Starting phenix.real_space_refine on Tue Aug 26 23:53:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8et2_28584/08_2025/8et2_28584.cif Found real_map, /net/cci-nas-00/data/ceres_data/8et2_28584/08_2025/8et2_28584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8et2_28584/08_2025/8et2_28584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8et2_28584/08_2025/8et2_28584.map" model { file = "/net/cci-nas-00/data/ceres_data/8et2_28584/08_2025/8et2_28584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8et2_28584/08_2025/8et2_28584.cif" } resolution = 4.96 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= 0.004 sd= 0.036 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 27672 2.51 5 N 7752 2.21 5 O 8016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.03s 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: 43584 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1816 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 1 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: 3.44, per 1000 atoms: 0.08 Number of scatterers: 43584 At special positions: 0 Unit cell: (273.9, 273.9, 73.04, 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 8016 8.00 N 7752 7.00 C 27672 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: 3.55 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 476.8 nanoseconds 10416 Ramachandran restraints generated. 5208 Oldfield, 0 Emsley, 5208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9984 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 144 sheets defined 14.5% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 removed outlier: 3.846A pdb=" N THR A 9 " --> pdb=" O PHE A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 135 removed outlier: 4.049A 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 removed outlier: 3.847A pdb=" N THR B 9 " --> pdb=" O PHE B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 135 removed outlier: 4.050A 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 removed outlier: 3.847A pdb=" N THR C 9 " --> pdb=" O PHE C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 135 removed outlier: 4.049A 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 removed outlier: 3.847A pdb=" N THR D 9 " --> pdb=" O PHE D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 135 removed outlier: 4.049A 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 removed outlier: 3.847A pdb=" N THR E 9 " --> pdb=" O PHE E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 135 removed outlier: 4.050A 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 removed outlier: 3.847A pdb=" N THR F 9 " --> pdb=" O PHE F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 135 removed outlier: 4.050A 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 removed outlier: 3.847A pdb=" N THR G 9 " --> pdb=" O PHE G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 135 removed outlier: 4.050A 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 removed outlier: 3.847A pdb=" N THR H 9 " --> pdb=" O PHE H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 135 removed outlier: 4.049A 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 removed outlier: 3.847A pdb=" N THR I 9 " --> pdb=" O PHE I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 135 removed outlier: 4.050A 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 removed outlier: 3.848A pdb=" N THR J 9 " --> pdb=" O PHE J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 135 removed outlier: 4.049A 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 removed outlier: 3.847A pdb=" N THR K 9 " --> pdb=" O PHE K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 135 removed outlier: 4.050A 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 removed outlier: 3.847A pdb=" N THR L 9 " --> pdb=" O PHE L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 135 removed outlier: 4.050A 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 removed outlier: 3.847A pdb=" N THR M 9 " --> pdb=" O PHE M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 135 removed outlier: 4.050A 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 removed outlier: 3.847A pdb=" N THR N 9 " --> pdb=" O PHE N 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 135 removed outlier: 4.050A 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 removed outlier: 3.847A pdb=" N THR O 9 " --> pdb=" O PHE O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 135 removed outlier: 4.049A 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 removed outlier: 3.847A pdb=" N THR P 9 " --> pdb=" O PHE P 5 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 135 removed outlier: 4.050A 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 removed outlier: 3.847A pdb=" N THR Q 9 " --> pdb=" O PHE Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 135 removed outlier: 4.049A 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 removed outlier: 3.846A pdb=" N THR R 9 " --> pdb=" O PHE R 5 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 135 removed outlier: 4.049A 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 removed outlier: 3.847A pdb=" N THR S 9 " --> pdb=" O PHE S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 135 removed outlier: 4.049A 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 removed outlier: 3.847A pdb=" N THR T 9 " --> pdb=" O PHE T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 135 removed outlier: 4.050A 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 removed outlier: 3.847A pdb=" N THR U 9 " --> pdb=" O PHE U 5 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 135 removed outlier: 4.049A 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 removed outlier: 3.847A pdb=" N THR V 9 " --> pdb=" O PHE V 5 " (cutoff:3.500A) Processing helix chain 'V' and resid 127 through 135 removed outlier: 4.050A 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 removed outlier: 3.847A pdb=" N THR W 9 " --> pdb=" O PHE W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 135 removed outlier: 4.049A 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 removed outlier: 3.846A pdb=" N THR X 9 " --> pdb=" O PHE X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 135 removed outlier: 4.050A 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 removed outlier: 3.744A pdb=" N ARG A 44 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG A 50 " --> pdb=" O ARG A 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 95 removed outlier: 3.712A pdb=" N THR A 161 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 180 Processing sheet with id=AA6, first strand: chain 'A' and resid 211 through 213 Processing sheet with id=AA7, first strand: chain 'B' and resid 23 through 24 Processing sheet with id=AA8, first strand: chain 'B' and resid 43 through 44 removed outlier: 3.743A pdb=" N ARG B 44 " --> pdb=" O ARG B 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 50 " --> pdb=" O ARG B 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 84 through 95 removed outlier: 3.712A pdb=" N THR B 161 " --> pdb=" O ASN B 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AB2, first strand: chain 'B' and resid 170 through 180 Processing sheet with id=AB3, first strand: chain 'B' and resid 211 through 213 Processing sheet with id=AB4, first strand: chain 'C' and resid 23 through 24 Processing sheet with id=AB5, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.745A pdb=" N ARG C 44 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG C 50 " --> pdb=" O ARG C 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 84 through 95 removed outlier: 3.710A pdb=" N THR C 161 " --> pdb=" O ASN C 123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 98 through 99 Processing sheet with id=AB8, first strand: chain 'C' and resid 170 through 180 Processing sheet with id=AB9, first strand: chain 'C' and resid 211 through 213 Processing sheet with id=AC1, first strand: chain 'D' and resid 23 through 24 Processing sheet with id=AC2, first strand: chain 'D' and resid 43 through 44 removed outlier: 3.745A pdb=" N ARG D 44 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG D 50 " --> pdb=" O ARG D 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR D 161 " --> pdb=" O ASN D 123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 98 through 99 Processing sheet with id=AC5, first strand: chain 'D' and resid 170 through 180 Processing sheet with id=AC6, first strand: chain 'D' and resid 211 through 213 Processing sheet with id=AC7, first strand: chain 'E' and resid 23 through 24 Processing sheet with id=AC8, first strand: chain 'E' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG E 44 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG E 50 " --> pdb=" O ARG E 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 84 through 95 removed outlier: 3.712A pdb=" N THR E 161 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 98 through 99 Processing sheet with id=AD2, first strand: chain 'E' and resid 170 through 180 Processing sheet with id=AD3, first strand: chain 'E' and resid 211 through 213 Processing sheet with id=AD4, first strand: chain 'F' and resid 23 through 24 Processing sheet with id=AD5, first strand: chain 'F' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG F 44 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG F 50 " --> pdb=" O ARG F 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR F 161 " --> pdb=" O ASN F 123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 98 through 99 Processing sheet with id=AD8, first strand: chain 'F' and resid 170 through 180 Processing sheet with id=AD9, first strand: chain 'F' and resid 211 through 213 Processing sheet with id=AE1, first strand: chain 'G' and resid 23 through 24 Processing sheet with id=AE2, first strand: chain 'G' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG G 44 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG G 50 " --> pdb=" O ARG G 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'G' and resid 84 through 95 removed outlier: 3.712A pdb=" N THR G 161 " --> pdb=" O ASN G 123 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 98 through 99 Processing sheet with id=AE5, first strand: chain 'G' and resid 170 through 180 Processing sheet with id=AE6, first strand: chain 'G' and resid 211 through 213 Processing sheet with id=AE7, first strand: chain 'H' and resid 23 through 24 Processing sheet with id=AE8, first strand: chain 'H' and resid 43 through 44 removed outlier: 3.743A pdb=" N ARG H 44 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG H 50 " --> pdb=" O ARG H 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'H' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR H 161 " --> pdb=" O ASN H 123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AF2, first strand: chain 'H' and resid 170 through 180 Processing sheet with id=AF3, first strand: chain 'H' and resid 211 through 213 Processing sheet with id=AF4, first strand: chain 'I' and resid 23 through 24 Processing sheet with id=AF5, first strand: chain 'I' and resid 43 through 44 removed outlier: 3.743A pdb=" N ARG I 44 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG I 50 " --> pdb=" O ARG I 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'I' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR I 161 " --> pdb=" O ASN I 123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 98 through 99 Processing sheet with id=AF8, first strand: chain 'I' and resid 170 through 180 Processing sheet with id=AF9, first strand: chain 'I' and resid 211 through 213 Processing sheet with id=AG1, first strand: chain 'J' and resid 23 through 24 Processing sheet with id=AG2, first strand: chain 'J' and resid 43 through 44 removed outlier: 3.745A pdb=" N ARG J 44 " --> pdb=" O ARG J 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG J 50 " --> pdb=" O ARG J 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'J' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR J 161 " --> pdb=" O ASN J 123 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 98 through 99 Processing sheet with id=AG5, first strand: chain 'J' and resid 170 through 180 Processing sheet with id=AG6, first strand: chain 'J' and resid 211 through 213 Processing sheet with id=AG7, first strand: chain 'K' and resid 23 through 24 Processing sheet with id=AG8, first strand: chain 'K' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG K 44 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG K 50 " --> pdb=" O ARG K 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'K' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR K 161 " --> pdb=" O ASN K 123 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 98 through 99 Processing sheet with id=AH2, first strand: chain 'K' and resid 170 through 180 Processing sheet with id=AH3, first strand: chain 'K' and resid 211 through 213 Processing sheet with id=AH4, first strand: chain 'L' and resid 23 through 24 Processing sheet with id=AH5, first strand: chain 'L' and resid 43 through 44 removed outlier: 3.745A pdb=" N ARG L 44 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG L 50 " --> pdb=" O ARG L 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'L' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR L 161 " --> pdb=" O ASN L 123 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 98 through 99 Processing sheet with id=AH8, first strand: chain 'L' and resid 170 through 180 Processing sheet with id=AH9, first strand: chain 'L' and resid 211 through 213 Processing sheet with id=AI1, first strand: chain 'M' and resid 23 through 24 Processing sheet with id=AI2, first strand: chain 'M' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG M 44 " --> pdb=" O ARG M 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG M 50 " --> pdb=" O ARG M 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'M' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR M 161 " --> pdb=" O ASN M 123 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 98 through 99 Processing sheet with id=AI5, first strand: chain 'M' and resid 170 through 180 Processing sheet with id=AI6, first strand: chain 'M' and resid 211 through 213 Processing sheet with id=AI7, first strand: chain 'N' and resid 23 through 24 Processing sheet with id=AI8, first strand: chain 'N' and resid 43 through 44 removed outlier: 3.745A pdb=" N ARG N 44 " --> pdb=" O ARG N 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG N 50 " --> pdb=" O ARG N 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'N' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR N 161 " --> pdb=" O ASN N 123 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'N' and resid 98 through 99 Processing sheet with id=AJ2, first strand: chain 'N' and resid 170 through 180 Processing sheet with id=AJ3, first strand: chain 'N' and resid 211 through 213 Processing sheet with id=AJ4, first strand: chain 'O' and resid 23 through 24 Processing sheet with id=AJ5, first strand: chain 'O' and resid 43 through 44 removed outlier: 3.745A pdb=" N ARG O 44 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG O 50 " --> pdb=" O ARG O 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ5 Processing sheet with id=AJ6, first strand: chain 'O' and resid 84 through 95 removed outlier: 3.712A pdb=" N THR O 161 " --> pdb=" O ASN O 123 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'O' and resid 98 through 99 Processing sheet with id=AJ8, first strand: chain 'O' and resid 170 through 180 Processing sheet with id=AJ9, first strand: chain 'O' and resid 211 through 213 Processing sheet with id=AK1, first strand: chain 'P' and resid 23 through 24 Processing sheet with id=AK2, first strand: chain 'P' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG P 44 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG P 50 " --> pdb=" O ARG P 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK2 Processing sheet with id=AK3, first strand: chain 'P' and resid 84 through 95 removed outlier: 3.712A pdb=" N THR P 161 " --> pdb=" O ASN P 123 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'P' and resid 98 through 99 Processing sheet with id=AK5, first strand: chain 'P' and resid 170 through 180 Processing sheet with id=AK6, first strand: chain 'P' and resid 211 through 213 Processing sheet with id=AK7, first strand: chain 'Q' and resid 23 through 24 Processing sheet with id=AK8, first strand: chain 'Q' and resid 43 through 44 removed outlier: 3.745A pdb=" N ARG Q 44 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG Q 50 " --> pdb=" O ARG Q 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK8 Processing sheet with id=AK9, first strand: chain 'Q' and resid 84 through 95 removed outlier: 3.710A pdb=" N THR Q 161 " --> pdb=" O ASN Q 123 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'Q' and resid 98 through 99 Processing sheet with id=AL2, first strand: chain 'Q' and resid 170 through 180 Processing sheet with id=AL3, first strand: chain 'Q' and resid 211 through 213 Processing sheet with id=AL4, first strand: chain 'R' and resid 23 through 24 Processing sheet with id=AL5, first strand: chain 'R' and resid 43 through 44 removed outlier: 3.745A pdb=" N ARG R 44 " --> pdb=" O ARG R 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG R 50 " --> pdb=" O ARG R 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL5 Processing sheet with id=AL6, first strand: chain 'R' and resid 84 through 95 removed outlier: 3.712A pdb=" N THR R 161 " --> pdb=" O ASN R 123 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'R' and resid 98 through 99 Processing sheet with id=AL8, first strand: chain 'R' and resid 170 through 180 Processing sheet with id=AL9, first strand: chain 'R' and resid 211 through 213 Processing sheet with id=AM1, first strand: chain 'S' and resid 23 through 24 Processing sheet with id=AM2, first strand: chain 'S' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG S 44 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG S 50 " --> pdb=" O ARG S 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM2 Processing sheet with id=AM3, first strand: chain 'S' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR S 161 " --> pdb=" O ASN S 123 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'S' and resid 98 through 99 Processing sheet with id=AM5, first strand: chain 'S' and resid 170 through 180 Processing sheet with id=AM6, first strand: chain 'S' and resid 211 through 213 Processing sheet with id=AM7, first strand: chain 'T' and resid 23 through 24 Processing sheet with id=AM8, first strand: chain 'T' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG T 44 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG T 50 " --> pdb=" O ARG T 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM8 Processing sheet with id=AM9, first strand: chain 'T' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR T 161 " --> pdb=" O ASN T 123 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'T' and resid 98 through 99 Processing sheet with id=AN2, first strand: chain 'T' and resid 170 through 180 Processing sheet with id=AN3, first strand: chain 'T' and resid 211 through 213 Processing sheet with id=AN4, first strand: chain 'U' and resid 23 through 24 Processing sheet with id=AN5, first strand: chain 'U' and resid 43 through 44 removed outlier: 3.745A pdb=" N ARG U 44 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG U 50 " --> pdb=" O ARG U 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN5 Processing sheet with id=AN6, first strand: chain 'U' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR U 161 " --> pdb=" O ASN U 123 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'U' and resid 98 through 99 Processing sheet with id=AN8, first strand: chain 'U' and resid 170 through 180 Processing sheet with id=AN9, first strand: chain 'U' and resid 211 through 213 Processing sheet with id=AO1, first strand: chain 'V' and resid 23 through 24 Processing sheet with id=AO2, first strand: chain 'V' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG V 44 " --> pdb=" O ARG V 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG V 50 " --> pdb=" O ARG V 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO2 Processing sheet with id=AO3, first strand: chain 'V' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR V 161 " --> pdb=" O ASN V 123 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'V' and resid 98 through 99 Processing sheet with id=AO5, first strand: chain 'V' and resid 170 through 180 Processing sheet with id=AO6, first strand: chain 'V' and resid 211 through 213 Processing sheet with id=AO7, first strand: chain 'W' and resid 23 through 24 Processing sheet with id=AO8, first strand: chain 'W' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG W 44 " --> pdb=" O ARG W 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG W 50 " --> pdb=" O ARG W 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AO8 Processing sheet with id=AO9, first strand: chain 'W' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR W 161 " --> pdb=" O ASN W 123 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'W' and resid 98 through 99 Processing sheet with id=AP2, first strand: chain 'W' and resid 170 through 180 Processing sheet with id=AP3, first strand: chain 'W' and resid 211 through 213 Processing sheet with id=AP4, first strand: chain 'X' and resid 23 through 24 Processing sheet with id=AP5, first strand: chain 'X' and resid 43 through 44 removed outlier: 3.744A pdb=" N ARG X 44 " --> pdb=" O ARG X 50 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG X 50 " --> pdb=" O ARG X 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP5 Processing sheet with id=AP6, first strand: chain 'X' and resid 84 through 95 removed outlier: 3.711A pdb=" N THR X 161 " --> pdb=" O ASN X 123 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'X' and resid 98 through 99 Processing sheet with id=AP8, first strand: chain 'X' and resid 170 through 180 Processing sheet with id=AP9, first strand: chain 'X' and resid 211 through 213 1272 hydrogen bonds defined for protein. 3312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.52 Time building geometry restraints manager: 4.81 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: 14299 1.34 - 1.46: 9038 1.46 - 1.58: 20823 1.58 - 1.70: 0 1.70 - 1.81: 240 Bond restraints: 44400 Sorted by residual: bond pdb=" CA VAL Q 165 " pdb=" CB VAL Q 165 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.08e-02 8.57e+03 1.71e+00 bond pdb=" CA VAL N 165 " pdb=" CB VAL N 165 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.08e-02 8.57e+03 1.69e+00 bond pdb=" CA VAL C 165 " pdb=" CB VAL C 165 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.08e-02 8.57e+03 1.63e+00 bond pdb=" CA VAL M 165 " pdb=" CB VAL M 165 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.08e-02 8.57e+03 1.61e+00 bond pdb=" CA VAL W 165 " pdb=" CB VAL W 165 " ideal model delta sigma weight residual 1.532 1.546 -0.014 1.08e-02 8.57e+03 1.61e+00 ... (remaining 44395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 56607 2.02 - 4.03: 2488 4.03 - 6.05: 353 6.05 - 8.07: 144 8.07 - 10.08: 24 Bond angle restraints: 59616 Sorted by residual: angle pdb=" CA ARG H 33 " pdb=" CB ARG H 33 " pdb=" CG ARG H 33 " ideal model delta sigma weight residual 114.10 121.95 -7.85 2.00e+00 2.50e-01 1.54e+01 angle pdb=" CA ARG E 33 " pdb=" CB ARG E 33 " pdb=" CG ARG E 33 " ideal model delta sigma weight residual 114.10 121.94 -7.84 2.00e+00 2.50e-01 1.54e+01 angle pdb=" CA ARG V 33 " pdb=" CB ARG V 33 " pdb=" CG ARG V 33 " ideal model delta sigma weight residual 114.10 121.94 -7.84 2.00e+00 2.50e-01 1.54e+01 angle pdb=" CA ARG O 33 " pdb=" CB ARG O 33 " pdb=" CG ARG O 33 " ideal model delta sigma weight residual 114.10 121.93 -7.83 2.00e+00 2.50e-01 1.53e+01 angle pdb=" CA ARG S 33 " pdb=" CB ARG S 33 " pdb=" CG ARG S 33 " ideal model delta sigma weight residual 114.10 121.93 -7.83 2.00e+00 2.50e-01 1.53e+01 ... (remaining 59611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 23998 16.95 - 33.91: 2430 33.91 - 50.86: 380 50.86 - 67.82: 24 67.82 - 84.77: 48 Dihedral angle restraints: 26880 sinusoidal: 11496 harmonic: 15384 Sorted by residual: dihedral pdb=" CA ALA E 222 " pdb=" C ALA E 222 " pdb=" N GLY E 223 " pdb=" CA GLY E 223 " ideal model delta harmonic sigma weight residual -180.00 -154.41 -25.59 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA ALA U 222 " pdb=" C ALA U 222 " pdb=" N GLY U 223 " pdb=" CA GLY U 223 " ideal model delta harmonic sigma weight residual -180.00 -154.44 -25.56 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA ALA T 222 " pdb=" C ALA T 222 " pdb=" N GLY T 223 " pdb=" CA GLY T 223 " ideal model delta harmonic sigma weight residual -180.00 -154.44 -25.56 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 26877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3835 0.036 - 0.072: 1795 0.072 - 0.108: 675 0.108 - 0.144: 175 0.144 - 0.179: 96 Chirality restraints: 6576 Sorted by residual: 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 2.33 0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CA ASN T 154 " pdb=" N ASN T 154 " pdb=" C ASN T 154 " pdb=" CB ASN T 154 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" CA ASN C 154 " pdb=" N ASN C 154 " pdb=" C ASN C 154 " pdb=" CB ASN C 154 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 6573 not shown) Planarity restraints: 7584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU F 168 " 0.014 2.00e-02 2.50e+03 2.64e-02 6.98e+00 pdb=" C GLU F 168 " -0.046 2.00e-02 2.50e+03 pdb=" O GLU F 168 " 0.016 2.00e-02 2.50e+03 pdb=" N THR F 169 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU P 168 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" C GLU P 168 " 0.046 2.00e-02 2.50e+03 pdb=" O GLU P 168 " -0.016 2.00e-02 2.50e+03 pdb=" N THR P 169 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU Q 168 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C GLU Q 168 " 0.045 2.00e-02 2.50e+03 pdb=" O GLU Q 168 " -0.016 2.00e-02 2.50e+03 pdb=" N THR Q 169 " -0.016 2.00e-02 2.50e+03 ... (remaining 7581 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 308 2.48 - 3.09: 30468 3.09 - 3.69: 66955 3.69 - 4.30: 92308 4.30 - 4.90: 148193 Nonbonded interactions: 338232 Sorted by model distance: nonbonded pdb=" O GLN W 85 " pdb=" OG1 THR X 198 " model vdw 1.879 3.040 nonbonded pdb=" O MET T 16 " pdb=" OG SER U 27 " model vdw 1.910 3.040 nonbonded pdb=" O GLN L 85 " pdb=" OG1 THR M 198 " model vdw 1.958 3.040 nonbonded pdb=" O GLN T 85 " pdb=" OG1 THR U 198 " model vdw 1.968 3.040 nonbonded pdb=" O MET S 16 " pdb=" OG SER T 27 " model vdw 2.017 3.040 ... (remaining 338227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.16 Found NCS groups: ncs_group { reference = chain '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 Number of NCS constrained groups: 1 pdb_interpretation.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 refine NCS operators NCS operators will be refined. 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: 1.130 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: 0.050 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.800 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5034 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 : 0.004 0.039 44400 Z= 0.199 Angle : 1.001 10.082 59616 Z= 0.558 Chirality : 0.050 0.179 6576 Planarity : 0.006 0.047 7584 Dihedral : 13.701 84.769 16896 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -4.06 (0.10), residues: 5208 helix: -1.06 (0.19), residues: 696 sheet: -2.17 (0.11), residues: 2136 loop : -3.71 (0.10), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 10 TYR 0.013 0.002 TYR L 207 PHE 0.013 0.002 PHE H 113 TRP 0.005 0.001 TRP L 69 HIS 0.015 0.002 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00370 (44400) covalent geometry : angle 1.00132 (59616) hydrogen bonds : bond 0.13868 ( 1272) hydrogen bonds : angle 9.10219 ( 3312) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10416 Ramachandran restraints generated. 5208 Oldfield, 0 Emsley, 5208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10416 Ramachandran restraints generated. 5208 Oldfield, 0 Emsley, 5208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.8509 (pmt-80) cc_final: 0.5208 (tmt170) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0715 time to fit residues: 2.2377 Evaluate side-chains 25 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 20.0000 chunk 497 optimal weight: 4.9990 chunk 414 optimal weight: 7.9990 chunk 310 optimal weight: 0.0060 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 0.5980 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 181 GLN O 186 HIS O 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.137991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.119271 restraints weight = 10156.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.120734 restraints weight = 8031.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.122520 restraints weight = 6727.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.123355 restraints weight = 5737.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.124517 restraints weight = 5158.316| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5125 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 44400 Z= 0.146 Angle : 0.742 7.377 59616 Z= 0.390 Chirality : 0.049 0.166 6576 Planarity : 0.005 0.050 7584 Dihedral : 6.969 23.696 5808 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.50 % Allowed : 5.94 % Favored : 93.56 % 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: -3.80 (0.11), residues: 5208 helix: -0.66 (0.19), residues: 744 sheet: -1.77 (0.13), residues: 1608 loop : -3.66 (0.09), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 174 TYR 0.005 0.001 TYR J 156 PHE 0.008 0.001 PHE C 113 TRP 0.003 0.001 TRP I 69 HIS 0.012 0.001 HIS P 38 Details of bonding type rmsd covalent geometry : bond 0.00283 (44400) covalent geometry : angle 0.74157 (59616) hydrogen bonds : bond 0.05116 ( 1272) hydrogen bonds : angle 8.49223 ( 3312) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.053 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 11 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.6447 (mp) REVERT: O 22 MET cc_start: 0.8209 (tpt) cc_final: 0.7850 (tpp) REVERT: O 26 ARG cc_start: 0.8739 (pmt-80) cc_final: 0.6280 (tmt170) REVERT: O 84 PHE cc_start: 0.6476 (t80) cc_final: 0.5904 (t80) REVERT: O 173 ASP cc_start: 0.6946 (t0) cc_final: 0.6411 (t0) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.0505 time to fit residues: 1.9111 Evaluate side-chains 23 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 100 optimal weight: 0.7980 chunk 482 optimal weight: 0.0870 chunk 33 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 293 optimal weight: 0.3980 chunk 37 optimal weight: 0.0270 chunk 0 optimal weight: 4.9990 chunk 385 optimal weight: 0.9980 chunk 345 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 181 GLN O 211 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.138538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.120434 restraints weight = 9888.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.122322 restraints weight = 7681.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.123975 restraints weight = 6282.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.124906 restraints weight = 5320.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.126069 restraints weight = 4739.177| |-----------------------------------------------------------------------------| r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5045 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 44400 Z= 0.125 Angle : 0.695 7.656 59616 Z= 0.365 Chirality : 0.047 0.149 6576 Planarity : 0.004 0.046 7584 Dihedral : 6.364 22.521 5808 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.50 % Allowed : 6.44 % Favored : 93.07 % 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: -3.68 (0.11), residues: 5208 helix: -0.84 (0.19), residues: 768 sheet: -1.89 (0.11), residues: 2184 loop : -3.57 (0.11), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 10 TYR 0.006 0.001 TYR X 156 PHE 0.014 0.001 PHE W 5 TRP 0.002 0.000 TRP M 69 HIS 0.010 0.001 HIS M 38 Details of bonding type rmsd covalent geometry : bond 0.00246 (44400) covalent geometry : angle 0.69539 (59616) hydrogen bonds : bond 0.04171 ( 1272) hydrogen bonds : angle 7.87539 ( 3312) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 11 ILE cc_start: 0.6542 (OUTLIER) cc_final: 0.6336 (mp) REVERT: O 22 MET cc_start: 0.7835 (tpt) cc_final: 0.7373 (tpp) REVERT: O 26 ARG cc_start: 0.8689 (pmt-80) cc_final: 0.6111 (tmt170) REVERT: O 199 ILE cc_start: 0.8988 (mm) cc_final: 0.8623 (pt) outliers start: 1 outliers final: 0 residues processed: 31 average time/residue: 0.0700 time to fit residues: 2.5107 Evaluate side-chains 24 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 387 optimal weight: 4.9990 chunk 404 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 146 optimal weight: 0.0870 chunk 451 optimal weight: 5.9990 chunk 78 optimal weight: 0.0030 chunk 294 optimal weight: 0.0570 chunk 158 optimal weight: 0.0040 chunk 192 optimal weight: 10.0000 chunk 501 optimal weight: 3.9990 chunk 358 optimal weight: 8.9990 overall best weight: 0.4300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.138223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.119983 restraints weight = 9688.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.121755 restraints weight = 7555.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.123494 restraints weight = 6232.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.124626 restraints weight = 5272.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.125594 restraints weight = 4644.801| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5015 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 44400 Z= 0.118 Angle : 0.679 7.524 59616 Z= 0.354 Chirality : 0.047 0.143 6576 Planarity : 0.004 0.045 7584 Dihedral : 6.154 22.104 5808 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.50 % Allowed : 5.94 % Favored : 93.56 % 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: -3.52 (0.11), residues: 5208 helix: -0.38 (0.19), residues: 768 sheet: -1.62 (0.12), residues: 1824 loop : -3.60 (0.10), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 203 TYR 0.005 0.001 TYR G 189 PHE 0.011 0.001 PHE G 84 TRP 0.002 0.000 TRP M 69 HIS 0.009 0.001 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00227 (44400) covalent geometry : angle 0.67860 (59616) hydrogen bonds : bond 0.03854 ( 1272) hydrogen bonds : angle 7.62112 ( 3312) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 11 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.6546 (mp) REVERT: O 26 ARG cc_start: 0.8710 (pmt-80) cc_final: 0.5545 (tmt170) REVERT: O 199 ILE cc_start: 0.8947 (mm) cc_final: 0.8702 (pt) outliers start: 1 outliers final: 0 residues processed: 31 average time/residue: 0.0697 time to fit residues: 2.4572 Evaluate side-chains 27 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 384 optimal weight: 10.0000 chunk 206 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 403 optimal weight: 4.9990 chunk 315 optimal weight: 0.0050 chunk 410 optimal weight: 0.2980 chunk 22 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 321 optimal weight: 5.9990 chunk 24 optimal weight: 0.0970 chunk 444 optimal weight: 0.5980 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.137352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.119571 restraints weight = 9819.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.121321 restraints weight = 7809.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.122318 restraints weight = 6467.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.123698 restraints weight = 5666.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.124330 restraints weight = 5009.257| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5090 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 44400 Z= 0.117 Angle : 0.668 7.850 59616 Z= 0.346 Chirality : 0.047 0.135 6576 Planarity : 0.004 0.044 7584 Dihedral : 6.046 21.099 5808 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.99 % Allowed : 4.46 % Favored : 94.55 % 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: -3.58 (0.11), residues: 5208 helix: -0.67 (0.19), residues: 768 sheet: -1.63 (0.12), residues: 1824 loop : -3.57 (0.10), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 203 TYR 0.006 0.001 TYR K 156 PHE 0.010 0.001 PHE N 46 TRP 0.001 0.000 TRP M 179 HIS 0.009 0.001 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00232 (44400) covalent geometry : angle 0.66798 (59616) hydrogen bonds : bond 0.03716 ( 1272) hydrogen bonds : angle 7.39316 ( 3312) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 11 ILE cc_start: 0.6653 (OUTLIER) cc_final: 0.6375 (mp) REVERT: O 26 ARG cc_start: 0.8806 (pmt-80) cc_final: 0.5348 (tmt170) REVERT: O 199 ILE cc_start: 0.9034 (mm) cc_final: 0.8780 (pt) outliers start: 2 outliers final: 0 residues processed: 29 average time/residue: 0.0718 time to fit residues: 2.3850 Evaluate side-chains 25 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 163 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 444 optimal weight: 10.0000 chunk 333 optimal weight: 0.2980 chunk 300 optimal weight: 0.0670 chunk 160 optimal weight: 8.9990 chunk 246 optimal weight: 4.9990 chunk 505 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 134 optimal weight: 0.3980 chunk 497 optimal weight: 3.9990 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.138353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.120994 restraints weight = 9807.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.122984 restraints weight = 7653.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.124089 restraints weight = 6304.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.124597 restraints weight = 5504.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.125891 restraints weight = 5067.213| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5010 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 44400 Z= 0.122 Angle : 0.678 8.050 59616 Z= 0.348 Chirality : 0.047 0.161 6576 Planarity : 0.004 0.042 7584 Dihedral : 5.937 20.907 5808 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % 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: -3.49 (0.11), residues: 5208 helix: -0.33 (0.19), residues: 768 sheet: -1.62 (0.12), residues: 1824 loop : -3.57 (0.10), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 203 TYR 0.008 0.001 TYR N 207 PHE 0.008 0.001 PHE B 46 TRP 0.000 0.000 TRP M 179 HIS 0.008 0.001 HIS K 38 Details of bonding type rmsd covalent geometry : bond 0.00235 (44400) covalent geometry : angle 0.67771 (59616) hydrogen bonds : bond 0.03368 ( 1272) hydrogen bonds : angle 7.25623 ( 3312) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9982 Ramachandran restraints generated. 4991 Oldfield, 0 Emsley, 4991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 11 ILE cc_start: 0.6385 (mp) cc_final: 0.6172 (mp) REVERT: O 16 MET cc_start: 0.5448 (tpt) cc_final: 0.5155 (tpt) REVERT: O 26 ARG cc_start: 0.8785 (pmt-80) cc_final: 0.6148 (tmt170) REVERT: O 171 LYS cc_start: 0.7045 (mmtt) cc_final: 0.6806 (mmtm) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0614 time to fit residues: 1.9004 Evaluate side-chains 24 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 46 optimal weight: 4.9990 chunk 272 optimal weight: 8.9990 chunk 497 optimal weight: 1.9990 chunk 437 optimal weight: 0.0040 chunk 123 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 263 optimal weight: 0.0980 chunk 199 optimal weight: 0.6980 chunk 237 optimal weight: 4.9990 chunk 321 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.145254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.123759 restraints weight = 12644.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.125214 restraints weight = 10478.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.126298 restraints weight = 9040.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.127219 restraints weight = 7996.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.127685 restraints weight = 7237.518| |-----------------------------------------------------------------------------| r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5185 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 44400 Z= 0.128 Angle : 0.706 9.412 59616 Z= 0.362 Chirality : 0.047 0.170 6576 Planarity : 0.004 0.043 7584 Dihedral : 5.982 21.456 5808 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: -3.53 (0.10), residues: 5208 helix: -0.83 (0.18), residues: 768 sheet: -1.74 (0.11), residues: 1824 loop : -3.35 (0.10), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 26 TYR 0.008 0.002 TYR K 207 PHE 0.008 0.001 PHE N 46 TRP 0.002 0.000 TRP E 69 HIS 0.008 0.001 HIS E 38 Details of bonding type rmsd covalent geometry : bond 0.00265 (44400) covalent geometry : angle 0.70634 (59616) hydrogen bonds : bond 0.03616 ( 1272) hydrogen bonds : angle 7.26245 ( 3312) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9548 Ramachandran restraints generated. 4774 Oldfield, 0 Emsley, 4774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 22 MET cc_start: 0.8504 (tpt) cc_final: 0.7431 (tpp) REVERT: R 176 TYR cc_start: 0.7835 (t80) cc_final: 0.7039 (m-80) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0600 time to fit residues: 2.1565 Evaluate side-chains 26 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 89 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 331 optimal weight: 3.9990 chunk 235 optimal weight: 0.1980 chunk 168 optimal weight: 0.3980 chunk 502 optimal weight: 4.9990 chunk 422 optimal weight: 0.0050 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.143861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.119819 restraints weight = 9161.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.122089 restraints weight = 7359.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.123392 restraints weight = 6191.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.124769 restraints weight = 5474.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.125389 restraints weight = 4932.716| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5253 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 44400 Z= 0.130 Angle : 0.701 8.482 59616 Z= 0.365 Chirality : 0.047 0.174 6576 Planarity : 0.004 0.043 7584 Dihedral : 5.994 20.286 5808 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: -3.52 (0.10), residues: 5208 helix: -0.59 (0.18), residues: 768 sheet: -1.81 (0.11), residues: 1824 loop : -3.35 (0.10), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 26 TYR 0.008 0.001 TYR K 207 PHE 0.008 0.001 PHE N 46 TRP 0.003 0.000 TRP J 69 HIS 0.008 0.001 HIS W 38 Details of bonding type rmsd covalent geometry : bond 0.00266 (44400) covalent geometry : angle 0.70116 (59616) hydrogen bonds : bond 0.03384 ( 1272) hydrogen bonds : angle 7.13690 ( 3312) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9114 Ramachandran restraints generated. 4557 Oldfield, 0 Emsley, 4557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 22 MET cc_start: 0.8917 (tpt) cc_final: 0.8106 (tpp) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0573 time to fit residues: 2.0597 Evaluate side-chains 22 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 517 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 394 optimal weight: 9.9990 chunk 416 optimal weight: 9.9990 chunk 401 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 468 optimal weight: 10.0000 chunk 306 optimal weight: 8.9990 chunk 389 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.127952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.110727 restraints weight = 10506.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.112009 restraints weight = 8634.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.113434 restraints weight = 7425.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.114465 restraints weight = 6528.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.115020 restraints weight = 5900.120| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5463 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 44400 Z= 0.174 Angle : 0.773 9.133 59616 Z= 0.403 Chirality : 0.049 0.168 6576 Planarity : 0.005 0.045 7584 Dihedral : 6.358 21.391 5808 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 24.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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 (0.10), residues: 5208 helix: -0.93 (0.17), residues: 768 sheet: -2.22 (0.11), residues: 1776 loop : -3.26 (0.10), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 26 TYR 0.013 0.002 TYR P 207 PHE 0.013 0.002 PHE X 84 TRP 0.006 0.001 TRP U 69 HIS 0.011 0.002 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00368 (44400) covalent geometry : angle 0.77323 (59616) hydrogen bonds : bond 0.04305 ( 1272) hydrogen bonds : angle 7.22124 ( 3312) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.079 Fit side-chains REVERT: I 22 MET cc_start: 0.8083 (tpt) cc_final: 0.7851 (tpt) REVERT: I 25 VAL cc_start: 0.6775 (p) cc_final: 0.6263 (p) REVERT: I 26 ARG cc_start: 0.8735 (pmt-80) cc_final: 0.6407 (tmt170) REVERT: I 176 TYR cc_start: 0.7686 (t80) cc_final: 0.7416 (m-80) REVERT: I 217 LYS cc_start: 0.7684 (mmpt) cc_final: 0.7362 (tptp) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0811 time to fit residues: 2.6894 Evaluate side-chains 21 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 43 optimal weight: 0.0070 chunk 382 optimal weight: 0.6980 chunk 383 optimal weight: 0.0170 chunk 316 optimal weight: 0.6980 chunk 260 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 0.0070 chunk 321 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 59 optimal weight: 0.4980 overall best weight: 0.2454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.134906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.117218 restraints weight = 10106.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.119256 restraints weight = 7848.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.120931 restraints weight = 6414.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.122226 restraints weight = 5429.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.122753 restraints weight = 4729.280| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5072 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 44400 Z= 0.133 Angle : 0.719 9.555 59616 Z= 0.377 Chirality : 0.049 0.167 6576 Planarity : 0.004 0.041 7584 Dihedral : 5.878 20.472 5808 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: -3.80 (0.10), residues: 5208 helix: -1.39 (0.17), residues: 768 sheet: -1.76 (0.12), residues: 1608 loop : -3.45 (0.09), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 26 TYR 0.010 0.002 TYR J 207 PHE 0.008 0.001 PHE I 113 TRP 0.002 0.000 TRP U 69 HIS 0.009 0.001 HIS I 38 Details of bonding type rmsd covalent geometry : bond 0.00268 (44400) covalent geometry : angle 0.71892 (59616) hydrogen bonds : bond 0.03143 ( 1272) hydrogen bonds : angle 7.15557 ( 3312) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8680 Ramachandran restraints generated. 4340 Oldfield, 0 Emsley, 4340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.083 Fit side-chains REVERT: I 25 VAL cc_start: 0.6238 (p) cc_final: 0.5857 (p) REVERT: I 26 ARG cc_start: 0.8417 (pmt-80) cc_final: 0.6581 (tmt170) REVERT: I 217 LYS cc_start: 0.7394 (mmpt) cc_final: 0.6824 (tptp) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.0811 time to fit residues: 2.9701 Evaluate side-chains 23 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 431 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 169 optimal weight: 0.0470 chunk 276 optimal weight: 0.0170 chunk 23 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 517 optimal weight: 0.0060 chunk 487 optimal weight: 0.0010 chunk 11 optimal weight: 0.7980 chunk 414 optimal weight: 0.0370 chunk 89 optimal weight: 0.9980 overall best weight: 0.0216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.145735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.125196 restraints weight = 9452.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.127094 restraints weight = 7660.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.128658 restraints weight = 6489.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.129833 restraints weight = 5694.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.130475 restraints weight = 5128.106| |-----------------------------------------------------------------------------| r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5080 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 44400 Z= 0.136 Angle : 0.747 10.864 59616 Z= 0.381 Chirality : 0.048 0.168 6576 Planarity : 0.004 0.041 7584 Dihedral : 5.796 19.929 5808 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.71 (0.10), residues: 5208 helix: -1.36 (0.17), residues: 768 sheet: -1.89 (0.12), residues: 1800 loop : -3.28 (0.10), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 208 TYR 0.020 0.003 TYR A 207 PHE 0.008 0.001 PHE I 113 TRP 0.002 0.000 TRP V 179 HIS 0.011 0.001 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00276 (44400) covalent geometry : angle 0.74697 (59616) hydrogen bonds : bond 0.03039 ( 1272) hydrogen bonds : angle 7.20342 ( 3312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2298.18 seconds wall clock time: 42 minutes 47.14 seconds (2567.14 seconds total)