Starting phenix.real_space_refine on Tue Jul 7 04:05:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8et2_28584/07_2026/8et2_28584.cif Found real_map, /net/cci-nas-00/data/ceres_data/8et2_28584/07_2026/8et2_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 { model { file = "/net/cci-nas-00/data/ceres_data/8et2_28584/07_2026/8et2_28584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8et2_28584/07_2026/8et2_28584.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8et2_28584/07_2026/8et2_28584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8et2_28584/07_2026/8et2_28584.map" } 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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 4.42, per 1000 atoms: 0.10 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: 4.06 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.38 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: 9.31 Time building geometry restraints manager: 5.48 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: 0.18 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: 1.230 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: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 35.670 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4867 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 are 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/Z covalent geometry : bond 0.00370 / 0.20 (44400) covalent geometry : angle 1.00132 / 0.56 (59616) hydrogen bonds : bond 0.13868 / 8.91 ( 1272) hydrogen bonds : angle 9.10219 / 6.36 ( 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: 0.8510 (pmt-80) cc_final: 0.5208 (tmt170) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0676 time to fit residues: 2.1352 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 : 0.080 ------------------------------------------------------------------------------- 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... ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN A 186 HIS A 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 = 0.4450 r_free = 0.4450 target = 0.137986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.119334 restraints weight = 9844.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.121377 restraints weight = 7677.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.122999 restraints weight = 6273.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.123958 restraints weight = 5321.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.124395 restraints weight = 4734.782| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4996 moved from start: 0.1352 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 : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.50 % Allowed : 5.45 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are 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/Z covalent geometry : bond 0.00283 / 0.15 (44400) covalent geometry : angle 0.74157 / 0.39 (59616) hydrogen bonds : bond 0.05116 / 3.27 ( 1272) hydrogen bonds : angle 8.49223 / 5.94 ( 3312) *********************** REFINEMENT MACRO_CYCLE 2 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 33 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 11 ILE cc_start: 0.6687 (OUTLIER) cc_final: 0.6437 (mp) REVERT: O 22 MET cc_start: 0.8193 (tpt) cc_final: 0.7840 (tpp) REVERT: O 26 ARG cc_start: 0.8731 (pmt-80) cc_final: 0.6265 (tmt170) REVERT: O 84 PHE cc_start: 0.6481 (t80) cc_final: 0.5906 (t80) REVERT: O 173 ASP cc_start: 0.6940 (t0) cc_final: 0.6403 (t0) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.0613 time to fit residues: 2.3359 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 : 0.093 ------------------------------------------------------------------------------- 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: 7.9990 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: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 181 GLN O 186 HIS O 211 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.137523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.120507 restraints weight = 9266.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.122305 restraints weight = 7230.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.123496 restraints weight = 5896.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.124514 restraints weight = 5083.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.124823 restraints weight = 4544.919| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4907 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 44400 Z= 0.125 Angle : 0.697 7.700 59616 Z= 0.366 Chirality : 0.047 0.147 6576 Planarity : 0.004 0.046 7584 Dihedral : 6.402 22.613 5808 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.50 % Allowed : 6.93 % Favored : 92.57 % 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 are not related in a simple way. whole: -3.69 (0.11), residues: 5208 helix: -0.84 (0.19), residues: 768 sheet: -1.91 (0.11), residues: 2184 loop : -3.56 (0.11), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 208 TYR 0.006 0.001 TYR R 156 PHE 0.015 0.001 PHE A 5 TRP 0.002 0.000 TRP M 69 HIS 0.010 0.001 HIS M 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 (44400) covalent geometry : angle 0.69693 / 0.37 (59616) hydrogen bonds : bond 0.04265 / 2.71 ( 1272) hydrogen bonds : angle 7.88731 / 5.52 ( 3312) *********************** REFINEMENT MACRO_CYCLE 3 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 31 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 11 ILE cc_start: 0.6552 (OUTLIER) cc_final: 0.6348 (mp) REVERT: O 22 MET cc_start: 0.7843 (tpt) cc_final: 0.7449 (tpt) REVERT: O 26 ARG cc_start: 0.8673 (pmt-80) cc_final: 0.6083 (tmt170) REVERT: O 199 ILE cc_start: 0.8950 (mm) cc_final: 0.8593 (pt) outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 0.0668 time to fit residues: 2.3242 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 : 0.080 ------------------------------------------------------------------------------- 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: 0.0970 chunk 404 optimal weight: 0.0170 chunk 36 optimal weight: 2.9990 chunk 146 optimal weight: 0.5980 chunk 451 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 294 optimal weight: 0.0980 chunk 158 optimal weight: 0.9980 chunk 192 optimal weight: 0.0980 chunk 501 optimal weight: 7.9990 chunk 358 optimal weight: 0.5980 overall best weight: 0.1816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.140221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.123709 restraints weight = 9957.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.125487 restraints weight = 7808.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.126888 restraints weight = 6434.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.127719 restraints weight = 5490.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.128768 restraints weight = 4900.776| |-----------------------------------------------------------------------------| r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4765 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 44400 Z= 0.119 Angle : 0.674 7.601 59616 Z= 0.351 Chirality : 0.047 0.143 6576 Planarity : 0.004 0.045 7584 Dihedral : 6.126 21.843 5808 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.50 % Allowed : 4.95 % 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 are not related in a simple way. whole: -3.49 (0.11), residues: 5208 helix: -0.32 (0.20), residues: 768 sheet: -1.61 (0.12), residues: 1824 loop : -3.58 (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 G 189 PHE 0.011 0.001 PHE I 113 TRP 0.003 0.001 TRP Q 179 HIS 0.009 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 (44400) covalent geometry : angle 0.67374 / 0.35 (59616) hydrogen bonds : bond 0.03850 / 2.45 ( 1272) hydrogen bonds : angle 7.55374 / 5.32 ( 3312) *********************** REFINEMENT MACRO_CYCLE 4 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 30 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 11 ILE cc_start: 0.6803 (OUTLIER) cc_final: 0.6485 (mp) REVERT: O 26 ARG cc_start: 0.8622 (pmt-80) cc_final: 0.5532 (tmt170) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.0666 time to fit residues: 2.2414 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 384 optimal weight: 10.0000 chunk 206 optimal weight: 0.0010 chunk 17 optimal weight: 3.9990 chunk 403 optimal weight: 6.9990 chunk 315 optimal weight: 0.0030 chunk 410 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 121 optimal weight: 0.0670 chunk 321 optimal weight: 5.9990 chunk 24 optimal weight: 0.0970 chunk 444 optimal weight: 0.9980 overall best weight: 0.2132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4523 r_free = 0.4523 target = 0.148764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.125686 restraints weight = 9430.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.127748 restraints weight = 7589.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.129242 restraints weight = 6425.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.130153 restraints weight = 5652.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.131556 restraints weight = 5173.661| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4869 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 44400 Z= 0.116 Angle : 0.681 7.800 59616 Z= 0.349 Chirality : 0.047 0.135 6576 Planarity : 0.004 0.043 7584 Dihedral : 5.975 21.381 5808 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.10), residues: 5208 helix: -0.56 (0.19), residues: 768 sheet: -1.59 (0.12), residues: 1824 loop : -3.60 (0.10), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 203 TYR 0.006 0.001 TYR C 156 PHE 0.009 0.001 PHE B 46 TRP 0.001 0.000 TRP M 69 HIS 0.008 0.001 HIS W 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 (44400) covalent geometry : angle 0.68078 / 0.35 (59616) hydrogen bonds : bond 0.03410 / 2.19 ( 1272) hydrogen bonds : angle 7.50214 / 5.27 ( 3312) *********************** REFINEMENT MACRO_CYCLE 5 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 31 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 5 PHE cc_start: 0.4462 (m-10) cc_final: 0.4232 (m-10) REVERT: M 16 MET cc_start: 0.6270 (tpt) cc_final: 0.5842 (tpp) REVERT: M 22 MET cc_start: 0.7877 (tpt) cc_final: 0.7371 (tpt) REVERT: M 26 ARG cc_start: 0.8370 (pmt-80) cc_final: 0.6584 (tmt170) REVERT: M 176 TYR cc_start: 0.7464 (t80) cc_final: 0.7192 (m-80) REVERT: M 217 LYS cc_start: 0.7737 (mmpt) cc_final: 0.7283 (tptp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0750 time to fit residues: 2.6822 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 : 0.074 ------------------------------------------------------------------------------- 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: 0.0370 chunk 241 optimal weight: 0.0040 chunk 444 optimal weight: 0.9990 chunk 333 optimal weight: 0.0670 chunk 300 optimal weight: 0.0570 chunk 160 optimal weight: 6.9990 chunk 246 optimal weight: 0.6980 chunk 505 optimal weight: 0.1980 chunk 7 optimal weight: 0.0770 chunk 134 optimal weight: 4.9990 chunk 497 optimal weight: 6.9990 overall best weight: 0.0484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 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 = 0.4521 r_free = 0.4521 target = 0.142190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.126279 restraints weight = 9870.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.128353 restraints weight = 7816.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.129772 restraints weight = 6465.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.130575 restraints weight = 5561.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.131643 restraints weight = 5008.167| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4686 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 44400 Z= 0.119 Angle : 0.674 7.932 59616 Z= 0.347 Chirality : 0.047 0.160 6576 Planarity : 0.004 0.042 7584 Dihedral : 5.851 21.180 5808 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.10), residues: 5208 helix: -0.33 (0.20), residues: 768 sheet: -1.35 (0.12), residues: 1704 loop : -3.65 (0.09), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 203 TYR 0.009 0.001 TYR U 156 PHE 0.009 0.001 PHE N 46 TRP 0.001 0.000 TRP K 69 HIS 0.008 0.001 HIS E 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (44400) covalent geometry : angle 0.67371 / 0.35 (59616) hydrogen bonds : bond 0.03199 / 2.06 ( 1272) hydrogen bonds : angle 7.24955 / 5.10 ( 3312) *********************** REFINEMENT MACRO_CYCLE 6 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 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: symmetry clash REVERT: O 11 ILE cc_start: 0.6137 (mp) cc_final: 0.5924 (mp) REVERT: O 16 MET cc_start: 0.5371 (tpt) cc_final: 0.4936 (tpt) REVERT: O 26 ARG cc_start: 0.8738 (pmt-80) cc_final: 0.5908 (tmt170) REVERT: O 84 PHE cc_start: 0.6366 (t80) cc_final: 0.6022 (t80) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0600 time to fit residues: 2.1160 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 : 0.048 ------------------------------------------------------------------------------- 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: 0.0010 chunk 272 optimal weight: 2.9990 chunk 497 optimal weight: 6.9990 chunk 437 optimal weight: 0.2980 chunk 123 optimal weight: 0.0030 chunk 174 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 237 optimal weight: 0.0970 chunk 321 optimal weight: 2.9990 chunk 184 optimal weight: 0.0020 overall best weight: 0.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4505 r_free = 0.4505 target = 0.147339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.125514 restraints weight = 9403.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.127606 restraints weight = 7608.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.129145 restraints weight = 6420.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.130639 restraints weight = 5640.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.131380 restraints weight = 5049.329| |-----------------------------------------------------------------------------| r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4804 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 44400 Z= 0.123 Angle : 0.700 8.143 59616 Z= 0.359 Chirality : 0.047 0.149 6576 Planarity : 0.004 0.041 7584 Dihedral : 5.817 20.993 5808 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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 are not related in a simple way. whole: -3.52 (0.10), residues: 5208 helix: -0.65 (0.19), residues: 768 sheet: -1.72 (0.12), residues: 1848 loop : -3.41 (0.10), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 26 TYR 0.008 0.001 TYR G 156 PHE 0.008 0.001 PHE N 46 TRP 0.001 0.000 TRP M 179 HIS 0.007 0.001 HIS W 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (44400) covalent geometry : angle 0.70013 / 0.36 (59616) hydrogen bonds : bond 0.03152 / 2.04 ( 1272) hydrogen bonds : angle 7.34765 / 5.15 ( 3312) *********************** REFINEMENT MACRO_CYCLE 7 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 31 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 16 MET cc_start: 0.6320 (tpt) cc_final: 0.6049 (tpt) REVERT: M 22 MET cc_start: 0.8470 (tpt) cc_final: 0.8108 (tpp) REVERT: M 26 ARG cc_start: 0.8512 (pmt-80) cc_final: 0.6665 (tmt170) REVERT: M 168 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7314 (mm-30) REVERT: M 173 ASP cc_start: 0.7470 (t0) cc_final: 0.7192 (t0) REVERT: M 176 TYR cc_start: 0.7443 (t80) cc_final: 0.7234 (m-80) REVERT: M 217 LYS cc_start: 0.7579 (mmpt) cc_final: 0.7262 (tptp) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0619 time to fit residues: 2.2390 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 : 0.080 ------------------------------------------------------------------------------- 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: 0.3980 chunk 18 optimal weight: 0.0070 chunk 261 optimal weight: 0.0010 chunk 92 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 242 optimal weight: 5.9990 chunk 331 optimal weight: 2.9990 chunk 235 optimal weight: 0.0870 chunk 168 optimal weight: 0.0030 chunk 502 optimal weight: 0.5980 chunk 422 optimal weight: 3.9990 overall best weight: 0.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 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 = 0.4531 r_free = 0.4531 target = 0.144034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.120135 restraints weight = 10944.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.123095 restraints weight = 8242.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.125160 restraints weight = 6566.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.126877 restraints weight = 5522.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.128318 restraints weight = 4784.640| |-----------------------------------------------------------------------------| r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4819 moved from start: 0.4122 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 : 0.667 8.321 59616 Z= 0.345 Chirality : 0.046 0.146 6576 Planarity : 0.004 0.041 7584 Dihedral : 5.655 21.149 5808 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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 are not related in a simple way. whole: -3.40 (0.10), residues: 5208 helix: -0.32 (0.19), residues: 720 sheet: -1.72 (0.11), residues: 1848 loop : -3.31 (0.10), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 10 TYR 0.009 0.001 TYR K 156 PHE 0.008 0.001 PHE N 46 TRP 0.001 0.000 TRP M 179 HIS 0.008 0.001 HIS K 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (44400) covalent geometry : angle 0.66679 / 0.34 (59616) hydrogen bonds : bond 0.03025 / 1.97 ( 1272) hydrogen bonds : angle 7.18261 / 5.05 ( 3312) *********************** REFINEMENT MACRO_CYCLE 8 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 34 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 16 MET cc_start: 0.5897 (tpt) cc_final: 0.5639 (tpt) REVERT: H 22 MET cc_start: 0.7563 (tpt) cc_final: 0.7331 (tpp) REVERT: H 26 ARG cc_start: 0.8488 (pmt-80) cc_final: 0.5629 (tmt170) REVERT: H 84 PHE cc_start: 0.5925 (t80) cc_final: 0.5165 (t80) REVERT: H 176 TYR cc_start: 0.7747 (t80) cc_final: 0.7085 (m-80) REVERT: H 217 LYS cc_start: 0.7712 (mmpt) cc_final: 0.7249 (tptp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0707 time to fit residues: 2.7692 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 : 0.057 ------------------------------------------------------------------------------- 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: 0.5980 chunk 89 optimal weight: 5.9990 chunk 157 optimal weight: 0.6980 chunk 394 optimal weight: 4.9990 chunk 416 optimal weight: 0.0070 chunk 401 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 468 optimal weight: 9.9990 chunk 306 optimal weight: 5.9990 chunk 389 optimal weight: 0.2980 chunk 110 optimal weight: 4.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 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 = 0.4563 r_free = 0.4563 target = 0.147491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.122545 restraints weight = 11506.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.125312 restraints weight = 8642.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.127460 restraints weight = 6926.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.129181 restraints weight = 5831.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.130242 restraints weight = 5083.321| |-----------------------------------------------------------------------------| r_work (final): 0.4317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4825 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 44400 Z= 0.119 Angle : 0.686 8.684 59616 Z= 0.351 Chirality : 0.046 0.144 6576 Planarity : 0.005 0.043 7584 Dihedral : 5.559 20.449 5808 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.50 % Allowed : 0.50 % 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 are not related in a simple way. whole: -3.28 (0.10), residues: 5208 helix: -0.02 (0.19), residues: 720 sheet: -1.82 (0.11), residues: 1896 loop : -3.15 (0.10), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 208 TYR 0.011 0.002 TYR C 156 PHE 0.009 0.001 PHE I 113 TRP 0.001 0.000 TRP K 69 HIS 0.008 0.001 HIS M 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (44400) covalent geometry : angle 0.68624 / 0.35 (59616) hydrogen bonds : bond 0.03137 / 2.04 ( 1272) hydrogen bonds : angle 6.99406 / 4.91 ( 3312) *********************** REFINEMENT MACRO_CYCLE 9 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 34 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 26 ARG cc_start: 0.8503 (pmt-80) cc_final: 0.5107 (tmt170) REVERT: H 176 TYR cc_start: 0.7773 (t80) cc_final: 0.7143 (m-80) REVERT: H 199 ILE cc_start: 0.8637 (mm) cc_final: 0.8211 (pt) REVERT: H 217 LYS cc_start: 0.7689 (mmpt) cc_final: 0.7339 (tptp) outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.0812 time to fit residues: 3.1403 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 : 0.078 ------------------------------------------------------------------------------- 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: 0.0670 chunk 382 optimal weight: 0.0870 chunk 383 optimal weight: 0.7980 chunk 316 optimal weight: 0.0040 chunk 260 optimal weight: 0.1980 chunk 66 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 chunk 321 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 59 optimal weight: 0.0770 overall best weight: 0.0866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 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 = 0.4556 r_free = 0.4556 target = 0.146636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.132150 restraints weight = 10543.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.134233 restraints weight = 7890.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.135724 restraints weight = 6222.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.137041 restraints weight = 5145.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.137732 restraints weight = 4355.784| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4596 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 44400 Z= 0.129 Angle : 0.729 10.525 59616 Z= 0.371 Chirality : 0.047 0.176 6576 Planarity : 0.004 0.043 7584 Dihedral : 5.532 20.585 5808 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % 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 are not related in a simple way. whole: -3.42 (0.10), residues: 5208 helix: 0.17 (0.19), residues: 720 sheet: -2.03 (0.11), residues: 1800 loop : -3.22 (0.10), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 26 TYR 0.007 0.001 TYR V 156 PHE 0.012 0.001 PHE F 84 TRP 0.001 0.000 TRP K 179 HIS 0.006 0.001 HIS M 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (44400) covalent geometry : angle 0.72910 / 0.37 (59616) hydrogen bonds : bond 0.03072 / 2.01 ( 1272) hydrogen bonds : angle 6.92361 / 4.86 ( 3312) ********************** REFINEMENT MACRO_CYCLE 10 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 31 residues out of total 202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 25 VAL cc_start: 0.6450 (p) cc_final: 0.6042 (p) REVERT: O 26 ARG cc_start: 0.8572 (pmt-80) cc_final: 0.5660 (tmt170) REVERT: O 84 PHE cc_start: 0.6742 (t80) cc_final: 0.5377 (t80) REVERT: O 171 LYS cc_start: 0.7886 (mptt) cc_final: 0.7662 (mmtm) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0677 time to fit residues: 2.4550 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 : 0.075 ------------------------------------------------------------------------------- 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: 5.9990 chunk 177 optimal weight: 0.2980 chunk 169 optimal weight: 0.0980 chunk 276 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 517 optimal weight: 0.0060 chunk 487 optimal weight: 0.4980 chunk 11 optimal weight: 0.1980 chunk 414 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4531 r_free = 0.4531 target = 0.144385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.120439 restraints weight = 11409.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.123074 restraints weight = 8716.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.125359 restraints weight = 7010.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.127047 restraints weight = 5903.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.127985 restraints weight = 5133.808| |-----------------------------------------------------------------------------| r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4732 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 44400 Z= 0.134 Angle : 0.738 8.793 59616 Z= 0.380 Chirality : 0.047 0.171 6576 Planarity : 0.005 0.056 7584 Dihedral : 5.575 20.509 5808 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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 are not related in a simple way. whole: -3.36 (0.10), residues: 5208 helix: 0.18 (0.19), residues: 768 sheet: -2.03 (0.11), residues: 1800 loop : -3.20 (0.10), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 203 TYR 0.008 0.001 TYR T 156 PHE 0.014 0.001 PHE S 84 TRP 0.001 0.000 TRP M 179 HIS 0.007 0.001 HIS M 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (44400) covalent geometry : angle 0.73806 / 0.38 (59616) hydrogen bonds : bond 0.03299 / 2.13 ( 1272) hydrogen bonds : angle 7.23833 / 5.06 ( 3312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2607.50 seconds wall clock time: 48 minutes 11.53 seconds (2891.53 seconds total)