cc_start: 0.8280 (mmm) cc_final: 0.7725 (mmm) REVERT: G 22 MET cc_start: 0.8427 (mmm) cc_final: 0.7597 (mmm) REVERT: L 22 MET cc_start: 0.8526 (mmm) cc_final: 0.7971 (mmm) REVERT: M 22 MET cc_start: 0.8451 (mmm) cc_final: 0.7703 (mmm) REVERT: M 37 PHE cc_start: 0.8328 (m-80) cc_final: 0.7992 (m-80) REVERT: M 85 GLN cc_start: 0.8629 (pp30) cc_final: 0.8327 (pp30) REVERT: N 37 PHE cc_start: 0.8411 (m-80) cc_final: 0.8052 (m-10) REVERT: P 220 MET cc_start: 0.0655 (mmm) cc_final: 0.0414 (mmt) REVERT: R 22 MET cc_start: 0.8606 (mmm) cc_final: 0.8208 (mmm) REVERT: R 37 PHE cc_start: 0.8101 (m-80) cc_final: 0.7796 (m-10) REVERT: S 22 MET cc_start: 0.8493 (mmm) cc_final: 0.7741 (mmm) REVERT: S 26 ARG cc_start: 0.6166 (tpt90) cc_final: 0.5381 (tpt90) REVERT: W 37 PHE cc_start: 0.8566 (m-80) cc_final: 0.8338 (m-10) REVERT: W 209 VAL cc_start: 0.5589 (t) cc_final: 0.5237 (t) REVERT: X 164 THR cc_start: 0.7123 (p) cc_final: 0.6763 (p) outliers start: 24 outliers final: 0 residues processed: 275 average time/residue: 0.2393 time to fit residues: 105.9597 Evaluate side-chains 162 residues out of total 4008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 35 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 356 optimal weight: 3.9990 chunk 322 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 230 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 154 ASN C 154 ASN D 154 ASN E 154 ASN F 154 ASN G 154 ASN H 154 ASN I 154 ASN J 154 ASN K 154 ASN M 154 ASN N 154 ASN O 154 ASN P 154 ASN Q 154 ASN R 154 ASN S 154 ASN T 154 ASN U 154 ASN V 154 ASN W 154 ASN X 154 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.087895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.077809 restraints weight = 266638.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.079216 restraints weight = 201285.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.080280 restraints weight = 158860.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.081095 restraints weight = 129836.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.081733 restraints weight = 109342.931| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 36528 Z= 0.179 Angle : 0.793 11.245 48960 Z= 0.434 Chirality : 0.050 0.200 5496 Planarity : 0.007 0.067 6240 Dihedral : 7.439 26.645 4752 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 30.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.59 % Favored : 84.41 % Rotamer: Outliers : 0.57 % Allowed : 0.60 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.81 (0.12), residues: 4176 helix: -0.63 (0.19), residues: 768 sheet: -1.23 (0.20), residues: 648 loop : -3.72 (0.10), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 195 TYR 0.016 0.002 TYR J 52 PHE 0.021 0.002 PHE E 5 TRP 0.009 0.002 TRP N 69 HIS 0.005 0.002 HIS V 38 Details of bonding type rmsd covalent geometry : bond 0.00390 (36528) covalent geometry : angle 0.79317 (48960) hydrogen bonds : bond 0.04559 ( 912) hydrogen bonds : angle 6.96579 ( 2232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4683.89 seconds wall clock time: 83 minutes 29.80 seconds (5009.80 seconds total)