Starting phenix.real_space_refine on Tue Aug 26 19:20:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5leg_4042/08_2025/5leg_4042_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5leg_4042/08_2025/5leg_4042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5leg_4042/08_2025/5leg_4042_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5leg_4042/08_2025/5leg_4042_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5leg_4042/08_2025/5leg_4042.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5leg_4042/08_2025/5leg_4042.map" } resolution = 3.6 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= 1.048 sd= 8.826 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: 5 Type Number sf(0) Gaussians P 75 5.49 5 S 320 5.16 5 C 28050 2.51 5 N 5680 2.21 5 O 7230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41355 Number of models: 1 Model: "" Number of chains: 3 Chain: "1A" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "1P" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "1A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: 1B, 1C, 1D, 1E, 1F, 1G, 1H, 1I, 1J, 1K, 1L, 1M, 1N, 1O, 2A, 2B, 2C, 2D, 2E, 2F, 2G, 2H, 2I, 2J, 2K, 2L, 2M, 2N, 2O, 3A, 3B, 3C, 3D, 3E, 3F, 3G, 3H, 3I, 3J, 3K, 3L, 3M, 3N, 3O, 4A, 4B, 4C, 4D, 4E, 4F, 4G, 4H, 4I, 4J, 4K, 4L, 4M, 4N, 4O, 5A, 5B, 5C, 5D, 5E, 5F, 5G, 5H, 5I, 5J, 5K, 5L, 5M, 5N, 5O, 2P, 3P, 4P, 5P Time building chain proxies: 2.96, per 1000 atoms: 0.07 Number of scatterers: 41355 At special positions: 0 Unit cell: (100.1, 100.1, 244.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 320 16.00 P 75 15.00 O 7230 8.00 N 5680 7.00 C 28050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS1B 24 " - pdb=" SG CYS1B 24 " distance=0.00 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9120 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 0 sheets defined 66.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain '1A' and resid 10 through 16 Processing helix chain '1A' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE1A 26 " --> pdb=" O MET1A 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU1A 29 " --> pdb=" O ILE1A 25 " (cutoff:3.500A) Processing helix chain '1A' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1A 51 " --> pdb=" O LEU1A 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL1A 52 " --> pdb=" O GLY1A 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1A 61 " --> pdb=" O THR1A 57 " (cutoff:3.500A) Processing helix chain '1B' and resid 10 through 16 Processing helix chain '1B' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE1B 26 " --> pdb=" O MET1B 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1B 29 " --> pdb=" O ILE1B 25 " (cutoff:3.500A) Processing helix chain '1B' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1B 51 " --> pdb=" O LEU1B 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL1B 52 " --> pdb=" O GLY1B 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1B 61 " --> pdb=" O THR1B 57 " (cutoff:3.500A) Processing helix chain '1C' and resid 10 through 16 Processing helix chain '1C' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE1C 26 " --> pdb=" O MET1C 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU1C 29 " --> pdb=" O ILE1C 25 " (cutoff:3.500A) Processing helix chain '1C' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1C 51 " --> pdb=" O LEU1C 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL1C 52 " --> pdb=" O GLY1C 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1C 61 " --> pdb=" O THR1C 57 " (cutoff:3.500A) Processing helix chain '1D' and resid 10 through 16 Processing helix chain '1D' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE1D 26 " --> pdb=" O MET1D 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1D 29 " --> pdb=" O ILE1D 25 " (cutoff:3.500A) Processing helix chain '1D' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1D 51 " --> pdb=" O LEU1D 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1D 52 " --> pdb=" O GLY1D 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR1D 61 " --> pdb=" O THR1D 57 " (cutoff:3.500A) Processing helix chain '1E' and resid 10 through 16 Processing helix chain '1E' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE1E 26 " --> pdb=" O MET1E 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1E 29 " --> pdb=" O ILE1E 25 " (cutoff:3.500A) Processing helix chain '1E' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1E 51 " --> pdb=" O LEU1E 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1E 52 " --> pdb=" O GLY1E 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1E 61 " --> pdb=" O THR1E 57 " (cutoff:3.500A) Processing helix chain '1F' and resid 10 through 16 Processing helix chain '1F' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE1F 26 " --> pdb=" O MET1F 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1F 29 " --> pdb=" O ILE1F 25 " (cutoff:3.500A) Processing helix chain '1F' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1F 51 " --> pdb=" O LEU1F 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1F 52 " --> pdb=" O GLY1F 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1F 61 " --> pdb=" O THR1F 57 " (cutoff:3.500A) Processing helix chain '1G' and resid 10 through 16 Processing helix chain '1G' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE1G 26 " --> pdb=" O MET1G 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1G 29 " --> pdb=" O ILE1G 25 " (cutoff:3.500A) Processing helix chain '1G' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1G 51 " --> pdb=" O LEU1G 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1G 52 " --> pdb=" O GLY1G 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1G 61 " --> pdb=" O THR1G 57 " (cutoff:3.500A) Processing helix chain '1H' and resid 10 through 16 Processing helix chain '1H' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE1H 26 " --> pdb=" O MET1H 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1H 29 " --> pdb=" O ILE1H 25 " (cutoff:3.500A) Processing helix chain '1H' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL1H 51 " --> pdb=" O LEU1H 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1H 52 " --> pdb=" O GLY1H 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1H 61 " --> pdb=" O THR1H 57 " (cutoff:3.500A) Processing helix chain '1I' and resid 10 through 16 Processing helix chain '1I' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE1I 26 " --> pdb=" O MET1I 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1I 29 " --> pdb=" O ILE1I 25 " (cutoff:3.500A) Processing helix chain '1I' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL1I 51 " --> pdb=" O LEU1I 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1I 52 " --> pdb=" O GLY1I 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1I 61 " --> pdb=" O THR1I 57 " (cutoff:3.500A) Processing helix chain '1J' and resid 10 through 16 Processing helix chain '1J' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE1J 26 " --> pdb=" O MET1J 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1J 29 " --> pdb=" O ILE1J 25 " (cutoff:3.500A) Processing helix chain '1J' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1J 51 " --> pdb=" O LEU1J 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1J 52 " --> pdb=" O GLY1J 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1J 61 " --> pdb=" O THR1J 57 " (cutoff:3.500A) Processing helix chain '1K' and resid 10 through 16 Processing helix chain '1K' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE1K 26 " --> pdb=" O MET1K 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1K 29 " --> pdb=" O ILE1K 25 " (cutoff:3.500A) Processing helix chain '1K' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1K 51 " --> pdb=" O LEU1K 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1K 52 " --> pdb=" O GLY1K 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR1K 61 " --> pdb=" O THR1K 57 " (cutoff:3.500A) Processing helix chain '1L' and resid 10 through 16 Processing helix chain '1L' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE1L 26 " --> pdb=" O MET1L 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1L 29 " --> pdb=" O ILE1L 25 " (cutoff:3.500A) Processing helix chain '1L' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1L 51 " --> pdb=" O LEU1L 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1L 52 " --> pdb=" O GLY1L 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1L 61 " --> pdb=" O THR1L 57 " (cutoff:3.500A) Processing helix chain '1M' and resid 10 through 16 Processing helix chain '1M' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE1M 26 " --> pdb=" O MET1M 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1M 29 " --> pdb=" O ILE1M 25 " (cutoff:3.500A) Processing helix chain '1M' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL1M 51 " --> pdb=" O LEU1M 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL1M 52 " --> pdb=" O GLY1M 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1M 61 " --> pdb=" O THR1M 57 " (cutoff:3.500A) Processing helix chain '1N' and resid 10 through 16 Processing helix chain '1N' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE1N 26 " --> pdb=" O MET1N 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1N 29 " --> pdb=" O ILE1N 25 " (cutoff:3.500A) Processing helix chain '1N' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1N 51 " --> pdb=" O LEU1N 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1N 52 " --> pdb=" O GLY1N 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1N 61 " --> pdb=" O THR1N 57 " (cutoff:3.500A) Processing helix chain '1O' and resid 10 through 16 Processing helix chain '1O' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE1O 26 " --> pdb=" O MET1O 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU1O 29 " --> pdb=" O ILE1O 25 " (cutoff:3.500A) Processing helix chain '1O' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1O 51 " --> pdb=" O LEU1O 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1O 52 " --> pdb=" O GLY1O 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR1O 61 " --> pdb=" O THR1O 57 " (cutoff:3.500A) Processing helix chain '1P' and resid 10 through 16 Processing helix chain '1P' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE1P 26 " --> pdb=" O MET1P 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1P 29 " --> pdb=" O ILE1P 25 " (cutoff:3.500A) Processing helix chain '1P' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL1P 51 " --> pdb=" O LEU1P 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1P 52 " --> pdb=" O GLY1P 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR1P 61 " --> pdb=" O THR1P 57 " (cutoff:3.500A) Processing helix chain '2A' and resid 10 through 16 Processing helix chain '2A' and resid 20 through 39 removed outlier: 3.528A pdb=" N ILE2A 26 " --> pdb=" O MET2A 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU2A 29 " --> pdb=" O ILE2A 25 " (cutoff:3.500A) Processing helix chain '2A' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2A 51 " --> pdb=" O LEU2A 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL2A 52 " --> pdb=" O GLY2A 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR2A 61 " --> pdb=" O THR2A 57 " (cutoff:3.500A) Processing helix chain '2B' and resid 10 through 16 Processing helix chain '2B' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE2B 26 " --> pdb=" O MET2B 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU2B 29 " --> pdb=" O ILE2B 25 " (cutoff:3.500A) Processing helix chain '2B' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2B 51 " --> pdb=" O LEU2B 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL2B 52 " --> pdb=" O GLY2B 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2B 61 " --> pdb=" O THR2B 57 " (cutoff:3.500A) Processing helix chain '2C' and resid 10 through 16 Processing helix chain '2C' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE2C 26 " --> pdb=" O MET2C 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU2C 29 " --> pdb=" O ILE2C 25 " (cutoff:3.500A) Processing helix chain '2C' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2C 51 " --> pdb=" O LEU2C 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL2C 52 " --> pdb=" O GLY2C 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2C 61 " --> pdb=" O THR2C 57 " (cutoff:3.500A) Processing helix chain '2D' and resid 10 through 16 Processing helix chain '2D' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE2D 26 " --> pdb=" O MET2D 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU2D 29 " --> pdb=" O ILE2D 25 " (cutoff:3.500A) Processing helix chain '2D' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2D 51 " --> pdb=" O LEU2D 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL2D 52 " --> pdb=" O GLY2D 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2D 61 " --> pdb=" O THR2D 57 " (cutoff:3.500A) Processing helix chain '2E' and resid 10 through 16 Processing helix chain '2E' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE2E 26 " --> pdb=" O MET2E 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU2E 29 " --> pdb=" O ILE2E 25 " (cutoff:3.500A) Processing helix chain '2E' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2E 51 " --> pdb=" O LEU2E 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL2E 52 " --> pdb=" O GLY2E 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2E 61 " --> pdb=" O THR2E 57 " (cutoff:3.500A) Processing helix chain '2F' and resid 10 through 16 Processing helix chain '2F' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE2F 26 " --> pdb=" O MET2F 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU2F 29 " --> pdb=" O ILE2F 25 " (cutoff:3.500A) Processing helix chain '2F' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2F 51 " --> pdb=" O LEU2F 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL2F 52 " --> pdb=" O GLY2F 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2F 61 " --> pdb=" O THR2F 57 " (cutoff:3.500A) Processing helix chain '2G' and resid 10 through 16 Processing helix chain '2G' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE2G 26 " --> pdb=" O MET2G 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU2G 29 " --> pdb=" O ILE2G 25 " (cutoff:3.500A) Processing helix chain '2G' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2G 51 " --> pdb=" O LEU2G 47 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL2G 52 " --> pdb=" O GLY2G 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2G 61 " --> pdb=" O THR2G 57 " (cutoff:3.500A) Processing helix chain '2H' and resid 10 through 16 Processing helix chain '2H' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE2H 26 " --> pdb=" O MET2H 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU2H 29 " --> pdb=" O ILE2H 25 " (cutoff:3.500A) Processing helix chain '2H' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL2H 51 " --> pdb=" O LEU2H 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL2H 52 " --> pdb=" O GLY2H 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR2H 61 " --> pdb=" O THR2H 57 " (cutoff:3.500A) Processing helix chain '2I' and resid 10 through 16 Processing helix chain '2I' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE2I 26 " --> pdb=" O MET2I 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU2I 29 " --> pdb=" O ILE2I 25 " (cutoff:3.500A) Processing helix chain '2I' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2I 51 " --> pdb=" O LEU2I 47 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL2I 52 " --> pdb=" O GLY2I 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2I 61 " --> pdb=" O THR2I 57 " (cutoff:3.500A) Processing helix chain '2J' and resid 10 through 16 Processing helix chain '2J' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE2J 26 " --> pdb=" O MET2J 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU2J 29 " --> pdb=" O ILE2J 25 " (cutoff:3.500A) Processing helix chain '2J' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2J 51 " --> pdb=" O LEU2J 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL2J 52 " --> pdb=" O GLY2J 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR2J 61 " --> pdb=" O THR2J 57 " (cutoff:3.500A) Processing helix chain '2K' and resid 10 through 16 Processing helix chain '2K' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE2K 26 " --> pdb=" O MET2K 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU2K 29 " --> pdb=" O ILE2K 25 " (cutoff:3.500A) Processing helix chain '2K' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2K 51 " --> pdb=" O LEU2K 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL2K 52 " --> pdb=" O GLY2K 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR2K 61 " --> pdb=" O THR2K 57 " (cutoff:3.500A) Processing helix chain '2L' and resid 10 through 16 Processing helix chain '2L' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE2L 26 " --> pdb=" O MET2L 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU2L 29 " --> pdb=" O ILE2L 25 " (cutoff:3.500A) Processing helix chain '2L' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL2L 51 " --> pdb=" O LEU2L 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL2L 52 " --> pdb=" O GLY2L 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2L 61 " --> pdb=" O THR2L 57 " (cutoff:3.500A) Processing helix chain '2M' and resid 10 through 16 Processing helix chain '2M' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE2M 26 " --> pdb=" O MET2M 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU2M 29 " --> pdb=" O ILE2M 25 " (cutoff:3.500A) Processing helix chain '2M' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL2M 51 " --> pdb=" O LEU2M 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL2M 52 " --> pdb=" O GLY2M 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2M 61 " --> pdb=" O THR2M 57 " (cutoff:3.500A) Processing helix chain '2N' and resid 10 through 16 Processing helix chain '2N' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE2N 26 " --> pdb=" O MET2N 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU2N 29 " --> pdb=" O ILE2N 25 " (cutoff:3.500A) Processing helix chain '2N' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL2N 51 " --> pdb=" O LEU2N 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL2N 52 " --> pdb=" O GLY2N 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR2N 61 " --> pdb=" O THR2N 57 " (cutoff:3.500A) Processing helix chain '2O' and resid 10 through 16 Processing helix chain '2O' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE2O 26 " --> pdb=" O MET2O 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU2O 29 " --> pdb=" O ILE2O 25 " (cutoff:3.500A) Processing helix chain '2O' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL2O 51 " --> pdb=" O LEU2O 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL2O 52 " --> pdb=" O GLY2O 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR2O 61 " --> pdb=" O THR2O 57 " (cutoff:3.500A) Processing helix chain '2P' and resid 10 through 16 Processing helix chain '2P' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE2P 26 " --> pdb=" O MET2P 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU2P 29 " --> pdb=" O ILE2P 25 " (cutoff:3.500A) Processing helix chain '2P' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL2P 51 " --> pdb=" O LEU2P 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL2P 52 " --> pdb=" O GLY2P 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2P 61 " --> pdb=" O THR2P 57 " (cutoff:3.500A) Processing helix chain '3A' and resid 10 through 16 Processing helix chain '3A' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE3A 26 " --> pdb=" O MET3A 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU3A 29 " --> pdb=" O ILE3A 25 " (cutoff:3.500A) Processing helix chain '3A' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL3A 51 " --> pdb=" O LEU3A 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL3A 52 " --> pdb=" O GLY3A 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3A 61 " --> pdb=" O THR3A 57 " (cutoff:3.500A) Processing helix chain '3B' and resid 10 through 16 Processing helix chain '3B' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE3B 26 " --> pdb=" O MET3B 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU3B 29 " --> pdb=" O ILE3B 25 " (cutoff:3.500A) Processing helix chain '3B' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL3B 51 " --> pdb=" O LEU3B 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL3B 52 " --> pdb=" O GLY3B 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR3B 61 " --> pdb=" O THR3B 57 " (cutoff:3.500A) Processing helix chain '3C' and resid 10 through 16 Processing helix chain '3C' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE3C 26 " --> pdb=" O MET3C 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU3C 29 " --> pdb=" O ILE3C 25 " (cutoff:3.500A) Processing helix chain '3C' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL3C 51 " --> pdb=" O LEU3C 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL3C 52 " --> pdb=" O GLY3C 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3C 61 " --> pdb=" O THR3C 57 " (cutoff:3.500A) Processing helix chain '3D' and resid 10 through 16 Processing helix chain '3D' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE3D 26 " --> pdb=" O MET3D 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU3D 29 " --> pdb=" O ILE3D 25 " (cutoff:3.500A) Processing helix chain '3D' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL3D 51 " --> pdb=" O LEU3D 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL3D 52 " --> pdb=" O GLY3D 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3D 61 " --> pdb=" O THR3D 57 " (cutoff:3.500A) Processing helix chain '3E' and resid 10 through 16 Processing helix chain '3E' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE3E 26 " --> pdb=" O MET3E 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU3E 29 " --> pdb=" O ILE3E 25 " (cutoff:3.500A) Processing helix chain '3E' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL3E 51 " --> pdb=" O LEU3E 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL3E 52 " --> pdb=" O GLY3E 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3E 61 " --> pdb=" O THR3E 57 " (cutoff:3.500A) Processing helix chain '3F' and resid 10 through 16 Processing helix chain '3F' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE3F 26 " --> pdb=" O MET3F 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU3F 29 " --> pdb=" O ILE3F 25 " (cutoff:3.500A) Processing helix chain '3F' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL3F 51 " --> pdb=" O LEU3F 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL3F 52 " --> pdb=" O GLY3F 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR3F 61 " --> pdb=" O THR3F 57 " (cutoff:3.500A) Processing helix chain '3G' and resid 10 through 16 Processing helix chain '3G' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE3G 26 " --> pdb=" O MET3G 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU3G 29 " --> pdb=" O ILE3G 25 " (cutoff:3.500A) Processing helix chain '3G' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL3G 51 " --> pdb=" O LEU3G 47 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL3G 52 " --> pdb=" O GLY3G 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3G 61 " --> pdb=" O THR3G 57 " (cutoff:3.500A) Processing helix chain '3H' and resid 10 through 16 Processing helix chain '3H' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE3H 26 " --> pdb=" O MET3H 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU3H 29 " --> pdb=" O ILE3H 25 " (cutoff:3.500A) Processing helix chain '3H' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL3H 51 " --> pdb=" O LEU3H 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL3H 52 " --> pdb=" O GLY3H 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3H 61 " --> pdb=" O THR3H 57 " (cutoff:3.500A) Processing helix chain '3I' and resid 10 through 16 Processing helix chain '3I' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE3I 26 " --> pdb=" O MET3I 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU3I 29 " --> pdb=" O ILE3I 25 " (cutoff:3.500A) Processing helix chain '3I' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL3I 51 " --> pdb=" O LEU3I 47 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL3I 52 " --> pdb=" O GLY3I 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3I 61 " --> pdb=" O THR3I 57 " (cutoff:3.500A) Processing helix chain '3J' and resid 10 through 16 Processing helix chain '3J' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE3J 26 " --> pdb=" O MET3J 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU3J 29 " --> pdb=" O ILE3J 25 " (cutoff:3.500A) Processing helix chain '3J' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL3J 51 " --> pdb=" O LEU3J 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL3J 52 " --> pdb=" O GLY3J 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3J 61 " --> pdb=" O THR3J 57 " (cutoff:3.500A) Processing helix chain '3K' and resid 10 through 16 Processing helix chain '3K' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE3K 26 " --> pdb=" O MET3K 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU3K 29 " --> pdb=" O ILE3K 25 " (cutoff:3.500A) Processing helix chain '3K' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL3K 51 " --> pdb=" O LEU3K 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL3K 52 " --> pdb=" O GLY3K 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR3K 61 " --> pdb=" O THR3K 57 " (cutoff:3.500A) Processing helix chain '3L' and resid 10 through 16 Processing helix chain '3L' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE3L 26 " --> pdb=" O MET3L 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU3L 29 " --> pdb=" O ILE3L 25 " (cutoff:3.500A) Processing helix chain '3L' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL3L 51 " --> pdb=" O LEU3L 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL3L 52 " --> pdb=" O GLY3L 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3L 61 " --> pdb=" O THR3L 57 " (cutoff:3.500A) Processing helix chain '3M' and resid 10 through 16 Processing helix chain '3M' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE3M 26 " --> pdb=" O MET3M 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU3M 29 " --> pdb=" O ILE3M 25 " (cutoff:3.500A) Processing helix chain '3M' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL3M 51 " --> pdb=" O LEU3M 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL3M 52 " --> pdb=" O GLY3M 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR3M 61 " --> pdb=" O THR3M 57 " (cutoff:3.500A) Processing helix chain '3N' and resid 10 through 16 Processing helix chain '3N' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE3N 26 " --> pdb=" O MET3N 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU3N 29 " --> pdb=" O ILE3N 25 " (cutoff:3.500A) Processing helix chain '3N' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL3N 51 " --> pdb=" O LEU3N 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL3N 52 " --> pdb=" O GLY3N 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR3N 61 " --> pdb=" O THR3N 57 " (cutoff:3.500A) Processing helix chain '3O' and resid 10 through 16 Processing helix chain '3O' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE3O 26 " --> pdb=" O MET3O 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU3O 29 " --> pdb=" O ILE3O 25 " (cutoff:3.500A) Processing helix chain '3O' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL3O 51 " --> pdb=" O LEU3O 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL3O 52 " --> pdb=" O GLY3O 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR3O 61 " --> pdb=" O THR3O 57 " (cutoff:3.500A) Processing helix chain '3P' and resid 10 through 16 Processing helix chain '3P' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE3P 26 " --> pdb=" O MET3P 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU3P 29 " --> pdb=" O ILE3P 25 " (cutoff:3.500A) Processing helix chain '3P' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL3P 51 " --> pdb=" O LEU3P 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL3P 52 " --> pdb=" O GLY3P 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3P 61 " --> pdb=" O THR3P 57 " (cutoff:3.500A) Processing helix chain '4A' and resid 10 through 16 Processing helix chain '4A' and resid 20 through 39 removed outlier: 3.528A pdb=" N ILE4A 26 " --> pdb=" O MET4A 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU4A 29 " --> pdb=" O ILE4A 25 " (cutoff:3.500A) Processing helix chain '4A' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4A 51 " --> pdb=" O LEU4A 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL4A 52 " --> pdb=" O GLY4A 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4A 61 " --> pdb=" O THR4A 57 " (cutoff:3.500A) Processing helix chain '4B' and resid 10 through 16 Processing helix chain '4B' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE4B 26 " --> pdb=" O MET4B 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU4B 29 " --> pdb=" O ILE4B 25 " (cutoff:3.500A) Processing helix chain '4B' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL4B 51 " --> pdb=" O LEU4B 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL4B 52 " --> pdb=" O GLY4B 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4B 61 " --> pdb=" O THR4B 57 " (cutoff:3.500A) Processing helix chain '4C' and resid 10 through 16 Processing helix chain '4C' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE4C 26 " --> pdb=" O MET4C 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU4C 29 " --> pdb=" O ILE4C 25 " (cutoff:3.500A) Processing helix chain '4C' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4C 51 " --> pdb=" O LEU4C 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL4C 52 " --> pdb=" O GLY4C 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4C 61 " --> pdb=" O THR4C 57 " (cutoff:3.500A) Processing helix chain '4D' and resid 10 through 16 Processing helix chain '4D' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE4D 26 " --> pdb=" O MET4D 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU4D 29 " --> pdb=" O ILE4D 25 " (cutoff:3.500A) Processing helix chain '4D' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL4D 51 " --> pdb=" O LEU4D 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL4D 52 " --> pdb=" O GLY4D 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4D 61 " --> pdb=" O THR4D 57 " (cutoff:3.500A) Processing helix chain '4E' and resid 10 through 16 Processing helix chain '4E' and resid 20 through 39 removed outlier: 3.528A pdb=" N ILE4E 26 " --> pdb=" O MET4E 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU4E 29 " --> pdb=" O ILE4E 25 " (cutoff:3.500A) Processing helix chain '4E' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4E 51 " --> pdb=" O LEU4E 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL4E 52 " --> pdb=" O GLY4E 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR4E 61 " --> pdb=" O THR4E 57 " (cutoff:3.500A) Processing helix chain '4F' and resid 10 through 16 Processing helix chain '4F' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE4F 26 " --> pdb=" O MET4F 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU4F 29 " --> pdb=" O ILE4F 25 " (cutoff:3.500A) Processing helix chain '4F' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4F 51 " --> pdb=" O LEU4F 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL4F 52 " --> pdb=" O GLY4F 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4F 61 " --> pdb=" O THR4F 57 " (cutoff:3.500A) Processing helix chain '4G' and resid 10 through 16 Processing helix chain '4G' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE4G 26 " --> pdb=" O MET4G 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU4G 29 " --> pdb=" O ILE4G 25 " (cutoff:3.500A) Processing helix chain '4G' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL4G 51 " --> pdb=" O LEU4G 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL4G 52 " --> pdb=" O GLY4G 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4G 61 " --> pdb=" O THR4G 57 " (cutoff:3.500A) Processing helix chain '4H' and resid 10 through 16 Processing helix chain '4H' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE4H 26 " --> pdb=" O MET4H 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU4H 29 " --> pdb=" O ILE4H 25 " (cutoff:3.500A) Processing helix chain '4H' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4H 51 " --> pdb=" O LEU4H 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL4H 52 " --> pdb=" O GLY4H 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4H 61 " --> pdb=" O THR4H 57 " (cutoff:3.500A) Processing helix chain '4I' and resid 10 through 16 Processing helix chain '4I' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE4I 26 " --> pdb=" O MET4I 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU4I 29 " --> pdb=" O ILE4I 25 " (cutoff:3.500A) Processing helix chain '4I' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL4I 51 " --> pdb=" O LEU4I 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL4I 52 " --> pdb=" O GLY4I 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4I 61 " --> pdb=" O THR4I 57 " (cutoff:3.500A) Processing helix chain '4J' and resid 10 through 16 Processing helix chain '4J' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE4J 26 " --> pdb=" O MET4J 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU4J 29 " --> pdb=" O ILE4J 25 " (cutoff:3.500A) Processing helix chain '4J' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL4J 51 " --> pdb=" O LEU4J 47 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL4J 52 " --> pdb=" O GLY4J 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4J 61 " --> pdb=" O THR4J 57 " (cutoff:3.500A) Processing helix chain '4K' and resid 10 through 16 Processing helix chain '4K' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE4K 26 " --> pdb=" O MET4K 22 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU4K 29 " --> pdb=" O ILE4K 25 " (cutoff:3.500A) Processing helix chain '4K' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4K 51 " --> pdb=" O LEU4K 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL4K 52 " --> pdb=" O GLY4K 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4K 61 " --> pdb=" O THR4K 57 " (cutoff:3.500A) Processing helix chain '4L' and resid 10 through 16 Processing helix chain '4L' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE4L 26 " --> pdb=" O MET4L 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU4L 29 " --> pdb=" O ILE4L 25 " (cutoff:3.500A) Processing helix chain '4L' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4L 51 " --> pdb=" O LEU4L 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL4L 52 " --> pdb=" O GLY4L 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4L 61 " --> pdb=" O THR4L 57 " (cutoff:3.500A) Processing helix chain '4M' and resid 10 through 16 Processing helix chain '4M' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE4M 26 " --> pdb=" O MET4M 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU4M 29 " --> pdb=" O ILE4M 25 " (cutoff:3.500A) Processing helix chain '4M' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4M 51 " --> pdb=" O LEU4M 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL4M 52 " --> pdb=" O GLY4M 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4M 61 " --> pdb=" O THR4M 57 " (cutoff:3.500A) Processing helix chain '4N' and resid 10 through 16 Processing helix chain '4N' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE4N 26 " --> pdb=" O MET4N 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU4N 29 " --> pdb=" O ILE4N 25 " (cutoff:3.500A) Processing helix chain '4N' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4N 51 " --> pdb=" O LEU4N 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL4N 52 " --> pdb=" O GLY4N 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR4N 61 " --> pdb=" O THR4N 57 " (cutoff:3.500A) Processing helix chain '4O' and resid 10 through 16 Processing helix chain '4O' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE4O 26 " --> pdb=" O MET4O 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU4O 29 " --> pdb=" O ILE4O 25 " (cutoff:3.500A) Processing helix chain '4O' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL4O 51 " --> pdb=" O LEU4O 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL4O 52 " --> pdb=" O GLY4O 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4O 61 " --> pdb=" O THR4O 57 " (cutoff:3.500A) Processing helix chain '4P' and resid 10 through 16 Processing helix chain '4P' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE4P 26 " --> pdb=" O MET4P 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU4P 29 " --> pdb=" O ILE4P 25 " (cutoff:3.500A) Processing helix chain '4P' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4P 51 " --> pdb=" O LEU4P 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL4P 52 " --> pdb=" O GLY4P 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4P 61 " --> pdb=" O THR4P 57 " (cutoff:3.500A) Processing helix chain '5A' and resid 10 through 16 Processing helix chain '5A' and resid 20 through 39 removed outlier: 3.528A pdb=" N ILE5A 26 " --> pdb=" O MET5A 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5A 29 " --> pdb=" O ILE5A 25 " (cutoff:3.500A) Processing helix chain '5A' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5A 51 " --> pdb=" O LEU5A 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL5A 52 " --> pdb=" O GLY5A 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5A 61 " --> pdb=" O THR5A 57 " (cutoff:3.500A) Processing helix chain '5B' and resid 10 through 16 Processing helix chain '5B' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE5B 26 " --> pdb=" O MET5B 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU5B 29 " --> pdb=" O ILE5B 25 " (cutoff:3.500A) Processing helix chain '5B' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5B 51 " --> pdb=" O LEU5B 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL5B 52 " --> pdb=" O GLY5B 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5B 61 " --> pdb=" O THR5B 57 " (cutoff:3.500A) Processing helix chain '5C' and resid 10 through 16 Processing helix chain '5C' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE5C 26 " --> pdb=" O MET5C 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU5C 29 " --> pdb=" O ILE5C 25 " (cutoff:3.500A) Processing helix chain '5C' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5C 51 " --> pdb=" O LEU5C 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL5C 52 " --> pdb=" O GLY5C 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR5C 61 " --> pdb=" O THR5C 57 " (cutoff:3.500A) Processing helix chain '5D' and resid 10 through 16 Processing helix chain '5D' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE5D 26 " --> pdb=" O MET5D 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5D 29 " --> pdb=" O ILE5D 25 " (cutoff:3.500A) Processing helix chain '5D' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5D 51 " --> pdb=" O LEU5D 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL5D 52 " --> pdb=" O GLY5D 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5D 61 " --> pdb=" O THR5D 57 " (cutoff:3.500A) Processing helix chain '5E' and resid 10 through 16 Processing helix chain '5E' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE5E 26 " --> pdb=" O MET5E 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5E 29 " --> pdb=" O ILE5E 25 " (cutoff:3.500A) Processing helix chain '5E' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL5E 51 " --> pdb=" O LEU5E 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL5E 52 " --> pdb=" O GLY5E 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR5E 61 " --> pdb=" O THR5E 57 " (cutoff:3.500A) Processing helix chain '5F' and resid 10 through 16 Processing helix chain '5F' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE5F 26 " --> pdb=" O MET5F 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5F 29 " --> pdb=" O ILE5F 25 " (cutoff:3.500A) Processing helix chain '5F' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5F 51 " --> pdb=" O LEU5F 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL5F 52 " --> pdb=" O GLY5F 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR5F 61 " --> pdb=" O THR5F 57 " (cutoff:3.500A) Processing helix chain '5G' and resid 10 through 16 Processing helix chain '5G' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE5G 26 " --> pdb=" O MET5G 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5G 29 " --> pdb=" O ILE5G 25 " (cutoff:3.500A) Processing helix chain '5G' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5G 51 " --> pdb=" O LEU5G 47 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL5G 52 " --> pdb=" O GLY5G 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5G 61 " --> pdb=" O THR5G 57 " (cutoff:3.500A) Processing helix chain '5H' and resid 10 through 16 Processing helix chain '5H' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE5H 26 " --> pdb=" O MET5H 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5H 29 " --> pdb=" O ILE5H 25 " (cutoff:3.500A) Processing helix chain '5H' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL5H 51 " --> pdb=" O LEU5H 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL5H 52 " --> pdb=" O GLY5H 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5H 61 " --> pdb=" O THR5H 57 " (cutoff:3.500A) Processing helix chain '5I' and resid 10 through 16 Processing helix chain '5I' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE5I 26 " --> pdb=" O MET5I 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5I 29 " --> pdb=" O ILE5I 25 " (cutoff:3.500A) Processing helix chain '5I' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL5I 51 " --> pdb=" O LEU5I 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL5I 52 " --> pdb=" O GLY5I 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5I 61 " --> pdb=" O THR5I 57 " (cutoff:3.500A) Processing helix chain '5J' and resid 10 through 16 Processing helix chain '5J' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE5J 26 " --> pdb=" O MET5J 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5J 29 " --> pdb=" O ILE5J 25 " (cutoff:3.500A) Processing helix chain '5J' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL5J 51 " --> pdb=" O LEU5J 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL5J 52 " --> pdb=" O GLY5J 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR5J 61 " --> pdb=" O THR5J 57 " (cutoff:3.500A) Processing helix chain '5K' and resid 10 through 16 Processing helix chain '5K' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE5K 26 " --> pdb=" O MET5K 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5K 29 " --> pdb=" O ILE5K 25 " (cutoff:3.500A) Processing helix chain '5K' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5K 51 " --> pdb=" O LEU5K 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL5K 52 " --> pdb=" O GLY5K 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR5K 61 " --> pdb=" O THR5K 57 " (cutoff:3.500A) Processing helix chain '5L' and resid 10 through 16 Processing helix chain '5L' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE5L 26 " --> pdb=" O MET5L 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5L 29 " --> pdb=" O ILE5L 25 " (cutoff:3.500A) Processing helix chain '5L' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5L 51 " --> pdb=" O LEU5L 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL5L 52 " --> pdb=" O GLY5L 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5L 61 " --> pdb=" O THR5L 57 " (cutoff:3.500A) Processing helix chain '5M' and resid 10 through 16 Processing helix chain '5M' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE5M 26 " --> pdb=" O MET5M 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU5M 29 " --> pdb=" O ILE5M 25 " (cutoff:3.500A) Processing helix chain '5M' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL5M 51 " --> pdb=" O LEU5M 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL5M 52 " --> pdb=" O GLY5M 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5M 61 " --> pdb=" O THR5M 57 " (cutoff:3.500A) Processing helix chain '5N' and resid 10 through 16 Processing helix chain '5N' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE5N 26 " --> pdb=" O MET5N 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU5N 29 " --> pdb=" O ILE5N 25 " (cutoff:3.500A) Processing helix chain '5N' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5N 51 " --> pdb=" O LEU5N 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL5N 52 " --> pdb=" O GLY5N 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5N 61 " --> pdb=" O THR5N 57 " (cutoff:3.500A) Processing helix chain '5O' and resid 10 through 16 Processing helix chain '5O' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE5O 26 " --> pdb=" O MET5O 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU5O 29 " --> pdb=" O ILE5O 25 " (cutoff:3.500A) Processing helix chain '5O' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5O 51 " --> pdb=" O LEU5O 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL5O 52 " --> pdb=" O GLY5O 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR5O 61 " --> pdb=" O THR5O 57 " (cutoff:3.500A) Processing helix chain '5P' and resid 10 through 16 Processing helix chain '5P' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE5P 26 " --> pdb=" O MET5P 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU5P 29 " --> pdb=" O ILE5P 25 " (cutoff:3.500A) Processing helix chain '5P' and resid 47 through 61 removed outlier: 3.512A pdb=" N VAL5P 51 " --> pdb=" O LEU5P 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL5P 52 " --> pdb=" O GLY5P 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5P 61 " --> pdb=" O THR5P 57 " (cutoff:3.500A) 2000 hydrogen bonds defined for protein. 6000 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: 5.87 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6099 1.32 - 1.44: 8736 1.44 - 1.56: 26055 1.56 - 1.68: 150 1.68 - 1.80: 560 Bond restraints: 41600 Sorted by residual: bond pdb=" C15 LHG4J 101 " pdb=" C16 LHG4J 101 " ideal model delta sigma weight residual 1.524 1.315 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C15 LHG2L 101 " pdb=" C16 LHG2L 101 " ideal model delta sigma weight residual 1.524 1.315 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C15 LHG4I 101 " pdb=" C16 LHG4I 101 " ideal model delta sigma weight residual 1.524 1.315 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C15 LHG3J 101 " pdb=" C16 LHG3J 101 " ideal model delta sigma weight residual 1.524 1.315 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C15 LHG5J 101 " pdb=" C16 LHG5J 101 " ideal model delta sigma weight residual 1.524 1.315 0.209 2.00e-02 2.50e+03 1.09e+02 ... (remaining 41595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 53930 2.72 - 5.44: 1095 5.44 - 8.16: 235 8.16 - 10.88: 0 10.88 - 13.60: 150 Bond angle restraints: 55410 Sorted by residual: angle pdb=" C15 LHG5L 101 " pdb=" C16 LHG5L 101 " pdb=" C17 LHG5L 101 " ideal model delta sigma weight residual 112.69 126.29 -13.60 3.00e+00 1.11e-01 2.06e+01 angle pdb=" C15 LHG4K 101 " pdb=" C16 LHG4K 101 " pdb=" C17 LHG4K 101 " ideal model delta sigma weight residual 112.69 126.27 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C15 LHG2K 101 " pdb=" C16 LHG2K 101 " pdb=" C17 LHG2K 101 " ideal model delta sigma weight residual 112.69 126.27 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C15 LHG2L 101 " pdb=" C16 LHG2L 101 " pdb=" C17 LHG2L 101 " ideal model delta sigma weight residual 112.69 126.25 -13.56 3.00e+00 1.11e-01 2.04e+01 angle pdb=" C15 LHG5K 101 " pdb=" C16 LHG5K 101 " pdb=" C17 LHG5K 101 " ideal model delta sigma weight residual 112.69 126.24 -13.55 3.00e+00 1.11e-01 2.04e+01 ... (remaining 55405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 23027 17.23 - 34.47: 1314 34.47 - 51.70: 896 51.70 - 68.94: 225 68.94 - 86.17: 315 Dihedral angle restraints: 25777 sinusoidal: 11617 harmonic: 14160 Sorted by residual: dihedral pdb=" CA GLY2C 7 " pdb=" C GLY2C 7 " pdb=" N LYS2C 8 " pdb=" CA LYS2C 8 " ideal model delta harmonic sigma weight residual 180.00 93.83 86.17 0 5.00e+00 4.00e-02 2.97e+02 dihedral pdb=" CA GLY3C 7 " pdb=" C GLY3C 7 " pdb=" N LYS3C 8 " pdb=" CA LYS3C 8 " ideal model delta harmonic sigma weight residual 180.00 93.88 86.12 0 5.00e+00 4.00e-02 2.97e+02 dihedral pdb=" CA GLY2B 7 " pdb=" C GLY2B 7 " pdb=" N LYS2B 8 " pdb=" CA LYS2B 8 " ideal model delta harmonic sigma weight residual 180.00 93.88 86.12 0 5.00e+00 4.00e-02 2.97e+02 ... (remaining 25774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3643 0.029 - 0.058: 2324 0.058 - 0.088: 1046 0.088 - 0.117: 97 0.117 - 0.146: 80 Chirality restraints: 7190 Sorted by residual: chirality pdb=" CB VAL5H 32 " pdb=" CA VAL5H 32 " pdb=" CG1 VAL5H 32 " pdb=" CG2 VAL5H 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CB VAL4F 32 " pdb=" CA VAL4F 32 " pdb=" CG1 VAL4F 32 " pdb=" CG2 VAL4F 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CB VAL3H 32 " pdb=" CA VAL3H 32 " pdb=" CG1 VAL3H 32 " pdb=" CG2 VAL3H 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 7187 not shown) Planarity restraints: 6070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET4L 23 " 0.003 2.00e-02 2.50e+03 6.31e-03 3.98e-01 pdb=" C MET4L 23 " -0.011 2.00e-02 2.50e+03 pdb=" O MET4L 23 " 0.004 2.00e-02 2.50e+03 pdb=" N CYS4L 24 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET5N 23 " 0.003 2.00e-02 2.50e+03 6.30e-03 3.97e-01 pdb=" C MET5N 23 " -0.011 2.00e-02 2.50e+03 pdb=" O MET5N 23 " 0.004 2.00e-02 2.50e+03 pdb=" N CYS5N 24 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET4A 23 " 0.003 2.00e-02 2.50e+03 6.27e-03 3.93e-01 pdb=" C MET4A 23 " -0.011 2.00e-02 2.50e+03 pdb=" O MET4A 23 " 0.004 2.00e-02 2.50e+03 pdb=" N CYS4A 24 " 0.004 2.00e-02 2.50e+03 ... (remaining 6067 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 15555 2.89 - 3.39: 42796 3.39 - 3.89: 67125 3.89 - 4.40: 74780 4.40 - 4.90: 119250 Nonbonded interactions: 319506 Sorted by model distance: nonbonded pdb=" O ASP4B 10 " pdb=" N ALA4B 13 " model vdw 2.383 3.120 nonbonded pdb=" O ASP5C 10 " pdb=" N ALA5C 13 " model vdw 2.383 3.120 nonbonded pdb=" O ASP4A 10 " pdb=" N ALA4A 13 " model vdw 2.383 3.120 nonbonded pdb=" O ASP3A 10 " pdb=" N ALA3A 13 " model vdw 2.383 3.120 nonbonded pdb=" O ASP2D 10 " pdb=" N ALA2D 13 " model vdw 2.384 3.120 ... (remaining 319501 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: 0.15 Found NCS groups: ncs_group { reference = chain '1A' selection = chain '1B' selection = chain '1C' selection = chain '1D' selection = chain '1E' selection = chain '1F' selection = chain '1G' selection = chain '1H' selection = chain '1I' selection = chain '1J' selection = chain '1K' selection = chain '1L' selection = chain '1M' selection = chain '1N' selection = chain '1O' selection = chain '2A' selection = chain '2B' selection = chain '2C' selection = chain '2D' selection = chain '2E' selection = chain '2F' selection = chain '2G' selection = chain '2H' selection = chain '2I' selection = chain '2J' selection = chain '2K' selection = chain '2L' selection = chain '2M' selection = chain '2N' selection = chain '2O' selection = chain '3A' selection = chain '3B' selection = chain '3C' selection = chain '3D' selection = chain '3E' selection = chain '3F' selection = chain '3G' selection = chain '3H' selection = chain '3I' selection = chain '3J' selection = chain '3K' selection = chain '3L' selection = chain '3M' selection = chain '3N' selection = chain '3O' selection = chain '4A' selection = chain '4B' selection = chain '4C' selection = chain '4D' selection = chain '4E' selection = chain '4F' selection = chain '4G' selection = chain '4H' selection = chain '4I' selection = chain '4J' selection = chain '4K' selection = chain '4L' selection = chain '4M' selection = chain '4N' selection = chain '4O' selection = chain '5A' selection = chain '5B' selection = chain '5C' selection = chain '5D' selection = chain '5E' selection = chain '5F' selection = chain '5G' selection = chain '5H' selection = chain '5I' selection = chain '5J' selection = chain '5K' selection = chain '5L' selection = chain '5M' selection = chain '5N' selection = chain '5O' } ncs_group { reference = chain '1P' selection = chain '2P' selection = chain '3P' selection = chain '4P' selection = chain '5P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 26.120 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 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 : 0.012 0.209 41600 Z= 0.599 Angle : 1.206 13.603 55411 Z= 0.569 Chirality : 0.043 0.146 7190 Planarity : 0.002 0.006 6070 Dihedral : 18.495 86.173 16655 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 44.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % 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 : 9.68 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.72 (0.09), residues: 4880 helix: -4.17 (0.05), residues: 3520 sheet: None (None), residues: 0 loop : -1.85 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG4N 39 TYR 0.005 0.002 TYR4N 37 PHE 0.010 0.001 PHE5P 62 Details of bonding type rmsd covalent geometry : bond 0.01248 (41600) covalent geometry : angle 1.20571 (55410) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.27467 ( 2000) hydrogen bonds : angle 10.65382 ( 6000) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2125 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2125 time to evaluate : 1.582 Fit side-chains REVERT: 1A 51 VAL cc_start: 0.8775 (m) cc_final: 0.8561 (t) REVERT: 1C 3 LEU cc_start: 0.7450 (tp) cc_final: 0.7238 (tp) REVERT: 1D 51 VAL cc_start: 0.8815 (m) cc_final: 0.8607 (t) REVERT: 1G 3 LEU cc_start: 0.7308 (tp) cc_final: 0.7031 (tp) REVERT: 1M 60 LEU cc_start: 0.8009 (mt) cc_final: 0.7717 (mt) REVERT: 2B 51 VAL cc_start: 0.8994 (m) cc_final: 0.8707 (t) REVERT: 2D 51 VAL cc_start: 0.8864 (m) cc_final: 0.8539 (t) REVERT: 3A 51 VAL cc_start: 0.8874 (m) cc_final: 0.8534 (t) REVERT: 3B 37 TYR cc_start: 0.8824 (t80) cc_final: 0.8559 (t80) REVERT: 3B 51 VAL cc_start: 0.9134 (m) cc_final: 0.8857 (t) REVERT: 4G 3 LEU cc_start: 0.7686 (tp) cc_final: 0.7461 (tp) REVERT: 4K 23 MET cc_start: 0.6289 (ttt) cc_final: 0.6024 (ttt) REVERT: 5B 20 PHE cc_start: 0.7913 (t80) cc_final: 0.7665 (t80) REVERT: 5B 29 GLU cc_start: 0.7265 (tp30) cc_final: 0.7045 (tp30) REVERT: 5C 3 LEU cc_start: 0.7638 (tp) cc_final: 0.7372 (tp) REVERT: 5G 3 LEU cc_start: 0.7351 (tp) cc_final: 0.7078 (tp) outliers start: 0 outliers final: 0 residues processed: 2125 average time/residue: 0.1983 time to fit residues: 720.3671 Evaluate side-chains 1695 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1695 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0070 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 470 optimal weight: 0.8980 overall best weight: 3.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.133045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.107954 restraints weight = 57091.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112287 restraints weight = 28039.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.115185 restraints weight = 17105.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.117085 restraints weight = 12202.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.118357 restraints weight = 9695.183| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 41600 Z= 0.167 Angle : 0.751 9.748 55411 Z= 0.392 Chirality : 0.041 0.162 7190 Planarity : 0.004 0.014 6070 Dihedral : 17.003 73.527 8495 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 5.07 % Allowed : 13.70 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.23 (0.11), residues: 4880 helix: -2.36 (0.07), residues: 3200 sheet: None (None), residues: 0 loop : -1.24 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG5F 39 TYR 0.025 0.003 TYR3N 37 PHE 0.021 0.001 PHE4G 15 Details of bonding type rmsd covalent geometry : bond 0.00403 (41600) covalent geometry : angle 0.75128 (55410) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.05079 ( 2000) hydrogen bonds : angle 5.89616 ( 6000) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2289 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 2078 time to evaluate : 0.955 Fit side-chains REVERT: 1B 23 MET cc_start: 0.8488 (ttp) cc_final: 0.8158 (ttm) REVERT: 1C 23 MET cc_start: 0.8177 (ttp) cc_final: 0.7942 (ttm) REVERT: 1C 47 LEU cc_start: 0.8744 (tt) cc_final: 0.8419 (mt) REVERT: 1E 23 MET cc_start: 0.8188 (ttp) cc_final: 0.7957 (ttm) REVERT: 1H 23 MET cc_start: 0.8035 (ttm) cc_final: 0.7804 (ttm) REVERT: 1I 23 MET cc_start: 0.7939 (ttm) cc_final: 0.7606 (ttm) REVERT: 1I 29 GLU cc_start: 0.8138 (tp30) cc_final: 0.7902 (tp30) REVERT: 1J 23 MET cc_start: 0.7706 (ttm) cc_final: 0.7340 (ttt) REVERT: 1J 29 GLU cc_start: 0.8249 (tp30) cc_final: 0.7994 (tp30) REVERT: 1J 57 THR cc_start: 0.8683 (m) cc_final: 0.8425 (p) REVERT: 1K 27 ILE cc_start: 0.9233 (pt) cc_final: 0.9033 (pt) REVERT: 1K 31 ILE cc_start: 0.9026 (tt) cc_final: 0.8800 (tt) REVERT: 1K 39 ARG cc_start: 0.7877 (ttp80) cc_final: 0.7654 (ttp80) REVERT: 1K 57 THR cc_start: 0.8956 (m) cc_final: 0.8663 (p) REVERT: 1L 29 GLU cc_start: 0.8384 (tp30) cc_final: 0.8172 (tp30) REVERT: 1M 29 GLU cc_start: 0.8224 (tp30) cc_final: 0.7830 (tp30) REVERT: 1M 60 LEU cc_start: 0.8834 (mt) cc_final: 0.8513 (mt) REVERT: 1P 39 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7687 (mmm160) REVERT: 2A 37 TYR cc_start: 0.9307 (t80) cc_final: 0.8907 (t80) REVERT: 2C 23 MET cc_start: 0.8243 (ttp) cc_final: 0.8024 (ttm) REVERT: 2D 3 LEU cc_start: 0.7990 (tp) cc_final: 0.7621 (tp) REVERT: 2E 22 MET cc_start: 0.8385 (tpp) cc_final: 0.7830 (tpp) REVERT: 2G 39 ARG cc_start: 0.8199 (ttp-170) cc_final: 0.7889 (ttp80) REVERT: 2L 39 ARG cc_start: 0.8260 (ttp80) cc_final: 0.7958 (ttp80) REVERT: 2M 23 MET cc_start: 0.7744 (ttt) cc_final: 0.7528 (ttm) REVERT: 2M 27 ILE cc_start: 0.9057 (tt) cc_final: 0.8826 (pt) REVERT: 2N 39 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7535 (ttp80) REVERT: 2O 23 MET cc_start: 0.7667 (ttm) cc_final: 0.7405 (ttm) REVERT: 3A 46 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8258 (mm) REVERT: 3B 37 TYR cc_start: 0.9290 (t80) cc_final: 0.8923 (t80) REVERT: 3C 12 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8029 (tttp) REVERT: 3C 47 LEU cc_start: 0.8911 (tt) cc_final: 0.8488 (mt) REVERT: 3D 23 MET cc_start: 0.7973 (ttm) cc_final: 0.7627 (ttm) REVERT: 3D 27 ILE cc_start: 0.9048 (tt) cc_final: 0.8791 (pt) REVERT: 3G 23 MET cc_start: 0.7961 (ttm) cc_final: 0.7662 (ttm) REVERT: 3J 23 MET cc_start: 0.7748 (ttm) cc_final: 0.7188 (ttm) REVERT: 3J 37 TYR cc_start: 0.9153 (t80) cc_final: 0.8952 (t80) REVERT: 3J 39 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7812 (ttp80) REVERT: 3L 60 LEU cc_start: 0.8729 (mt) cc_final: 0.8090 (tt) REVERT: 3M 37 TYR cc_start: 0.8872 (t80) cc_final: 0.8604 (t80) REVERT: 3M 39 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7623 (ttp80) REVERT: 3N 37 TYR cc_start: 0.8691 (t80) cc_final: 0.8291 (t80) REVERT: 3N 53 ILE cc_start: 0.9011 (mm) cc_final: 0.8797 (mm) REVERT: 4A 47 LEU cc_start: 0.8833 (tt) cc_final: 0.8588 (tp) REVERT: 4C 37 TYR cc_start: 0.9171 (t80) cc_final: 0.8933 (t80) REVERT: 4E 23 MET cc_start: 0.8115 (ttp) cc_final: 0.7871 (ttm) REVERT: 4G 23 MET cc_start: 0.7773 (ttm) cc_final: 0.7327 (ttm) REVERT: 4H 23 MET cc_start: 0.8087 (ttp) cc_final: 0.7871 (ttm) REVERT: 4I 23 MET cc_start: 0.7798 (ttt) cc_final: 0.7539 (ttm) REVERT: 4J 39 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7685 (ttp80) REVERT: 4L 26 ILE cc_start: 0.9045 (mm) cc_final: 0.8817 (mt) REVERT: 4M 23 MET cc_start: 0.7796 (ttm) cc_final: 0.7523 (ttm) REVERT: 4N 53 ILE cc_start: 0.9073 (mm) cc_final: 0.8831 (mm) REVERT: 4N 60 LEU cc_start: 0.8791 (mt) cc_final: 0.8469 (mt) REVERT: 4O 53 ILE cc_start: 0.9061 (mm) cc_final: 0.8851 (mm) REVERT: 5B 23 MET cc_start: 0.8210 (ttp) cc_final: 0.7993 (ttm) REVERT: 5E 23 MET cc_start: 0.7945 (ttm) cc_final: 0.7560 (ttm) REVERT: 5F 23 MET cc_start: 0.8010 (ttm) cc_final: 0.7548 (ttm) REVERT: 5H 54 VAL cc_start: 0.9390 (p) cc_final: 0.9157 (t) REVERT: 5I 57 THR cc_start: 0.8725 (m) cc_final: 0.8446 (p) REVERT: 5J 23 MET cc_start: 0.7686 (ttm) cc_final: 0.7356 (ttm) REVERT: 5K 39 ARG cc_start: 0.7905 (ttp80) cc_final: 0.7568 (ttp80) REVERT: 5L 23 MET cc_start: 0.7785 (ttm) cc_final: 0.7389 (ttm) REVERT: 5L 39 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7910 (ttp80) REVERT: 5L 60 LEU cc_start: 0.8869 (mt) cc_final: 0.8529 (mt) REVERT: 5N 23 MET cc_start: 0.7828 (ttm) cc_final: 0.7563 (ttm) REVERT: 5N 60 LEU cc_start: 0.8803 (mt) cc_final: 0.8494 (mt) REVERT: 5O 39 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7726 (ttp80) REVERT: 5P 29 GLU cc_start: 0.8016 (tp30) cc_final: 0.7539 (tp30) outliers start: 211 outliers final: 138 residues processed: 2123 average time/residue: 0.2076 time to fit residues: 745.9510 Evaluate side-chains 1907 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 1767 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 21 VAL Chi-restraints excluded: chain 1B residue 26 ILE Chi-restraints excluded: chain 1B residue 31 ILE Chi-restraints excluded: chain 1B residue 47 LEU Chi-restraints excluded: chain 1C residue 50 VAL Chi-restraints excluded: chain 1D residue 26 ILE Chi-restraints excluded: chain 1D residue 58 VAL Chi-restraints excluded: chain 1E residue 21 VAL Chi-restraints excluded: chain 1E residue 31 ILE Chi-restraints excluded: chain 1F residue 58 VAL Chi-restraints excluded: chain 1G residue 26 ILE Chi-restraints excluded: chain 1G residue 50 VAL Chi-restraints excluded: chain 1G residue 58 VAL Chi-restraints excluded: chain 1H residue 26 ILE Chi-restraints excluded: chain 1H residue 58 VAL Chi-restraints excluded: chain 1I residue 26 ILE Chi-restraints excluded: chain 1I residue 58 VAL Chi-restraints excluded: chain 1J residue 21 VAL Chi-restraints excluded: chain 1J residue 50 VAL Chi-restraints excluded: chain 1J residue 58 VAL Chi-restraints excluded: chain 1L residue 58 VAL Chi-restraints excluded: chain 1L residue 61 THR Chi-restraints excluded: chain 1M residue 50 VAL Chi-restraints excluded: chain 1M residue 57 THR Chi-restraints excluded: chain 1M residue 58 VAL Chi-restraints excluded: chain 1M residue 61 THR Chi-restraints excluded: chain 1N residue 50 VAL Chi-restraints excluded: chain 1O residue 49 LEU Chi-restraints excluded: chain 1P residue 50 VAL Chi-restraints excluded: chain 1P residue 52 VAL Chi-restraints excluded: chain 1P residue 53 ILE Chi-restraints excluded: chain 2A residue 47 LEU Chi-restraints excluded: chain 2A residue 51 VAL Chi-restraints excluded: chain 2A residue 58 VAL Chi-restraints excluded: chain 2B residue 47 LEU Chi-restraints excluded: chain 2C residue 11 VAL Chi-restraints excluded: chain 2C residue 26 ILE Chi-restraints excluded: chain 2C residue 58 VAL Chi-restraints excluded: chain 2D residue 50 VAL Chi-restraints excluded: chain 2E residue 26 ILE Chi-restraints excluded: chain 2E residue 53 ILE Chi-restraints excluded: chain 2G residue 26 ILE Chi-restraints excluded: chain 2G residue 58 VAL Chi-restraints excluded: chain 2H residue 31 ILE Chi-restraints excluded: chain 2I residue 21 VAL Chi-restraints excluded: chain 2I residue 26 ILE Chi-restraints excluded: chain 2K residue 50 VAL Chi-restraints excluded: chain 2K residue 61 THR Chi-restraints excluded: chain 2L residue 21 VAL Chi-restraints excluded: chain 2L residue 58 VAL Chi-restraints excluded: chain 2M residue 11 VAL Chi-restraints excluded: chain 2M residue 50 VAL Chi-restraints excluded: chain 2N residue 50 VAL Chi-restraints excluded: chain 2N residue 58 VAL Chi-restraints excluded: chain 2N residue 61 THR Chi-restraints excluded: chain 3A residue 4 LEU Chi-restraints excluded: chain 3A residue 21 VAL Chi-restraints excluded: chain 3A residue 46 LEU Chi-restraints excluded: chain 3A residue 58 VAL Chi-restraints excluded: chain 3C residue 12 LYS Chi-restraints excluded: chain 3C residue 61 THR Chi-restraints excluded: chain 3D residue 58 VAL Chi-restraints excluded: chain 3E residue 11 VAL Chi-restraints excluded: chain 3E residue 21 VAL Chi-restraints excluded: chain 3F residue 11 VAL Chi-restraints excluded: chain 3F residue 26 ILE Chi-restraints excluded: chain 3F residue 50 VAL Chi-restraints excluded: chain 3F residue 58 VAL Chi-restraints excluded: chain 3G residue 11 VAL Chi-restraints excluded: chain 3G residue 47 LEU Chi-restraints excluded: chain 3G residue 58 VAL Chi-restraints excluded: chain 3H residue 11 VAL Chi-restraints excluded: chain 3H residue 21 VAL Chi-restraints excluded: chain 3H residue 26 ILE Chi-restraints excluded: chain 3I residue 58 VAL Chi-restraints excluded: chain 3J residue 50 VAL Chi-restraints excluded: chain 3K residue 61 THR Chi-restraints excluded: chain 3L residue 21 VAL Chi-restraints excluded: chain 3L residue 50 VAL Chi-restraints excluded: chain 3M residue 50 VAL Chi-restraints excluded: chain 3N residue 21 VAL Chi-restraints excluded: chain 3N residue 50 VAL Chi-restraints excluded: chain 3O residue 50 VAL Chi-restraints excluded: chain 3O residue 57 THR Chi-restraints excluded: chain 3O residue 61 THR Chi-restraints excluded: chain 3P residue 53 ILE Chi-restraints excluded: chain 4C residue 58 VAL Chi-restraints excluded: chain 4D residue 58 VAL Chi-restraints excluded: chain 4E residue 58 VAL Chi-restraints excluded: chain 4F residue 11 VAL Chi-restraints excluded: chain 4F residue 21 VAL Chi-restraints excluded: chain 4F residue 26 ILE Chi-restraints excluded: chain 4F residue 51 VAL Chi-restraints excluded: chain 4F residue 53 ILE Chi-restraints excluded: chain 4F residue 57 THR Chi-restraints excluded: chain 4H residue 21 VAL Chi-restraints excluded: chain 4H residue 26 ILE Chi-restraints excluded: chain 4I residue 21 VAL Chi-restraints excluded: chain 4I residue 26 ILE Chi-restraints excluded: chain 4I residue 50 VAL Chi-restraints excluded: chain 4J residue 58 VAL Chi-restraints excluded: chain 4K residue 21 VAL Chi-restraints excluded: chain 4K residue 26 ILE Chi-restraints excluded: chain 4K residue 50 VAL Chi-restraints excluded: chain 4M residue 21 VAL Chi-restraints excluded: chain 4M residue 50 VAL Chi-restraints excluded: chain 4M residue 58 VAL Chi-restraints excluded: chain 4N residue 50 VAL Chi-restraints excluded: chain 4N residue 61 THR Chi-restraints excluded: chain 4O residue 50 VAL Chi-restraints excluded: chain 4O residue 61 THR Chi-restraints excluded: chain 5A residue 58 VAL Chi-restraints excluded: chain 5B residue 26 ILE Chi-restraints excluded: chain 5B residue 53 ILE Chi-restraints excluded: chain 5B residue 58 VAL Chi-restraints excluded: chain 5C residue 50 VAL Chi-restraints excluded: chain 5D residue 58 VAL Chi-restraints excluded: chain 5E residue 21 VAL Chi-restraints excluded: chain 5F residue 4 LEU Chi-restraints excluded: chain 5F residue 58 VAL Chi-restraints excluded: chain 5G residue 58 VAL Chi-restraints excluded: chain 5H residue 26 ILE Chi-restraints excluded: chain 5I residue 53 ILE Chi-restraints excluded: chain 5I residue 58 VAL Chi-restraints excluded: chain 5I residue 61 THR Chi-restraints excluded: chain 5J residue 26 ILE Chi-restraints excluded: chain 5J residue 50 VAL Chi-restraints excluded: chain 5K residue 50 VAL Chi-restraints excluded: chain 5L residue 21 VAL Chi-restraints excluded: chain 5L residue 27 ILE Chi-restraints excluded: chain 5L residue 50 VAL Chi-restraints excluded: chain 5L residue 58 VAL Chi-restraints excluded: chain 5M residue 11 VAL Chi-restraints excluded: chain 5M residue 21 VAL Chi-restraints excluded: chain 5M residue 50 VAL Chi-restraints excluded: chain 5M residue 61 THR Chi-restraints excluded: chain 5N residue 50 VAL Chi-restraints excluded: chain 5N residue 61 THR Chi-restraints excluded: chain 5O residue 61 THR Chi-restraints excluded: chain 5P residue 52 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 303 optimal weight: 5.9990 chunk 430 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 chunk 271 optimal weight: 5.9990 chunk 331 optimal weight: 9.9990 chunk 170 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 377 optimal weight: 1.9990 chunk 326 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 283 optimal weight: 50.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.127061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102061 restraints weight = 57209.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.106296 restraints weight = 27948.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.109138 restraints weight = 17164.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111022 restraints weight = 12302.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.112101 restraints weight = 9826.401| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 41600 Z= 0.161 Angle : 0.642 8.732 55411 Z= 0.329 Chirality : 0.039 0.159 7190 Planarity : 0.003 0.011 6070 Dihedral : 15.737 77.311 8495 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 5.53 % Allowed : 19.04 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.11), residues: 4880 helix: -1.32 (0.08), residues: 3280 sheet: None (None), residues: 0 loop : -1.14 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG3K 39 TYR 0.020 0.002 TYR5M 37 PHE 0.017 0.001 PHE4C 15 Details of bonding type rmsd covalent geometry : bond 0.00392 (41600) covalent geometry : angle 0.64246 (55410) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.04609 ( 2000) hydrogen bonds : angle 5.24672 ( 6000) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2126 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 1896 time to evaluate : 1.325 Fit side-chains REVERT: 1B 23 MET cc_start: 0.8493 (ttp) cc_final: 0.8119 (ttm) REVERT: 1B 40 THR cc_start: 0.9223 (m) cc_final: 0.8941 (p) REVERT: 1C 22 MET cc_start: 0.8476 (tpp) cc_final: 0.8018 (tpp) REVERT: 1C 40 THR cc_start: 0.9401 (m) cc_final: 0.9035 (p) REVERT: 1D 22 MET cc_start: 0.8278 (tpp) cc_final: 0.8030 (tpp) REVERT: 1E 40 THR cc_start: 0.9351 (m) cc_final: 0.8895 (p) REVERT: 1G 40 THR cc_start: 0.9198 (m) cc_final: 0.8942 (p) REVERT: 1I 40 THR cc_start: 0.9243 (m) cc_final: 0.8842 (p) REVERT: 1J 23 MET cc_start: 0.7862 (ttm) cc_final: 0.7620 (ttt) REVERT: 1J 40 THR cc_start: 0.9122 (m) cc_final: 0.8589 (p) REVERT: 1K 26 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8341 (tt) REVERT: 1K 39 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7642 (ttp80) REVERT: 1K 40 THR cc_start: 0.9129 (m) cc_final: 0.8752 (p) REVERT: 1L 29 GLU cc_start: 0.8592 (tp30) cc_final: 0.8351 (tp30) REVERT: 1M 23 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7906 (ttm) REVERT: 1M 60 LEU cc_start: 0.8990 (mt) cc_final: 0.8694 (mt) REVERT: 2A 37 TYR cc_start: 0.9327 (t80) cc_final: 0.8897 (t80) REVERT: 2A 40 THR cc_start: 0.9407 (m) cc_final: 0.8933 (p) REVERT: 2A 47 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8793 (mt) REVERT: 2B 40 THR cc_start: 0.9297 (m) cc_final: 0.8897 (p) REVERT: 2C 37 TYR cc_start: 0.9263 (t80) cc_final: 0.9033 (t80) REVERT: 2D 3 LEU cc_start: 0.8204 (tp) cc_final: 0.7707 (tp) REVERT: 2E 22 MET cc_start: 0.8507 (tpp) cc_final: 0.8042 (tpp) REVERT: 2E 40 THR cc_start: 0.9289 (m) cc_final: 0.8826 (p) REVERT: 2E 41 LYS cc_start: 0.8662 (mttp) cc_final: 0.8448 (mttp) REVERT: 2F 40 THR cc_start: 0.9165 (m) cc_final: 0.8930 (p) REVERT: 2G 39 ARG cc_start: 0.8206 (ttp-170) cc_final: 0.7919 (ttp80) REVERT: 2H 40 THR cc_start: 0.9267 (m) cc_final: 0.8912 (p) REVERT: 2I 40 THR cc_start: 0.9321 (m) cc_final: 0.8969 (p) REVERT: 2J 40 THR cc_start: 0.9108 (m) cc_final: 0.8784 (p) REVERT: 2K 37 TYR cc_start: 0.9106 (t80) cc_final: 0.8688 (t80) REVERT: 2L 39 ARG cc_start: 0.8125 (ttp80) cc_final: 0.7894 (ttp80) REVERT: 2L 40 THR cc_start: 0.9206 (m) cc_final: 0.8845 (p) REVERT: 2L 60 LEU cc_start: 0.8865 (mt) cc_final: 0.8653 (mt) REVERT: 2N 39 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7839 (ttp80) REVERT: 2N 60 LEU cc_start: 0.8866 (mt) cc_final: 0.8518 (mt) REVERT: 3A 40 THR cc_start: 0.9240 (m) cc_final: 0.8830 (p) REVERT: 3A 46 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8297 (mm) REVERT: 3B 23 MET cc_start: 0.7798 (ttm) cc_final: 0.7527 (ttm) REVERT: 3B 40 THR cc_start: 0.9242 (m) cc_final: 0.8809 (p) REVERT: 3C 26 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8404 (mt) REVERT: 3C 40 THR cc_start: 0.9199 (m) cc_final: 0.8780 (p) REVERT: 3D 40 THR cc_start: 0.9391 (m) cc_final: 0.8960 (p) REVERT: 3E 36 MET cc_start: 0.7913 (mtm) cc_final: 0.7691 (mtm) REVERT: 3E 40 THR cc_start: 0.9226 (m) cc_final: 0.8804 (p) REVERT: 3F 40 THR cc_start: 0.9261 (m) cc_final: 0.8947 (p) REVERT: 3H 40 THR cc_start: 0.9332 (m) cc_final: 0.9062 (p) REVERT: 3H 46 LEU cc_start: 0.9222 (mt) cc_final: 0.8947 (mt) REVERT: 3I 40 THR cc_start: 0.9377 (m) cc_final: 0.9088 (p) REVERT: 3J 39 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7834 (ttp80) REVERT: 3K 40 THR cc_start: 0.9230 (m) cc_final: 0.8794 (p) REVERT: 3L 40 THR cc_start: 0.9203 (m) cc_final: 0.8848 (p) REVERT: 3L 60 LEU cc_start: 0.8886 (mt) cc_final: 0.8212 (tt) REVERT: 3M 22 MET cc_start: 0.8383 (tpp) cc_final: 0.8176 (tpp) REVERT: 3M 37 TYR cc_start: 0.8975 (t80) cc_final: 0.8773 (t80) REVERT: 3M 39 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7775 (ttp80) REVERT: 3O 23 MET cc_start: 0.8030 (ttm) cc_final: 0.7626 (ttm) REVERT: 3O 29 GLU cc_start: 0.8594 (tp30) cc_final: 0.8218 (tp30) REVERT: 3O 37 TYR cc_start: 0.8970 (t80) cc_final: 0.8536 (t80) REVERT: 3O 46 LEU cc_start: 0.9261 (mt) cc_final: 0.9060 (mt) REVERT: 4A 40 THR cc_start: 0.9328 (m) cc_final: 0.8866 (p) REVERT: 4B 40 THR cc_start: 0.9163 (m) cc_final: 0.8868 (p) REVERT: 4C 40 THR cc_start: 0.9246 (m) cc_final: 0.8854 (p) REVERT: 4E 43 LEU cc_start: 0.8654 (mt) cc_final: 0.8212 (mt) REVERT: 4F 40 THR cc_start: 0.9337 (m) cc_final: 0.8942 (p) REVERT: 4G 40 THR cc_start: 0.9092 (m) cc_final: 0.8831 (p) REVERT: 4H 40 THR cc_start: 0.9253 (m) cc_final: 0.8797 (p) REVERT: 4J 39 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7672 (ttp80) REVERT: 4K 40 THR cc_start: 0.9401 (m) cc_final: 0.9083 (p) REVERT: 4K 60 LEU cc_start: 0.8935 (mt) cc_final: 0.8680 (mt) REVERT: 4L 40 THR cc_start: 0.9268 (m) cc_final: 0.8865 (p) REVERT: 4L 46 LEU cc_start: 0.9166 (mt) cc_final: 0.8918 (mt) REVERT: 4N 46 LEU cc_start: 0.9151 (mt) cc_final: 0.8927 (mt) REVERT: 4N 60 LEU cc_start: 0.8950 (mt) cc_final: 0.8546 (mt) REVERT: 4O 37 TYR cc_start: 0.9181 (t80) cc_final: 0.8945 (t80) REVERT: 4O 53 ILE cc_start: 0.9158 (mm) cc_final: 0.8917 (mm) REVERT: 5B 23 MET cc_start: 0.8176 (ttp) cc_final: 0.7890 (ttm) REVERT: 5C 26 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8980 (mt) REVERT: 5C 40 THR cc_start: 0.9223 (m) cc_final: 0.8956 (p) REVERT: 5D 40 THR cc_start: 0.9273 (m) cc_final: 0.8913 (p) REVERT: 5E 23 MET cc_start: 0.8110 (ttm) cc_final: 0.7846 (ttm) REVERT: 5E 37 TYR cc_start: 0.9157 (t80) cc_final: 0.8908 (t80) REVERT: 5E 40 THR cc_start: 0.9256 (m) cc_final: 0.8695 (p) REVERT: 5F 23 MET cc_start: 0.7886 (ttm) cc_final: 0.7680 (ttm) REVERT: 5F 40 THR cc_start: 0.9216 (m) cc_final: 0.8852 (p) REVERT: 5G 40 THR cc_start: 0.9180 (m) cc_final: 0.8792 (p) REVERT: 5H 43 LEU cc_start: 0.8860 (mp) cc_final: 0.8656 (mp) REVERT: 5I 40 THR cc_start: 0.9236 (m) cc_final: 0.8801 (p) REVERT: 5J 40 THR cc_start: 0.9162 (m) cc_final: 0.8711 (p) REVERT: 5K 40 THR cc_start: 0.9238 (m) cc_final: 0.8936 (p) REVERT: 5L 23 MET cc_start: 0.7861 (ttm) cc_final: 0.7393 (ttm) REVERT: 5L 39 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7866 (ttp80) REVERT: 5L 60 LEU cc_start: 0.8936 (mt) cc_final: 0.8573 (mt) REVERT: 5N 23 MET cc_start: 0.7942 (ttm) cc_final: 0.7676 (ttm) REVERT: 5N 60 LEU cc_start: 0.8850 (mt) cc_final: 0.8568 (mt) REVERT: 5O 23 MET cc_start: 0.7856 (ttm) cc_final: 0.7421 (ttm) REVERT: 5O 39 ARG cc_start: 0.8228 (ttp80) cc_final: 0.7886 (ttp80) REVERT: 5O 53 ILE cc_start: 0.8947 (mm) cc_final: 0.8717 (mm) REVERT: 5O 60 LEU cc_start: 0.9027 (mt) cc_final: 0.8752 (mt) REVERT: 5P 29 GLU cc_start: 0.8392 (tp30) cc_final: 0.8147 (tp30) outliers start: 230 outliers final: 141 residues processed: 1958 average time/residue: 0.2190 time to fit residues: 713.6486 Evaluate side-chains 1851 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1704 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 21 VAL Chi-restraints excluded: chain 1A residue 51 VAL Chi-restraints excluded: chain 1B residue 26 ILE Chi-restraints excluded: chain 1C residue 50 VAL Chi-restraints excluded: chain 1D residue 26 ILE Chi-restraints excluded: chain 1D residue 31 ILE Chi-restraints excluded: chain 1E residue 21 VAL Chi-restraints excluded: chain 1E residue 31 ILE Chi-restraints excluded: chain 1G residue 26 ILE Chi-restraints excluded: chain 1G residue 31 ILE Chi-restraints excluded: chain 1G residue 50 VAL Chi-restraints excluded: chain 1G residue 58 VAL Chi-restraints excluded: chain 1H residue 26 ILE Chi-restraints excluded: chain 1I residue 26 ILE Chi-restraints excluded: chain 1I residue 31 ILE Chi-restraints excluded: chain 1J residue 19 SER Chi-restraints excluded: chain 1J residue 21 VAL Chi-restraints excluded: chain 1J residue 26 ILE Chi-restraints excluded: chain 1J residue 50 VAL Chi-restraints excluded: chain 1K residue 23 MET Chi-restraints excluded: chain 1K residue 26 ILE Chi-restraints excluded: chain 1L residue 61 THR Chi-restraints excluded: chain 1M residue 23 MET Chi-restraints excluded: chain 1M residue 50 VAL Chi-restraints excluded: chain 1N residue 50 VAL Chi-restraints excluded: chain 1P residue 52 VAL Chi-restraints excluded: chain 1P residue 54 VAL Chi-restraints excluded: chain 2A residue 4 LEU Chi-restraints excluded: chain 2A residue 23 MET Chi-restraints excluded: chain 2A residue 31 ILE Chi-restraints excluded: chain 2A residue 47 LEU Chi-restraints excluded: chain 2A residue 51 VAL Chi-restraints excluded: chain 2B residue 47 LEU Chi-restraints excluded: chain 2C residue 26 ILE Chi-restraints excluded: chain 2C residue 50 VAL Chi-restraints excluded: chain 2C residue 58 VAL Chi-restraints excluded: chain 2D residue 4 LEU Chi-restraints excluded: chain 2D residue 26 ILE Chi-restraints excluded: chain 2D residue 50 VAL Chi-restraints excluded: chain 2D residue 51 VAL Chi-restraints excluded: chain 2D residue 53 ILE Chi-restraints excluded: chain 2E residue 26 ILE Chi-restraints excluded: chain 2E residue 51 VAL Chi-restraints excluded: chain 2F residue 31 ILE Chi-restraints excluded: chain 2G residue 26 ILE Chi-restraints excluded: chain 2G residue 61 THR Chi-restraints excluded: chain 2H residue 26 ILE Chi-restraints excluded: chain 2H residue 31 ILE Chi-restraints excluded: chain 2I residue 21 VAL Chi-restraints excluded: chain 2I residue 26 ILE Chi-restraints excluded: chain 2I residue 47 LEU Chi-restraints excluded: chain 2J residue 4 LEU Chi-restraints excluded: chain 2J residue 26 ILE Chi-restraints excluded: chain 2J residue 31 ILE Chi-restraints excluded: chain 2K residue 4 LEU Chi-restraints excluded: chain 2K residue 61 THR Chi-restraints excluded: chain 2L residue 23 MET Chi-restraints excluded: chain 2L residue 58 VAL Chi-restraints excluded: chain 2N residue 23 MET Chi-restraints excluded: chain 2N residue 50 VAL Chi-restraints excluded: chain 2N residue 61 THR Chi-restraints excluded: chain 2N residue 63 ILE Chi-restraints excluded: chain 2O residue 50 VAL Chi-restraints excluded: chain 2P residue 50 VAL Chi-restraints excluded: chain 3A residue 21 VAL Chi-restraints excluded: chain 3A residue 46 LEU Chi-restraints excluded: chain 3A residue 58 VAL Chi-restraints excluded: chain 3C residue 26 ILE Chi-restraints excluded: chain 3C residue 31 ILE Chi-restraints excluded: chain 3C residue 41 LYS Chi-restraints excluded: chain 3E residue 46 LEU Chi-restraints excluded: chain 3F residue 11 VAL Chi-restraints excluded: chain 3F residue 26 ILE Chi-restraints excluded: chain 3F residue 47 LEU Chi-restraints excluded: chain 3F residue 50 VAL Chi-restraints excluded: chain 3G residue 31 ILE Chi-restraints excluded: chain 3G residue 58 VAL Chi-restraints excluded: chain 3H residue 21 VAL Chi-restraints excluded: chain 3H residue 31 ILE Chi-restraints excluded: chain 3H residue 50 VAL Chi-restraints excluded: chain 3I residue 11 VAL Chi-restraints excluded: chain 3I residue 31 ILE Chi-restraints excluded: chain 3I residue 50 VAL Chi-restraints excluded: chain 3I residue 51 VAL Chi-restraints excluded: chain 3I residue 58 VAL Chi-restraints excluded: chain 3I residue 61 THR Chi-restraints excluded: chain 3J residue 4 LEU Chi-restraints excluded: chain 3J residue 11 VAL Chi-restraints excluded: chain 3K residue 4 LEU Chi-restraints excluded: chain 3M residue 58 VAL Chi-restraints excluded: chain 3N residue 21 VAL Chi-restraints excluded: chain 3N residue 52 VAL Chi-restraints excluded: chain 3O residue 61 THR Chi-restraints excluded: chain 3P residue 53 ILE Chi-restraints excluded: chain 4A residue 31 ILE Chi-restraints excluded: chain 4A residue 58 VAL Chi-restraints excluded: chain 4B residue 31 ILE Chi-restraints excluded: chain 4C residue 26 ILE Chi-restraints excluded: chain 4C residue 61 THR Chi-restraints excluded: chain 4D residue 31 ILE Chi-restraints excluded: chain 4E residue 58 VAL Chi-restraints excluded: chain 4F residue 4 LEU Chi-restraints excluded: chain 4F residue 26 ILE Chi-restraints excluded: chain 4F residue 54 VAL Chi-restraints excluded: chain 4H residue 21 VAL Chi-restraints excluded: chain 4H residue 50 VAL Chi-restraints excluded: chain 4I residue 21 VAL Chi-restraints excluded: chain 4I residue 26 ILE Chi-restraints excluded: chain 4I residue 50 VAL Chi-restraints excluded: chain 4J residue 58 VAL Chi-restraints excluded: chain 4J residue 61 THR Chi-restraints excluded: chain 4K residue 21 VAL Chi-restraints excluded: chain 4K residue 26 ILE Chi-restraints excluded: chain 4L residue 31 ILE Chi-restraints excluded: chain 4M residue 21 VAL Chi-restraints excluded: chain 4M residue 50 VAL Chi-restraints excluded: chain 4N residue 23 MET Chi-restraints excluded: chain 4N residue 50 VAL Chi-restraints excluded: chain 4O residue 57 THR Chi-restraints excluded: chain 4P residue 53 ILE Chi-restraints excluded: chain 5A residue 31 ILE Chi-restraints excluded: chain 5B residue 11 VAL Chi-restraints excluded: chain 5B residue 26 ILE Chi-restraints excluded: chain 5B residue 53 ILE Chi-restraints excluded: chain 5C residue 26 ILE Chi-restraints excluded: chain 5C residue 31 ILE Chi-restraints excluded: chain 5C residue 61 THR Chi-restraints excluded: chain 5D residue 4 LEU Chi-restraints excluded: chain 5E residue 21 VAL Chi-restraints excluded: chain 5E residue 50 VAL Chi-restraints excluded: chain 5F residue 4 LEU Chi-restraints excluded: chain 5F residue 11 VAL Chi-restraints excluded: chain 5F residue 31 ILE Chi-restraints excluded: chain 5H residue 26 ILE Chi-restraints excluded: chain 5I residue 31 ILE Chi-restraints excluded: chain 5I residue 50 VAL Chi-restraints excluded: chain 5I residue 58 VAL Chi-restraints excluded: chain 5I residue 61 THR Chi-restraints excluded: chain 5J residue 50 VAL Chi-restraints excluded: chain 5L residue 50 VAL Chi-restraints excluded: chain 5M residue 23 MET Chi-restraints excluded: chain 5M residue 43 LEU Chi-restraints excluded: chain 5M residue 50 VAL Chi-restraints excluded: chain 5M residue 61 THR Chi-restraints excluded: chain 5N residue 50 VAL Chi-restraints excluded: chain 5P residue 52 VAL Chi-restraints excluded: chain 5P residue 53 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 111 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 60 optimal weight: 0.0000 chunk 375 optimal weight: 9.9990 chunk 332 optimal weight: 5.9990 chunk 309 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 403 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 175 optimal weight: 0.5980 overall best weight: 2.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.128629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.103831 restraints weight = 57646.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.108050 restraints weight = 28733.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.110875 restraints weight = 17722.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.112678 restraints weight = 12710.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.113932 restraints weight = 10184.470| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 41600 Z= 0.127 Angle : 0.593 9.370 55411 Z= 0.294 Chirality : 0.037 0.166 7190 Planarity : 0.002 0.020 6070 Dihedral : 14.589 77.706 8495 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.02 % Allowed : 21.73 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.12), residues: 4880 helix: -0.64 (0.09), residues: 3280 sheet: None (None), residues: 0 loop : -1.07 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG3A 39 TYR 0.019 0.002 TYR4I 37 PHE 0.017 0.001 PHE3N 15 Details of bonding type rmsd covalent geometry : bond 0.00305 (41600) covalent geometry : angle 0.59295 (55410) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.03803 ( 2000) hydrogen bonds : angle 4.93784 ( 6000) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2042 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 1833 time to evaluate : 1.232 Fit side-chains REVERT: 1B 40 THR cc_start: 0.9267 (m) cc_final: 0.8960 (p) REVERT: 1C 22 MET cc_start: 0.8437 (tpp) cc_final: 0.8002 (tpp) REVERT: 1C 23 MET cc_start: 0.8025 (ttm) cc_final: 0.7718 (ttm) REVERT: 1C 40 THR cc_start: 0.9264 (m) cc_final: 0.8776 (p) REVERT: 1E 40 THR cc_start: 0.9229 (m) cc_final: 0.8831 (p) REVERT: 1F 37 TYR cc_start: 0.9134 (t80) cc_final: 0.8859 (t80) REVERT: 1F 40 THR cc_start: 0.9225 (m) cc_final: 0.8968 (p) REVERT: 1G 40 THR cc_start: 0.9225 (m) cc_final: 0.8935 (p) REVERT: 1I 40 THR cc_start: 0.9323 (m) cc_final: 0.8917 (p) REVERT: 1J 40 THR cc_start: 0.9033 (m) cc_final: 0.8449 (p) REVERT: 1K 40 THR cc_start: 0.9246 (m) cc_final: 0.8874 (p) REVERT: 1M 29 GLU cc_start: 0.8408 (tp30) cc_final: 0.7896 (tp30) REVERT: 1M 60 LEU cc_start: 0.8923 (mt) cc_final: 0.8610 (mt) REVERT: 2A 4 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7826 (tt) REVERT: 2A 37 TYR cc_start: 0.9305 (t80) cc_final: 0.8882 (t80) REVERT: 2A 47 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8842 (mt) REVERT: 2B 40 THR cc_start: 0.9231 (m) cc_final: 0.8809 (p) REVERT: 2C 37 TYR cc_start: 0.9119 (t80) cc_final: 0.8880 (t80) REVERT: 2D 3 LEU cc_start: 0.8180 (tp) cc_final: 0.7744 (tp) REVERT: 2E 22 MET cc_start: 0.8457 (tpp) cc_final: 0.7983 (tpp) REVERT: 2E 40 THR cc_start: 0.9269 (m) cc_final: 0.8804 (p) REVERT: 2G 39 ARG cc_start: 0.8113 (ttp-170) cc_final: 0.7806 (ttp80) REVERT: 2H 27 ILE cc_start: 0.9271 (tt) cc_final: 0.8922 (pt) REVERT: 2H 40 THR cc_start: 0.9290 (m) cc_final: 0.8822 (p) REVERT: 2I 37 TYR cc_start: 0.9124 (t80) cc_final: 0.8603 (t80) REVERT: 2I 40 THR cc_start: 0.9207 (m) cc_final: 0.8766 (p) REVERT: 2J 40 THR cc_start: 0.9084 (m) cc_final: 0.8767 (p) REVERT: 2L 40 THR cc_start: 0.9316 (m) cc_final: 0.8871 (p) REVERT: 2L 49 LEU cc_start: 0.9290 (tp) cc_final: 0.9074 (tt) REVERT: 2L 60 LEU cc_start: 0.8866 (mt) cc_final: 0.8658 (mt) REVERT: 2N 60 LEU cc_start: 0.8881 (mt) cc_final: 0.8492 (tt) REVERT: 2O 23 MET cc_start: 0.7824 (ttm) cc_final: 0.7566 (ttm) REVERT: 2P 37 TYR cc_start: 0.8863 (t80) cc_final: 0.8542 (t80) REVERT: 3A 40 THR cc_start: 0.9167 (m) cc_final: 0.8919 (p) REVERT: 3B 23 MET cc_start: 0.7849 (ttm) cc_final: 0.7559 (ttm) REVERT: 3B 40 THR cc_start: 0.9150 (m) cc_final: 0.8741 (p) REVERT: 3C 22 MET cc_start: 0.8124 (tpp) cc_final: 0.7715 (tpp) REVERT: 3C 36 MET cc_start: 0.8136 (mtm) cc_final: 0.7889 (mtm) REVERT: 3C 40 THR cc_start: 0.9076 (m) cc_final: 0.8607 (p) REVERT: 3D 10 ASP cc_start: 0.7566 (p0) cc_final: 0.7357 (p0) REVERT: 3D 40 THR cc_start: 0.9365 (m) cc_final: 0.8953 (p) REVERT: 3E 40 THR cc_start: 0.9191 (m) cc_final: 0.8798 (p) REVERT: 3F 40 THR cc_start: 0.9265 (m) cc_final: 0.8955 (p) REVERT: 3G 41 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8463 (tttp) REVERT: 3H 40 THR cc_start: 0.9325 (m) cc_final: 0.8920 (p) REVERT: 3H 46 LEU cc_start: 0.9272 (mt) cc_final: 0.9061 (mt) REVERT: 3I 40 THR cc_start: 0.9275 (m) cc_final: 0.8993 (p) REVERT: 3I 41 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8554 (ttmm) REVERT: 3J 39 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7791 (ttp80) REVERT: 3J 40 THR cc_start: 0.9306 (m) cc_final: 0.8823 (p) REVERT: 3K 4 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7939 (tp) REVERT: 3K 40 THR cc_start: 0.9247 (m) cc_final: 0.8769 (p) REVERT: 3L 40 THR cc_start: 0.9216 (m) cc_final: 0.8578 (p) REVERT: 3M 39 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7660 (ttp80) REVERT: 3M 46 LEU cc_start: 0.9164 (mt) cc_final: 0.8919 (mt) REVERT: 3N 46 LEU cc_start: 0.9157 (mt) cc_final: 0.8936 (mt) REVERT: 3O 37 TYR cc_start: 0.9095 (t80) cc_final: 0.8726 (t80) REVERT: 3O 46 LEU cc_start: 0.9288 (mt) cc_final: 0.9053 (mt) REVERT: 4A 40 THR cc_start: 0.9170 (m) cc_final: 0.8698 (p) REVERT: 4B 40 THR cc_start: 0.9155 (m) cc_final: 0.8817 (p) REVERT: 4C 22 MET cc_start: 0.8197 (tpp) cc_final: 0.7955 (tpp) REVERT: 4C 40 THR cc_start: 0.9235 (m) cc_final: 0.8839 (p) REVERT: 4D 36 MET cc_start: 0.8311 (mtm) cc_final: 0.7968 (mtm) REVERT: 4D 40 THR cc_start: 0.9137 (m) cc_final: 0.8678 (p) REVERT: 4E 43 LEU cc_start: 0.8698 (mt) cc_final: 0.8455 (mt) REVERT: 4F 40 THR cc_start: 0.9233 (m) cc_final: 0.8815 (p) REVERT: 4G 27 ILE cc_start: 0.9200 (pt) cc_final: 0.8925 (mt) REVERT: 4G 40 THR cc_start: 0.9015 (m) cc_final: 0.8746 (p) REVERT: 4G 41 LYS cc_start: 0.8491 (mttp) cc_final: 0.8276 (ttmm) REVERT: 4H 40 THR cc_start: 0.9128 (m) cc_final: 0.8626 (p) REVERT: 4J 39 ARG cc_start: 0.7812 (ttp80) cc_final: 0.7589 (ttp80) REVERT: 4K 40 THR cc_start: 0.9264 (m) cc_final: 0.8853 (p) REVERT: 4K 60 LEU cc_start: 0.8838 (mt) cc_final: 0.8626 (mt) REVERT: 4L 40 THR cc_start: 0.9124 (m) cc_final: 0.8778 (p) REVERT: 4L 46 LEU cc_start: 0.9161 (mt) cc_final: 0.8904 (mt) REVERT: 4N 46 LEU cc_start: 0.9155 (mt) cc_final: 0.8862 (mt) REVERT: 4N 60 LEU cc_start: 0.8944 (mt) cc_final: 0.8514 (mt) REVERT: 4O 37 TYR cc_start: 0.9145 (t80) cc_final: 0.8816 (t80) REVERT: 4O 46 LEU cc_start: 0.9117 (mt) cc_final: 0.8840 (mt) REVERT: 4O 60 LEU cc_start: 0.8976 (mt) cc_final: 0.8668 (mt) REVERT: 5B 39 ARG cc_start: 0.8160 (ttp-170) cc_final: 0.7909 (ttp80) REVERT: 5C 40 THR cc_start: 0.9220 (m) cc_final: 0.8729 (p) REVERT: 5D 40 THR cc_start: 0.9222 (m) cc_final: 0.8797 (p) REVERT: 5E 26 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8446 (mt) REVERT: 5F 40 THR cc_start: 0.9071 (m) cc_final: 0.8592 (p) REVERT: 5G 10 ASP cc_start: 0.7982 (p0) cc_final: 0.7740 (p0) REVERT: 5G 40 THR cc_start: 0.9161 (m) cc_final: 0.8750 (p) REVERT: 5H 40 THR cc_start: 0.9085 (m) cc_final: 0.8562 (p) REVERT: 5I 4 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7841 (tt) REVERT: 5I 40 THR cc_start: 0.9156 (m) cc_final: 0.8711 (p) REVERT: 5J 40 THR cc_start: 0.9225 (m) cc_final: 0.8715 (p) REVERT: 5K 40 THR cc_start: 0.9295 (m) cc_final: 0.9079 (p) REVERT: 5L 23 MET cc_start: 0.7646 (ttm) cc_final: 0.7293 (ttm) REVERT: 5N 23 MET cc_start: 0.7936 (ttm) cc_final: 0.7648 (ttm) REVERT: 5N 60 LEU cc_start: 0.8839 (mt) cc_final: 0.8585 (mt) REVERT: 5O 23 MET cc_start: 0.7822 (ttm) cc_final: 0.7604 (ttm) REVERT: 5P 46 LEU cc_start: 0.9270 (mt) cc_final: 0.8916 (mt) outliers start: 209 outliers final: 134 residues processed: 1898 average time/residue: 0.2116 time to fit residues: 669.2356 Evaluate side-chains 1858 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1717 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 21 VAL Chi-restraints excluded: chain 1A residue 23 MET Chi-restraints excluded: chain 1A residue 51 VAL Chi-restraints excluded: chain 1B residue 11 VAL Chi-restraints excluded: chain 1B residue 26 ILE Chi-restraints excluded: chain 1C residue 26 ILE Chi-restraints excluded: chain 1C residue 50 VAL Chi-restraints excluded: chain 1D residue 26 ILE Chi-restraints excluded: chain 1D residue 31 ILE Chi-restraints excluded: chain 1E residue 21 VAL Chi-restraints excluded: chain 1E residue 26 ILE Chi-restraints excluded: chain 1E residue 31 ILE Chi-restraints excluded: chain 1F residue 26 ILE Chi-restraints excluded: chain 1G residue 25 ILE Chi-restraints excluded: chain 1G residue 26 ILE Chi-restraints excluded: chain 1G residue 31 ILE Chi-restraints excluded: chain 1G residue 47 LEU Chi-restraints excluded: chain 1G residue 51 VAL Chi-restraints excluded: chain 1G residue 58 VAL Chi-restraints excluded: chain 1H residue 26 ILE Chi-restraints excluded: chain 1I residue 26 ILE Chi-restraints excluded: chain 1I residue 31 ILE Chi-restraints excluded: chain 1J residue 19 SER Chi-restraints excluded: chain 1J residue 21 VAL Chi-restraints excluded: chain 1J residue 26 ILE Chi-restraints excluded: chain 1M residue 50 VAL Chi-restraints excluded: chain 1N residue 50 VAL Chi-restraints excluded: chain 1P residue 53 ILE Chi-restraints excluded: chain 2A residue 4 LEU Chi-restraints excluded: chain 2A residue 23 MET Chi-restraints excluded: chain 2A residue 47 LEU Chi-restraints excluded: chain 2A residue 51 VAL Chi-restraints excluded: chain 2B residue 12 LYS Chi-restraints excluded: chain 2B residue 23 MET Chi-restraints excluded: chain 2B residue 26 ILE Chi-restraints excluded: chain 2B residue 47 LEU Chi-restraints excluded: chain 2C residue 26 ILE Chi-restraints excluded: chain 2C residue 50 VAL Chi-restraints excluded: chain 2D residue 26 ILE Chi-restraints excluded: chain 2D residue 53 ILE Chi-restraints excluded: chain 2E residue 26 ILE Chi-restraints excluded: chain 2F residue 31 ILE Chi-restraints excluded: chain 2F residue 36 MET Chi-restraints excluded: chain 2F residue 47 LEU Chi-restraints excluded: chain 2F residue 51 VAL Chi-restraints excluded: chain 2G residue 23 MET Chi-restraints excluded: chain 2G residue 26 ILE Chi-restraints excluded: chain 2H residue 26 ILE Chi-restraints excluded: chain 2I residue 21 VAL Chi-restraints excluded: chain 2I residue 26 ILE Chi-restraints excluded: chain 2I residue 47 LEU Chi-restraints excluded: chain 2I residue 51 VAL Chi-restraints excluded: chain 2I residue 52 VAL Chi-restraints excluded: chain 2J residue 4 LEU Chi-restraints excluded: chain 2J residue 26 ILE Chi-restraints excluded: chain 2K residue 61 THR Chi-restraints excluded: chain 2L residue 23 MET Chi-restraints excluded: chain 2L residue 58 VAL Chi-restraints excluded: chain 2M residue 23 MET Chi-restraints excluded: chain 2M residue 31 ILE Chi-restraints excluded: chain 2N residue 63 ILE Chi-restraints excluded: chain 2P residue 41 LYS Chi-restraints excluded: chain 3A residue 21 VAL Chi-restraints excluded: chain 3B residue 26 ILE Chi-restraints excluded: chain 3C residue 12 LYS Chi-restraints excluded: chain 3C residue 41 LYS Chi-restraints excluded: chain 3C residue 51 VAL Chi-restraints excluded: chain 3E residue 26 ILE Chi-restraints excluded: chain 3F residue 11 VAL Chi-restraints excluded: chain 3F residue 26 ILE Chi-restraints excluded: chain 3F residue 47 LEU Chi-restraints excluded: chain 3F residue 50 VAL Chi-restraints excluded: chain 3G residue 31 ILE Chi-restraints excluded: chain 3G residue 41 LYS Chi-restraints excluded: chain 3G residue 47 LEU Chi-restraints excluded: chain 3G residue 51 VAL Chi-restraints excluded: chain 3G residue 58 VAL Chi-restraints excluded: chain 3H residue 21 VAL Chi-restraints excluded: chain 3I residue 11 VAL Chi-restraints excluded: chain 3I residue 31 ILE Chi-restraints excluded: chain 3I residue 41 LYS Chi-restraints excluded: chain 3I residue 58 VAL Chi-restraints excluded: chain 3K residue 4 LEU Chi-restraints excluded: chain 3K residue 46 LEU Chi-restraints excluded: chain 3K residue 50 VAL Chi-restraints excluded: chain 3M residue 58 VAL Chi-restraints excluded: chain 3N residue 21 VAL Chi-restraints excluded: chain 3O residue 50 VAL Chi-restraints excluded: chain 3O residue 61 THR Chi-restraints excluded: chain 4B residue 31 ILE Chi-restraints excluded: chain 4C residue 26 ILE Chi-restraints excluded: chain 4D residue 31 ILE Chi-restraints excluded: chain 4H residue 21 VAL Chi-restraints excluded: chain 4I residue 21 VAL Chi-restraints excluded: chain 4I residue 23 MET Chi-restraints excluded: chain 4I residue 26 ILE Chi-restraints excluded: chain 4J residue 4 LEU Chi-restraints excluded: chain 4J residue 51 VAL Chi-restraints excluded: chain 4K residue 21 VAL Chi-restraints excluded: chain 4K residue 26 ILE Chi-restraints excluded: chain 4L residue 31 ILE Chi-restraints excluded: chain 4M residue 21 VAL Chi-restraints excluded: chain 4M residue 50 VAL Chi-restraints excluded: chain 4O residue 21 VAL Chi-restraints excluded: chain 4O residue 23 MET Chi-restraints excluded: chain 4O residue 27 ILE Chi-restraints excluded: chain 4O residue 31 ILE Chi-restraints excluded: chain 4P residue 50 VAL Chi-restraints excluded: chain 5B residue 11 VAL Chi-restraints excluded: chain 5B residue 26 ILE Chi-restraints excluded: chain 5B residue 47 LEU Chi-restraints excluded: chain 5C residue 11 VAL Chi-restraints excluded: chain 5C residue 31 ILE Chi-restraints excluded: chain 5C residue 43 LEU Chi-restraints excluded: chain 5D residue 4 LEU Chi-restraints excluded: chain 5E residue 21 VAL Chi-restraints excluded: chain 5E residue 26 ILE Chi-restraints excluded: chain 5E residue 31 ILE Chi-restraints excluded: chain 5E residue 50 VAL Chi-restraints excluded: chain 5F residue 3 LEU Chi-restraints excluded: chain 5F residue 11 VAL Chi-restraints excluded: chain 5F residue 26 ILE Chi-restraints excluded: chain 5F residue 53 ILE Chi-restraints excluded: chain 5G residue 31 ILE Chi-restraints excluded: chain 5H residue 26 ILE Chi-restraints excluded: chain 5H residue 31 ILE Chi-restraints excluded: chain 5I residue 4 LEU Chi-restraints excluded: chain 5I residue 23 MET Chi-restraints excluded: chain 5I residue 31 ILE Chi-restraints excluded: chain 5I residue 61 THR Chi-restraints excluded: chain 5K residue 4 LEU Chi-restraints excluded: chain 5L residue 4 LEU Chi-restraints excluded: chain 5L residue 21 VAL Chi-restraints excluded: chain 5L residue 50 VAL Chi-restraints excluded: chain 5M residue 11 VAL Chi-restraints excluded: chain 5M residue 23 MET Chi-restraints excluded: chain 5M residue 50 VAL Chi-restraints excluded: chain 5N residue 31 ILE Chi-restraints excluded: chain 5O residue 50 VAL Chi-restraints excluded: chain 5P residue 50 VAL Chi-restraints excluded: chain 5P residue 52 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 415 optimal weight: 20.0000 chunk 340 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 275 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 chunk 316 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 174 optimal weight: 0.0370 chunk 455 optimal weight: 10.0000 chunk 258 optimal weight: 20.0000 overall best weight: 5.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.122245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097684 restraints weight = 58370.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101841 restraints weight = 29255.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.104612 restraints weight = 18117.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.106452 restraints weight = 12992.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.107583 restraints weight = 10344.255| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.6630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 41600 Z= 0.174 Angle : 0.635 9.973 55411 Z= 0.312 Chirality : 0.038 0.177 7190 Planarity : 0.002 0.033 6070 Dihedral : 14.872 76.304 8495 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 5.36 % Allowed : 24.38 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.12), residues: 4880 helix: -0.58 (0.09), residues: 3280 sheet: None (None), residues: 0 loop : -1.12 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG3A 39 TYR 0.017 0.002 TYR4L 37 PHE 0.019 0.001 PHE3N 15 Details of bonding type rmsd covalent geometry : bond 0.00438 (41600) covalent geometry : angle 0.63548 (55410) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.04350 ( 2000) hydrogen bonds : angle 4.98965 ( 6000) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1922 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 1699 time to evaluate : 1.709 Fit side-chains REVERT: 1B 40 THR cc_start: 0.9306 (m) cc_final: 0.9035 (p) REVERT: 1C 22 MET cc_start: 0.8433 (tpp) cc_final: 0.8080 (tpp) REVERT: 1C 40 THR cc_start: 0.9410 (m) cc_final: 0.9007 (p) REVERT: 1E 40 THR cc_start: 0.9321 (m) cc_final: 0.8880 (p) REVERT: 1F 40 THR cc_start: 0.9247 (m) cc_final: 0.9008 (p) REVERT: 1G 40 THR cc_start: 0.9265 (m) cc_final: 0.8981 (p) REVERT: 1I 10 ASP cc_start: 0.7737 (p0) cc_final: 0.7505 (p0) REVERT: 1I 36 MET cc_start: 0.8455 (mtp) cc_final: 0.8166 (mtm) REVERT: 1I 40 THR cc_start: 0.9337 (m) cc_final: 0.8907 (p) REVERT: 1J 40 THR cc_start: 0.9234 (m) cc_final: 0.8657 (p) REVERT: 1K 40 THR cc_start: 0.9270 (m) cc_final: 0.9007 (p) REVERT: 1L 22 MET cc_start: 0.8523 (mmt) cc_final: 0.8172 (tpp) REVERT: 1M 29 GLU cc_start: 0.8357 (tp30) cc_final: 0.8000 (tp30) REVERT: 2A 4 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8016 (tt) REVERT: 2A 37 TYR cc_start: 0.9343 (t80) cc_final: 0.8786 (t80) REVERT: 2B 40 THR cc_start: 0.9293 (m) cc_final: 0.8893 (p) REVERT: 2C 37 TYR cc_start: 0.9172 (t80) cc_final: 0.8885 (t80) REVERT: 2D 3 LEU cc_start: 0.8308 (tp) cc_final: 0.7998 (tp) REVERT: 2D 46 LEU cc_start: 0.9258 (mt) cc_final: 0.9037 (mt) REVERT: 2E 22 MET cc_start: 0.8487 (tpp) cc_final: 0.7904 (tpp) REVERT: 2E 40 THR cc_start: 0.9307 (m) cc_final: 0.8851 (p) REVERT: 2G 39 ARG cc_start: 0.8159 (ttp-170) cc_final: 0.7901 (ttp80) REVERT: 2H 40 THR cc_start: 0.9291 (m) cc_final: 0.8872 (p) REVERT: 2I 12 LYS cc_start: 0.8715 (ttpt) cc_final: 0.8506 (ttmm) REVERT: 2I 40 THR cc_start: 0.9234 (m) cc_final: 0.8805 (p) REVERT: 2J 40 THR cc_start: 0.9137 (m) cc_final: 0.8847 (p) REVERT: 2L 40 THR cc_start: 0.9360 (m) cc_final: 0.8936 (p) REVERT: 2L 60 LEU cc_start: 0.8862 (mt) cc_final: 0.8625 (mt) REVERT: 2N 60 LEU cc_start: 0.8931 (mt) cc_final: 0.8587 (mt) REVERT: 3A 40 THR cc_start: 0.9215 (m) cc_final: 0.8975 (p) REVERT: 3B 23 MET cc_start: 0.7926 (ttm) cc_final: 0.7700 (ttm) REVERT: 3B 40 THR cc_start: 0.9250 (m) cc_final: 0.8864 (p) REVERT: 3C 40 THR cc_start: 0.9133 (m) cc_final: 0.8731 (p) REVERT: 3D 40 THR cc_start: 0.9378 (m) cc_final: 0.8973 (p) REVERT: 3E 40 THR cc_start: 0.9208 (m) cc_final: 0.8899 (p) REVERT: 3F 40 THR cc_start: 0.9285 (m) cc_final: 0.8994 (p) REVERT: 3H 3 LEU cc_start: 0.8468 (tp) cc_final: 0.8212 (tp) REVERT: 3H 40 THR cc_start: 0.9297 (m) cc_final: 0.8999 (p) REVERT: 3H 46 LEU cc_start: 0.9354 (mt) cc_final: 0.9130 (mt) REVERT: 3I 40 THR cc_start: 0.9326 (m) cc_final: 0.9098 (p) REVERT: 3J 39 ARG cc_start: 0.8095 (ttp80) cc_final: 0.7845 (ttp80) REVERT: 3J 40 THR cc_start: 0.9336 (m) cc_final: 0.8848 (p) REVERT: 3K 40 THR cc_start: 0.9306 (m) cc_final: 0.8897 (p) REVERT: 3L 40 THR cc_start: 0.9303 (m) cc_final: 0.8865 (p) REVERT: 3M 39 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7936 (ttp80) REVERT: 3O 23 MET cc_start: 0.8158 (ttm) cc_final: 0.7917 (ttm) REVERT: 3O 37 TYR cc_start: 0.9216 (t80) cc_final: 0.8962 (t80) REVERT: 4A 40 THR cc_start: 0.9218 (m) cc_final: 0.8767 (p) REVERT: 4B 40 THR cc_start: 0.9164 (m) cc_final: 0.8830 (p) REVERT: 4C 22 MET cc_start: 0.8155 (tpp) cc_final: 0.7677 (tpp) REVERT: 4C 40 THR cc_start: 0.9237 (m) cc_final: 0.8820 (p) REVERT: 4D 36 MET cc_start: 0.8337 (mtm) cc_final: 0.7995 (mtm) REVERT: 4D 40 THR cc_start: 0.9252 (m) cc_final: 0.8843 (p) REVERT: 4E 37 TYR cc_start: 0.9283 (t80) cc_final: 0.9025 (t80) REVERT: 4E 43 LEU cc_start: 0.8855 (mt) cc_final: 0.8597 (mt) REVERT: 4F 40 THR cc_start: 0.9287 (m) cc_final: 0.8909 (p) REVERT: 4H 40 THR cc_start: 0.9282 (m) cc_final: 0.8950 (p) REVERT: 4K 40 THR cc_start: 0.9301 (m) cc_final: 0.8969 (p) REVERT: 4K 60 LEU cc_start: 0.8945 (mt) cc_final: 0.8691 (mt) REVERT: 4L 40 THR cc_start: 0.9097 (m) cc_final: 0.8810 (p) REVERT: 4L 46 LEU cc_start: 0.9279 (mt) cc_final: 0.9042 (mt) REVERT: 4L 60 LEU cc_start: 0.8854 (mt) cc_final: 0.8649 (mt) REVERT: 4N 46 LEU cc_start: 0.9301 (mt) cc_final: 0.9062 (mt) REVERT: 4N 60 LEU cc_start: 0.8964 (mt) cc_final: 0.8566 (mt) REVERT: 4O 37 TYR cc_start: 0.9328 (t80) cc_final: 0.8991 (t80) REVERT: 4O 46 LEU cc_start: 0.9302 (mt) cc_final: 0.9055 (mt) REVERT: 5C 36 MET cc_start: 0.8448 (mtp) cc_final: 0.8203 (mtp) REVERT: 5C 40 THR cc_start: 0.9298 (m) cc_final: 0.8757 (p) REVERT: 5D 40 THR cc_start: 0.9303 (m) cc_final: 0.8956 (p) REVERT: 5E 26 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8393 (mt) REVERT: 5E 40 THR cc_start: 0.9223 (m) cc_final: 0.8650 (p) REVERT: 5F 40 THR cc_start: 0.9150 (m) cc_final: 0.8825 (p) REVERT: 5G 40 THR cc_start: 0.9282 (m) cc_final: 0.8915 (p) REVERT: 5H 40 THR cc_start: 0.9272 (m) cc_final: 0.8739 (p) REVERT: 5I 4 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7838 (tt) REVERT: 5I 40 THR cc_start: 0.9155 (m) cc_final: 0.8722 (p) REVERT: 5J 40 THR cc_start: 0.9290 (m) cc_final: 0.8830 (p) REVERT: 5K 40 THR cc_start: 0.9320 (m) cc_final: 0.8935 (p) REVERT: 5L 23 MET cc_start: 0.7892 (ttm) cc_final: 0.7462 (ttm) REVERT: 5N 60 LEU cc_start: 0.8920 (mt) cc_final: 0.8691 (mt) REVERT: 5P 46 LEU cc_start: 0.9369 (mt) cc_final: 0.9062 (mt) outliers start: 223 outliers final: 178 residues processed: 1792 average time/residue: 0.2118 time to fit residues: 632.2839 Evaluate side-chains 1817 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 1636 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 21 VAL Chi-restraints excluded: chain 1A residue 23 MET Chi-restraints excluded: chain 1A residue 51 VAL Chi-restraints excluded: chain 1A residue 57 THR Chi-restraints excluded: chain 1B residue 26 ILE Chi-restraints excluded: chain 1C residue 26 ILE Chi-restraints excluded: chain 1D residue 11 VAL Chi-restraints excluded: chain 1D residue 26 ILE Chi-restraints excluded: chain 1D residue 31 ILE Chi-restraints excluded: chain 1E residue 21 VAL Chi-restraints excluded: chain 1E residue 26 ILE Chi-restraints excluded: chain 1E residue 31 ILE Chi-restraints excluded: chain 1F residue 26 ILE Chi-restraints excluded: chain 1G residue 25 ILE Chi-restraints excluded: chain 1G residue 26 ILE Chi-restraints excluded: chain 1G residue 31 ILE Chi-restraints excluded: chain 1G residue 47 LEU Chi-restraints excluded: chain 1G residue 51 VAL Chi-restraints excluded: chain 1G residue 58 VAL Chi-restraints excluded: chain 1H residue 19 SER Chi-restraints excluded: chain 1H residue 23 MET Chi-restraints excluded: chain 1H residue 26 ILE Chi-restraints excluded: chain 1I residue 23 MET Chi-restraints excluded: chain 1I residue 26 ILE Chi-restraints excluded: chain 1I residue 31 ILE Chi-restraints excluded: chain 1I residue 57 THR Chi-restraints excluded: chain 1J residue 19 SER Chi-restraints excluded: chain 1J residue 21 VAL Chi-restraints excluded: chain 1J residue 26 ILE Chi-restraints excluded: chain 1L residue 26 ILE Chi-restraints excluded: chain 1L residue 53 ILE Chi-restraints excluded: chain 1M residue 23 MET Chi-restraints excluded: chain 1M residue 50 VAL Chi-restraints excluded: chain 1N residue 57 THR Chi-restraints excluded: chain 1O residue 31 ILE Chi-restraints excluded: chain 1P residue 52 VAL Chi-restraints excluded: chain 2A residue 4 LEU Chi-restraints excluded: chain 2A residue 23 MET Chi-restraints excluded: chain 2A residue 31 ILE Chi-restraints excluded: chain 2A residue 47 LEU Chi-restraints excluded: chain 2A residue 51 VAL Chi-restraints excluded: chain 2B residue 12 LYS Chi-restraints excluded: chain 2B residue 23 MET Chi-restraints excluded: chain 2B residue 26 ILE Chi-restraints excluded: chain 2B residue 31 ILE Chi-restraints excluded: chain 2B residue 47 LEU Chi-restraints excluded: chain 2C residue 26 ILE Chi-restraints excluded: chain 2D residue 26 ILE Chi-restraints excluded: chain 2D residue 53 ILE Chi-restraints excluded: chain 2E residue 47 LEU Chi-restraints excluded: chain 2F residue 4 LEU Chi-restraints excluded: chain 2F residue 31 ILE Chi-restraints excluded: chain 2F residue 47 LEU Chi-restraints excluded: chain 2F residue 51 VAL Chi-restraints excluded: chain 2G residue 23 MET Chi-restraints excluded: chain 2G residue 26 ILE Chi-restraints excluded: chain 2H residue 26 ILE Chi-restraints excluded: chain 2H residue 31 ILE Chi-restraints excluded: chain 2I residue 21 VAL Chi-restraints excluded: chain 2I residue 26 ILE Chi-restraints excluded: chain 2I residue 47 LEU Chi-restraints excluded: chain 2I residue 51 VAL Chi-restraints excluded: chain 2I residue 52 VAL Chi-restraints excluded: chain 2I residue 53 ILE Chi-restraints excluded: chain 2J residue 4 LEU Chi-restraints excluded: chain 2J residue 26 ILE Chi-restraints excluded: chain 2J residue 47 LEU Chi-restraints excluded: chain 2K residue 4 LEU Chi-restraints excluded: chain 2K residue 51 VAL Chi-restraints excluded: chain 2K residue 61 THR Chi-restraints excluded: chain 2L residue 23 MET Chi-restraints excluded: chain 2L residue 52 VAL Chi-restraints excluded: chain 2L residue 58 VAL Chi-restraints excluded: chain 2M residue 11 VAL Chi-restraints excluded: chain 2M residue 31 ILE Chi-restraints excluded: chain 2N residue 50 VAL Chi-restraints excluded: chain 2N residue 58 VAL Chi-restraints excluded: chain 2N residue 63 ILE Chi-restraints excluded: chain 2P residue 41 LYS Chi-restraints excluded: chain 2P residue 53 ILE Chi-restraints excluded: chain 3A residue 21 VAL Chi-restraints excluded: chain 3B residue 26 ILE Chi-restraints excluded: chain 3C residue 12 LYS Chi-restraints excluded: chain 3C residue 31 ILE Chi-restraints excluded: chain 3C residue 41 LYS Chi-restraints excluded: chain 3C residue 51 VAL Chi-restraints excluded: chain 3C residue 57 THR Chi-restraints excluded: chain 3E residue 11 VAL Chi-restraints excluded: chain 3E residue 26 ILE Chi-restraints excluded: chain 3E residue 46 LEU Chi-restraints excluded: chain 3F residue 11 VAL Chi-restraints excluded: chain 3F residue 26 ILE Chi-restraints excluded: chain 3F residue 47 LEU Chi-restraints excluded: chain 3F residue 50 VAL Chi-restraints excluded: chain 3F residue 51 VAL Chi-restraints excluded: chain 3G residue 23 MET Chi-restraints excluded: chain 3G residue 31 ILE Chi-restraints excluded: chain 3G residue 47 LEU Chi-restraints excluded: chain 3G residue 51 VAL Chi-restraints excluded: chain 3G residue 57 THR Chi-restraints excluded: chain 3G residue 58 VAL Chi-restraints excluded: chain 3H residue 11 VAL Chi-restraints excluded: chain 3H residue 21 VAL Chi-restraints excluded: chain 3I residue 11 VAL Chi-restraints excluded: chain 3I residue 23 MET Chi-restraints excluded: chain 3I residue 31 ILE Chi-restraints excluded: chain 3I residue 58 VAL Chi-restraints excluded: chain 3I residue 61 THR Chi-restraints excluded: chain 3J residue 11 VAL Chi-restraints excluded: chain 3K residue 4 LEU Chi-restraints excluded: chain 3K residue 23 MET Chi-restraints excluded: chain 3K residue 46 LEU Chi-restraints excluded: chain 3K residue 50 VAL Chi-restraints excluded: chain 3K residue 51 VAL Chi-restraints excluded: chain 3L residue 51 VAL Chi-restraints excluded: chain 3L residue 53 ILE Chi-restraints excluded: chain 3M residue 21 VAL Chi-restraints excluded: chain 3M residue 58 VAL Chi-restraints excluded: chain 3N residue 21 VAL Chi-restraints excluded: chain 4B residue 31 ILE Chi-restraints excluded: chain 4C residue 26 ILE Chi-restraints excluded: chain 4D residue 31 ILE Chi-restraints excluded: chain 4D residue 41 LYS Chi-restraints excluded: chain 4D residue 47 LEU Chi-restraints excluded: chain 4F residue 4 LEU Chi-restraints excluded: chain 4F residue 26 ILE Chi-restraints excluded: chain 4H residue 21 VAL Chi-restraints excluded: chain 4I residue 21 VAL Chi-restraints excluded: chain 4I residue 23 MET Chi-restraints excluded: chain 4I residue 26 ILE Chi-restraints excluded: chain 4J residue 4 LEU Chi-restraints excluded: chain 4J residue 51 VAL Chi-restraints excluded: chain 4K residue 21 VAL Chi-restraints excluded: chain 4K residue 26 ILE Chi-restraints excluded: chain 4L residue 23 MET Chi-restraints excluded: chain 4L residue 31 ILE Chi-restraints excluded: chain 4M residue 21 VAL Chi-restraints excluded: chain 4M residue 43 LEU Chi-restraints excluded: chain 4N residue 23 MET Chi-restraints excluded: chain 4O residue 21 VAL Chi-restraints excluded: chain 4O residue 31 ILE Chi-restraints excluded: chain 4O residue 50 VAL Chi-restraints excluded: chain 4O residue 57 THR Chi-restraints excluded: chain 4P residue 52 VAL Chi-restraints excluded: chain 5A residue 31 ILE Chi-restraints excluded: chain 5A residue 57 THR Chi-restraints excluded: chain 5B residue 11 VAL Chi-restraints excluded: chain 5B residue 26 ILE Chi-restraints excluded: chain 5B residue 47 LEU Chi-restraints excluded: chain 5B residue 53 ILE Chi-restraints excluded: chain 5C residue 11 VAL Chi-restraints excluded: chain 5C residue 31 ILE Chi-restraints excluded: chain 5C residue 43 LEU Chi-restraints excluded: chain 5C residue 57 THR Chi-restraints excluded: chain 5D residue 4 LEU Chi-restraints excluded: chain 5E residue 21 VAL Chi-restraints excluded: chain 5E residue 26 ILE Chi-restraints excluded: chain 5E residue 31 ILE Chi-restraints excluded: chain 5E residue 50 VAL Chi-restraints excluded: chain 5F residue 4 LEU Chi-restraints excluded: chain 5F residue 11 VAL Chi-restraints excluded: chain 5F residue 26 ILE Chi-restraints excluded: chain 5G residue 31 ILE Chi-restraints excluded: chain 5G residue 57 THR Chi-restraints excluded: chain 5H residue 26 ILE Chi-restraints excluded: chain 5H residue 31 ILE Chi-restraints excluded: chain 5I residue 4 LEU Chi-restraints excluded: chain 5I residue 23 MET Chi-restraints excluded: chain 5I residue 31 ILE Chi-restraints excluded: chain 5I residue 53 ILE Chi-restraints excluded: chain 5I residue 57 THR Chi-restraints excluded: chain 5I residue 61 THR Chi-restraints excluded: chain 5J residue 50 VAL Chi-restraints excluded: chain 5J residue 52 VAL Chi-restraints excluded: chain 5K residue 4 LEU Chi-restraints excluded: chain 5K residue 31 ILE Chi-restraints excluded: chain 5L residue 4 LEU Chi-restraints excluded: chain 5L residue 21 VAL Chi-restraints excluded: chain 5M residue 11 VAL Chi-restraints excluded: chain 5M residue 23 MET Chi-restraints excluded: chain 5P residue 52 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 2 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 352 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 467 optimal weight: 2.9990 chunk 345 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 183 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.124613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.100191 restraints weight = 57980.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.104410 restraints weight = 28746.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.107216 restraints weight = 17625.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109105 restraints weight = 12535.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.110314 restraints weight = 9901.961| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.6972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 41600 Z= 0.128 Angle : 0.593 9.560 55411 Z= 0.292 Chirality : 0.037 0.179 7190 Planarity : 0.002 0.029 6070 Dihedral : 14.293 74.224 8495 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.95 % Allowed : 27.69 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.12), residues: 4880 helix: -0.34 (0.09), residues: 3280 sheet: None (None), residues: 0 loop : -1.08 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG3A 39 TYR 0.021 0.002 TYR3N 37 PHE 0.016 0.001 PHE5A 15 Details of bonding type rmsd covalent geometry : bond 0.00322 (41600) covalent geometry : angle 0.59336 (55410) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.03860 ( 2000) hydrogen bonds : angle 4.84979 ( 6000) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1952 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 1746 time to evaluate : 1.446 Fit side-chains REVERT: 1B 40 THR cc_start: 0.9201 (m) cc_final: 0.8936 (p) REVERT: 1C 22 MET cc_start: 0.8435 (tpp) cc_final: 0.8110 (tpp) REVERT: 1C 40 THR cc_start: 0.9310 (m) cc_final: 0.8879 (p) REVERT: 1E 40 THR cc_start: 0.9207 (m) cc_final: 0.8775 (p) REVERT: 1F 22 MET cc_start: 0.7913 (tpp) cc_final: 0.7675 (tpp) REVERT: 1F 40 THR cc_start: 0.9229 (m) cc_final: 0.9013 (p) REVERT: 1G 40 THR cc_start: 0.9204 (m) cc_final: 0.8918 (p) REVERT: 1H 40 THR cc_start: 0.9341 (m) cc_final: 0.8866 (p) REVERT: 1I 40 THR cc_start: 0.9270 (m) cc_final: 0.8796 (p) REVERT: 1I 46 LEU cc_start: 0.9415 (mt) cc_final: 0.9186 (mp) REVERT: 1J 40 THR cc_start: 0.9093 (m) cc_final: 0.8384 (p) REVERT: 1K 40 THR cc_start: 0.9217 (m) cc_final: 0.8936 (p) REVERT: 1L 22 MET cc_start: 0.8426 (mmt) cc_final: 0.8109 (tpp) REVERT: 1M 29 GLU cc_start: 0.8421 (tp30) cc_final: 0.8127 (tp30) REVERT: 1P 47 LEU cc_start: 0.8910 (tt) cc_final: 0.8290 (mt) REVERT: 2A 4 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7843 (tt) REVERT: 2A 23 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7831 (ptm) REVERT: 2A 37 TYR cc_start: 0.9325 (t80) cc_final: 0.8714 (t80) REVERT: 2B 36 MET cc_start: 0.8216 (mtm) cc_final: 0.7991 (mtm) REVERT: 2B 40 THR cc_start: 0.9254 (m) cc_final: 0.8858 (p) REVERT: 2C 37 TYR cc_start: 0.9127 (t80) cc_final: 0.8799 (t80) REVERT: 2D 3 LEU cc_start: 0.8306 (tp) cc_final: 0.7974 (tp) REVERT: 2D 26 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8717 (mt) REVERT: 2E 22 MET cc_start: 0.8478 (tpp) cc_final: 0.7883 (tpp) REVERT: 2E 40 THR cc_start: 0.9260 (m) cc_final: 0.8832 (p) REVERT: 2G 39 ARG cc_start: 0.8101 (ttp-170) cc_final: 0.7805 (ttp80) REVERT: 2H 40 THR cc_start: 0.9176 (m) cc_final: 0.8743 (p) REVERT: 2I 40 THR cc_start: 0.9114 (m) cc_final: 0.8647 (p) REVERT: 2J 40 THR cc_start: 0.9122 (m) cc_final: 0.8753 (p) REVERT: 2L 29 GLU cc_start: 0.8359 (tp30) cc_final: 0.7873 (tp30) REVERT: 2L 40 THR cc_start: 0.9279 (m) cc_final: 0.8799 (p) REVERT: 2L 46 LEU cc_start: 0.9199 (mt) cc_final: 0.8999 (mt) REVERT: 2N 29 GLU cc_start: 0.8473 (tp30) cc_final: 0.8058 (tp30) REVERT: 2N 60 LEU cc_start: 0.8913 (mt) cc_final: 0.8590 (mt) REVERT: 3A 40 THR cc_start: 0.9143 (m) cc_final: 0.8839 (p) REVERT: 3B 40 THR cc_start: 0.9270 (m) cc_final: 0.8864 (p) REVERT: 3C 40 THR cc_start: 0.9042 (m) cc_final: 0.8660 (p) REVERT: 3D 40 THR cc_start: 0.9322 (m) cc_final: 0.8965 (p) REVERT: 3E 40 THR cc_start: 0.9168 (m) cc_final: 0.8827 (p) REVERT: 3E 41 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8330 (tttt) REVERT: 3F 40 THR cc_start: 0.9164 (m) cc_final: 0.8858 (p) REVERT: 3G 41 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8501 (tttp) REVERT: 3H 40 THR cc_start: 0.9198 (m) cc_final: 0.8923 (p) REVERT: 3H 46 LEU cc_start: 0.9298 (mt) cc_final: 0.8993 (mt) REVERT: 3J 39 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7778 (ttp80) REVERT: 3J 40 THR cc_start: 0.9278 (m) cc_final: 0.8792 (p) REVERT: 3K 40 THR cc_start: 0.9240 (m) cc_final: 0.8816 (p) REVERT: 3L 40 THR cc_start: 0.9232 (m) cc_final: 0.8704 (p) REVERT: 3M 39 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7894 (ttp80) REVERT: 3M 47 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8754 (mt) REVERT: 4A 22 MET cc_start: 0.8259 (tpp) cc_final: 0.8046 (tpp) REVERT: 4A 40 THR cc_start: 0.9127 (m) cc_final: 0.8731 (p) REVERT: 4B 40 THR cc_start: 0.9095 (m) cc_final: 0.8772 (p) REVERT: 4C 22 MET cc_start: 0.8176 (tpp) cc_final: 0.7744 (tpp) REVERT: 4C 40 THR cc_start: 0.9257 (m) cc_final: 0.8824 (p) REVERT: 4D 40 THR cc_start: 0.9175 (m) cc_final: 0.8778 (p) REVERT: 4D 41 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8399 (tttt) REVERT: 4E 37 TYR cc_start: 0.9268 (t80) cc_final: 0.8967 (t80) REVERT: 4F 40 THR cc_start: 0.9311 (m) cc_final: 0.8902 (p) REVERT: 4H 40 THR cc_start: 0.9235 (m) cc_final: 0.8892 (p) REVERT: 4K 40 THR cc_start: 0.9266 (m) cc_final: 0.8905 (p) REVERT: 4K 60 LEU cc_start: 0.8939 (mt) cc_final: 0.8686 (mt) REVERT: 4L 40 THR cc_start: 0.9055 (m) cc_final: 0.8788 (p) REVERT: 4L 46 LEU cc_start: 0.9276 (mt) cc_final: 0.9062 (mt) REVERT: 4N 46 LEU cc_start: 0.9287 (mt) cc_final: 0.8998 (mt) REVERT: 4N 60 LEU cc_start: 0.8965 (mt) cc_final: 0.8532 (mt) REVERT: 4O 37 TYR cc_start: 0.9304 (t80) cc_final: 0.8999 (t80) REVERT: 4O 46 LEU cc_start: 0.9314 (mt) cc_final: 0.9065 (mt) REVERT: 5B 39 ARG cc_start: 0.8159 (ttp-170) cc_final: 0.7913 (ttp80) REVERT: 5C 36 MET cc_start: 0.8400 (mtp) cc_final: 0.8151 (mtp) REVERT: 5C 40 THR cc_start: 0.9288 (m) cc_final: 0.8713 (p) REVERT: 5D 40 THR cc_start: 0.9231 (m) cc_final: 0.8884 (p) REVERT: 5E 40 THR cc_start: 0.9093 (m) cc_final: 0.8516 (p) REVERT: 5F 40 THR cc_start: 0.9119 (m) cc_final: 0.8741 (p) REVERT: 5G 40 THR cc_start: 0.9230 (m) cc_final: 0.8877 (p) REVERT: 5G 47 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8673 (mt) REVERT: 5H 40 THR cc_start: 0.9188 (m) cc_final: 0.8632 (p) REVERT: 5I 4 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7817 (tt) REVERT: 5I 40 THR cc_start: 0.9248 (m) cc_final: 0.8782 (p) REVERT: 5J 40 THR cc_start: 0.9206 (m) cc_final: 0.8777 (p) REVERT: 5K 40 THR cc_start: 0.9303 (m) cc_final: 0.9039 (p) REVERT: 5L 23 MET cc_start: 0.7812 (ttm) cc_final: 0.7356 (ttm) REVERT: 5N 60 LEU cc_start: 0.8934 (mt) cc_final: 0.8693 (mt) REVERT: 5O 29 GLU cc_start: 0.8294 (tp30) cc_final: 0.7842 (tp30) REVERT: 5O 60 LEU cc_start: 0.8914 (mt) cc_final: 0.8534 (mt) REVERT: 5P 46 LEU cc_start: 0.9355 (mt) cc_final: 0.9024 (mt) outliers start: 206 outliers final: 161 residues processed: 1816 average time/residue: 0.2237 time to fit residues: 675.6759 Evaluate side-chains 1846 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 1676 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 21 VAL Chi-restraints excluded: chain 1A residue 23 MET Chi-restraints excluded: chain 1A residue 57 THR Chi-restraints excluded: chain 1B residue 26 ILE Chi-restraints excluded: chain 1C residue 26 ILE Chi-restraints excluded: chain 1C residue 53 ILE Chi-restraints excluded: chain 1D residue 11 VAL Chi-restraints excluded: chain 1D residue 26 ILE Chi-restraints excluded: chain 1D residue 31 ILE Chi-restraints excluded: chain 1D residue 47 LEU Chi-restraints excluded: chain 1D residue 51 VAL Chi-restraints excluded: chain 1E residue 21 VAL Chi-restraints excluded: chain 1E residue 26 ILE Chi-restraints excluded: chain 1E residue 31 ILE Chi-restraints excluded: chain 1F residue 26 ILE Chi-restraints excluded: chain 1G residue 25 ILE Chi-restraints excluded: chain 1G residue 26 ILE Chi-restraints excluded: chain 1G residue 31 ILE Chi-restraints excluded: chain 1G residue 47 LEU Chi-restraints excluded: chain 1G residue 51 VAL Chi-restraints excluded: chain 1H residue 19 SER Chi-restraints excluded: chain 1H residue 23 MET Chi-restraints excluded: chain 1H residue 26 ILE Chi-restraints excluded: chain 1H residue 46 LEU Chi-restraints excluded: chain 1H residue 47 LEU Chi-restraints excluded: chain 1I residue 23 MET Chi-restraints excluded: chain 1I residue 26 ILE Chi-restraints excluded: chain 1I residue 31 ILE Chi-restraints excluded: chain 1J residue 19 SER Chi-restraints excluded: chain 1J residue 21 VAL Chi-restraints excluded: chain 1J residue 26 ILE Chi-restraints excluded: chain 1K residue 23 MET Chi-restraints excluded: chain 1L residue 23 MET Chi-restraints excluded: chain 1L residue 26 ILE Chi-restraints excluded: chain 1L residue 49 LEU Chi-restraints excluded: chain 1L residue 53 ILE Chi-restraints excluded: chain 1M residue 11 VAL Chi-restraints excluded: chain 1M residue 47 LEU Chi-restraints excluded: chain 1O residue 31 ILE Chi-restraints excluded: chain 2A residue 4 LEU Chi-restraints excluded: chain 2A residue 12 LYS Chi-restraints excluded: chain 2A residue 23 MET Chi-restraints excluded: chain 2A residue 47 LEU Chi-restraints excluded: chain 2A residue 51 VAL Chi-restraints excluded: chain 2B residue 23 MET Chi-restraints excluded: chain 2B residue 26 ILE Chi-restraints excluded: chain 2C residue 26 ILE Chi-restraints excluded: chain 2D residue 26 ILE Chi-restraints excluded: chain 2E residue 47 LEU Chi-restraints excluded: chain 2F residue 4 LEU Chi-restraints excluded: chain 2F residue 31 ILE Chi-restraints excluded: chain 2F residue 47 LEU Chi-restraints excluded: chain 2F residue 51 VAL Chi-restraints excluded: chain 2G residue 23 MET Chi-restraints excluded: chain 2G residue 26 ILE Chi-restraints excluded: chain 2H residue 26 ILE Chi-restraints excluded: chain 2I residue 26 ILE Chi-restraints excluded: chain 2I residue 47 LEU Chi-restraints excluded: chain 2I residue 51 VAL Chi-restraints excluded: chain 2I residue 52 VAL Chi-restraints excluded: chain 2J residue 4 LEU Chi-restraints excluded: chain 2J residue 26 ILE Chi-restraints excluded: chain 2J residue 47 LEU Chi-restraints excluded: chain 2J residue 52 VAL Chi-restraints excluded: chain 2K residue 4 LEU Chi-restraints excluded: chain 2K residue 51 VAL Chi-restraints excluded: chain 2L residue 57 THR Chi-restraints excluded: chain 2L residue 58 VAL Chi-restraints excluded: chain 2M residue 11 VAL Chi-restraints excluded: chain 2N residue 50 VAL Chi-restraints excluded: chain 2N residue 58 VAL Chi-restraints excluded: chain 2N residue 63 ILE Chi-restraints excluded: chain 2P residue 41 LYS Chi-restraints excluded: chain 3A residue 21 VAL Chi-restraints excluded: chain 3B residue 4 LEU Chi-restraints excluded: chain 3B residue 26 ILE Chi-restraints excluded: chain 3C residue 12 LYS Chi-restraints excluded: chain 3C residue 31 ILE Chi-restraints excluded: chain 3C residue 51 VAL Chi-restraints excluded: chain 3E residue 26 ILE Chi-restraints excluded: chain 3E residue 41 LYS Chi-restraints excluded: chain 3E residue 46 LEU Chi-restraints excluded: chain 3F residue 11 VAL Chi-restraints excluded: chain 3F residue 26 ILE Chi-restraints excluded: chain 3F residue 43 LEU Chi-restraints excluded: chain 3F residue 50 VAL Chi-restraints excluded: chain 3G residue 23 MET Chi-restraints excluded: chain 3G residue 31 ILE Chi-restraints excluded: chain 3G residue 41 LYS Chi-restraints excluded: chain 3G residue 47 LEU Chi-restraints excluded: chain 3G residue 51 VAL Chi-restraints excluded: chain 3H residue 11 VAL Chi-restraints excluded: chain 3H residue 21 VAL Chi-restraints excluded: chain 3H residue 23 MET Chi-restraints excluded: chain 3I residue 11 VAL Chi-restraints excluded: chain 3I residue 23 MET Chi-restraints excluded: chain 3I residue 47 LEU Chi-restraints excluded: chain 3I residue 52 VAL Chi-restraints excluded: chain 3I residue 58 VAL Chi-restraints excluded: chain 3K residue 4 LEU Chi-restraints excluded: chain 3K residue 23 MET Chi-restraints excluded: chain 3K residue 46 LEU Chi-restraints excluded: chain 3K residue 47 LEU Chi-restraints excluded: chain 3K residue 50 VAL Chi-restraints excluded: chain 3K residue 51 VAL Chi-restraints excluded: chain 3L residue 53 ILE Chi-restraints excluded: chain 3M residue 21 VAL Chi-restraints excluded: chain 3M residue 47 LEU Chi-restraints excluded: chain 3M residue 58 VAL Chi-restraints excluded: chain 3N residue 21 VAL Chi-restraints excluded: chain 3N residue 23 MET Chi-restraints excluded: chain 4A residue 43 LEU Chi-restraints excluded: chain 4B residue 31 ILE Chi-restraints excluded: chain 4C residue 26 ILE Chi-restraints excluded: chain 4D residue 31 ILE Chi-restraints excluded: chain 4D residue 41 LYS Chi-restraints excluded: chain 4D residue 47 LEU Chi-restraints excluded: chain 4E residue 23 MET Chi-restraints excluded: chain 4F residue 4 LEU Chi-restraints excluded: chain 4F residue 26 ILE Chi-restraints excluded: chain 4H residue 21 VAL Chi-restraints excluded: chain 4I residue 21 VAL Chi-restraints excluded: chain 4I residue 23 MET Chi-restraints excluded: chain 4I residue 26 ILE Chi-restraints excluded: chain 4J residue 4 LEU Chi-restraints excluded: chain 4K residue 21 VAL Chi-restraints excluded: chain 4K residue 26 ILE Chi-restraints excluded: chain 4K residue 47 LEU Chi-restraints excluded: chain 4L residue 31 ILE Chi-restraints excluded: chain 4M residue 21 VAL Chi-restraints excluded: chain 4M residue 23 MET Chi-restraints excluded: chain 4N residue 23 MET Chi-restraints excluded: chain 4O residue 21 VAL Chi-restraints excluded: chain 4O residue 31 ILE Chi-restraints excluded: chain 4P residue 47 LEU Chi-restraints excluded: chain 4P residue 52 VAL Chi-restraints excluded: chain 5B residue 11 VAL Chi-restraints excluded: chain 5B residue 26 ILE Chi-restraints excluded: chain 5B residue 47 LEU Chi-restraints excluded: chain 5B residue 53 ILE Chi-restraints excluded: chain 5C residue 11 VAL Chi-restraints excluded: chain 5C residue 31 ILE Chi-restraints excluded: chain 5C residue 43 LEU Chi-restraints excluded: chain 5D residue 4 LEU Chi-restraints excluded: chain 5E residue 21 VAL Chi-restraints excluded: chain 5E residue 26 ILE Chi-restraints excluded: chain 5E residue 31 ILE Chi-restraints excluded: chain 5E residue 50 VAL Chi-restraints excluded: chain 5F residue 4 LEU Chi-restraints excluded: chain 5F residue 11 VAL Chi-restraints excluded: chain 5F residue 26 ILE Chi-restraints excluded: chain 5F residue 47 LEU Chi-restraints excluded: chain 5F residue 53 ILE Chi-restraints excluded: chain 5G residue 27 ILE Chi-restraints excluded: chain 5G residue 31 ILE Chi-restraints excluded: chain 5G residue 47 LEU Chi-restraints excluded: chain 5H residue 26 ILE Chi-restraints excluded: chain 5I residue 4 LEU Chi-restraints excluded: chain 5I residue 31 ILE Chi-restraints excluded: chain 5I residue 53 ILE Chi-restraints excluded: chain 5I residue 61 THR Chi-restraints excluded: chain 5J residue 50 VAL Chi-restraints excluded: chain 5J residue 52 VAL Chi-restraints excluded: chain 5K residue 4 LEU Chi-restraints excluded: chain 5L residue 21 VAL Chi-restraints excluded: chain 5L residue 52 VAL Chi-restraints excluded: chain 5M residue 11 VAL Chi-restraints excluded: chain 5N residue 21 VAL Chi-restraints excluded: chain 5P residue 50 VAL Chi-restraints excluded: chain 5P residue 52 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 9.9990 chunk 243 optimal weight: 4.9990 chunk 418 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 368 optimal weight: 10.0000 chunk 120 optimal weight: 40.0000 chunk 265 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 178 optimal weight: 10.0000 chunk 269 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.118741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.094537 restraints weight = 58566.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098678 restraints weight = 29278.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.101420 restraints weight = 17999.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.103270 restraints weight = 12827.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.104420 restraints weight = 10137.646| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.7012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 41600 Z= 0.206 Angle : 0.668 10.542 55411 Z= 0.327 Chirality : 0.039 0.199 7190 Planarity : 0.002 0.033 6070 Dihedral : 15.054 75.101 8495 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 6.03 % Allowed : 28.08 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.12), residues: 4880 helix: -0.52 (0.08), residues: 3280 sheet: None (None), residues: 0 loop : -1.12 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG3A 39 TYR 0.020 0.002 TYR3N 37 PHE 0.022 0.001 PHE3N 15 Details of bonding type rmsd covalent geometry : bond 0.00521 (41600) covalent geometry : angle 0.66829 (55410) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.04609 ( 2000) hydrogen bonds : angle 5.04166 ( 6000) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1918 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 251 poor density : 1667 time to evaluate : 2.182 Fit side-chains REVERT: 1A 40 THR cc_start: 0.9213 (m) cc_final: 0.8797 (p) REVERT: 1B 40 THR cc_start: 0.9216 (m) cc_final: 0.8986 (p) REVERT: 1C 22 MET cc_start: 0.8437 (tpp) cc_final: 0.8026 (tpp) REVERT: 1C 40 THR cc_start: 0.9364 (m) cc_final: 0.8924 (p) REVERT: 1E 40 THR cc_start: 0.9301 (m) cc_final: 0.8897 (p) REVERT: 1F 40 THR cc_start: 0.9259 (m) cc_final: 0.9046 (p) REVERT: 1G 40 THR cc_start: 0.9369 (m) cc_final: 0.9117 (p) REVERT: 1H 40 THR cc_start: 0.9424 (m) cc_final: 0.8997 (p) REVERT: 1I 40 THR cc_start: 0.9238 (m) cc_final: 0.8738 (p) REVERT: 1J 40 THR cc_start: 0.9094 (m) cc_final: 0.8455 (p) REVERT: 1K 40 THR cc_start: 0.9166 (m) cc_final: 0.8885 (p) REVERT: 1L 22 MET cc_start: 0.8442 (mmt) cc_final: 0.8062 (tpp) REVERT: 1L 40 THR cc_start: 0.9254 (m) cc_final: 0.8684 (p) REVERT: 1M 29 GLU cc_start: 0.8342 (tp30) cc_final: 0.8126 (tp30) REVERT: 1P 39 ARG cc_start: 0.6257 (mmt180) cc_final: 0.5216 (mmm160) REVERT: 2A 4 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7915 (tt) REVERT: 2A 47 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9008 (mt) REVERT: 2B 40 THR cc_start: 0.9291 (m) cc_final: 0.8879 (p) REVERT: 2C 40 THR cc_start: 0.9365 (m) cc_final: 0.9029 (p) REVERT: 2D 26 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8666 (mt) REVERT: 2E 22 MET cc_start: 0.8484 (tpp) cc_final: 0.7808 (tpp) REVERT: 2E 40 THR cc_start: 0.9249 (m) cc_final: 0.8866 (p) REVERT: 2G 39 ARG cc_start: 0.8210 (ttp-170) cc_final: 0.7936 (ttp80) REVERT: 2H 40 THR cc_start: 0.9212 (m) cc_final: 0.8836 (p) REVERT: 2I 40 THR cc_start: 0.9174 (m) cc_final: 0.8726 (p) REVERT: 2J 40 THR cc_start: 0.9109 (m) cc_final: 0.8764 (p) REVERT: 2K 40 THR cc_start: 0.9337 (m) cc_final: 0.8932 (p) REVERT: 2K 46 LEU cc_start: 0.9347 (tp) cc_final: 0.9119 (mt) REVERT: 2L 29 GLU cc_start: 0.8321 (tp30) cc_final: 0.7745 (tp30) REVERT: 2L 40 THR cc_start: 0.9351 (m) cc_final: 0.8896 (p) REVERT: 2M 40 THR cc_start: 0.9257 (m) cc_final: 0.8717 (p) REVERT: 2N 29 GLU cc_start: 0.8445 (tp30) cc_final: 0.8108 (tp30) REVERT: 2N 60 LEU cc_start: 0.9014 (mt) cc_final: 0.8776 (mt) REVERT: 3A 40 THR cc_start: 0.9209 (m) cc_final: 0.8980 (p) REVERT: 3A 47 LEU cc_start: 0.9076 (tt) cc_final: 0.8755 (mt) REVERT: 3B 40 THR cc_start: 0.9292 (m) cc_final: 0.8924 (p) REVERT: 3C 40 THR cc_start: 0.9144 (m) cc_final: 0.8792 (p) REVERT: 3D 40 THR cc_start: 0.9337 (m) cc_final: 0.8988 (p) REVERT: 3E 40 THR cc_start: 0.9206 (m) cc_final: 0.8912 (p) REVERT: 3F 40 THR cc_start: 0.9215 (m) cc_final: 0.8912 (p) REVERT: 3G 12 LYS cc_start: 0.8891 (ttmt) cc_final: 0.8603 (tttt) REVERT: 3G 41 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8464 (tttp) REVERT: 3H 40 THR cc_start: 0.9152 (m) cc_final: 0.8922 (p) REVERT: 3H 46 LEU cc_start: 0.9393 (mt) cc_final: 0.9152 (mt) REVERT: 3J 39 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7819 (ttp80) REVERT: 3J 40 THR cc_start: 0.9289 (m) cc_final: 0.8825 (p) REVERT: 3K 40 THR cc_start: 0.9325 (m) cc_final: 0.8967 (p) REVERT: 3L 40 THR cc_start: 0.9319 (m) cc_final: 0.8852 (p) REVERT: 3M 39 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7932 (ttp80) REVERT: 4A 40 THR cc_start: 0.9248 (m) cc_final: 0.8836 (p) REVERT: 4B 40 THR cc_start: 0.9161 (m) cc_final: 0.8896 (p) REVERT: 4C 22 MET cc_start: 0.8183 (tpp) cc_final: 0.7691 (tpp) REVERT: 4C 40 THR cc_start: 0.9248 (m) cc_final: 0.8863 (p) REVERT: 4D 40 THR cc_start: 0.9249 (m) cc_final: 0.8847 (p) REVERT: 4F 40 THR cc_start: 0.9373 (m) cc_final: 0.9102 (p) REVERT: 4H 40 THR cc_start: 0.9377 (m) cc_final: 0.9022 (p) REVERT: 4I 22 MET cc_start: 0.8441 (tpp) cc_final: 0.8210 (tpp) REVERT: 4K 40 THR cc_start: 0.9267 (m) cc_final: 0.8938 (p) REVERT: 4K 60 LEU cc_start: 0.9015 (mt) cc_final: 0.8740 (mt) REVERT: 4L 40 THR cc_start: 0.8991 (m) cc_final: 0.8765 (p) REVERT: 4L 46 LEU cc_start: 0.9326 (mt) cc_final: 0.9091 (mt) REVERT: 4N 46 LEU cc_start: 0.9341 (mt) cc_final: 0.8992 (mt) REVERT: 4N 47 LEU cc_start: 0.8914 (tt) cc_final: 0.8685 (mt) REVERT: 4N 60 LEU cc_start: 0.8943 (mt) cc_final: 0.8525 (mt) REVERT: 4O 37 TYR cc_start: 0.9409 (t80) cc_final: 0.9060 (t80) REVERT: 4O 46 LEU cc_start: 0.9419 (mt) cc_final: 0.9178 (mt) REVERT: 5C 36 MET cc_start: 0.8461 (mtp) cc_final: 0.8234 (mtp) REVERT: 5C 40 THR cc_start: 0.9267 (m) cc_final: 0.8776 (p) REVERT: 5D 40 THR cc_start: 0.9273 (m) cc_final: 0.8927 (p) REVERT: 5E 40 THR cc_start: 0.9252 (m) cc_final: 0.8651 (p) REVERT: 5F 40 THR cc_start: 0.9187 (m) cc_final: 0.8878 (p) REVERT: 5G 40 THR cc_start: 0.9242 (m) cc_final: 0.8946 (p) REVERT: 5H 40 THR cc_start: 0.9288 (m) cc_final: 0.8760 (p) REVERT: 5I 4 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7999 (tt) REVERT: 5I 40 THR cc_start: 0.9289 (m) cc_final: 0.8828 (p) REVERT: 5J 36 MET cc_start: 0.8144 (mtm) cc_final: 0.7934 (mtm) REVERT: 5J 40 THR cc_start: 0.9267 (m) cc_final: 0.8853 (p) REVERT: 5K 40 THR cc_start: 0.9243 (m) cc_final: 0.8972 (p) REVERT: 5L 23 MET cc_start: 0.7827 (ttm) cc_final: 0.7492 (ttm) REVERT: 5N 60 LEU cc_start: 0.8963 (mt) cc_final: 0.8736 (mt) REVERT: 5O 29 GLU cc_start: 0.8266 (tp30) cc_final: 0.7894 (tp30) REVERT: 5O 60 LEU cc_start: 0.9057 (mt) cc_final: 0.8716 (mt) REVERT: 5P 46 LEU cc_start: 0.9437 (mt) cc_final: 0.9170 (mt) outliers start: 251 outliers final: 207 residues processed: 1774 average time/residue: 0.2250 time to fit residues: 662.7139 Evaluate side-chains 1841 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 1629 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 23 MET Chi-restraints excluded: chain 1A residue 51 VAL Chi-restraints excluded: chain 1A residue 57 THR Chi-restraints excluded: chain 1B residue 26 ILE Chi-restraints excluded: chain 1C residue 23 MET Chi-restraints excluded: chain 1C residue 26 ILE Chi-restraints excluded: chain 1C residue 53 ILE Chi-restraints excluded: chain 1D residue 11 VAL Chi-restraints excluded: chain 1D residue 21 VAL Chi-restraints excluded: chain 1D residue 26 ILE Chi-restraints excluded: chain 1D residue 31 ILE Chi-restraints excluded: chain 1E residue 21 VAL Chi-restraints excluded: chain 1E residue 26 ILE Chi-restraints excluded: chain 1E residue 31 ILE Chi-restraints excluded: chain 1F residue 26 ILE Chi-restraints excluded: chain 1G residue 25 ILE Chi-restraints excluded: chain 1G residue 26 ILE Chi-restraints excluded: chain 1G residue 31 ILE Chi-restraints excluded: chain 1G residue 47 LEU Chi-restraints excluded: chain 1G residue 51 VAL Chi-restraints excluded: chain 1G residue 53 ILE Chi-restraints excluded: chain 1H residue 23 MET Chi-restraints excluded: chain 1H residue 26 ILE Chi-restraints excluded: chain 1H residue 47 LEU Chi-restraints excluded: chain 1I residue 23 MET Chi-restraints excluded: chain 1I residue 26 ILE Chi-restraints excluded: chain 1I residue 31 ILE Chi-restraints excluded: chain 1I residue 47 LEU Chi-restraints excluded: chain 1I residue 57 THR Chi-restraints excluded: chain 1J residue 19 SER Chi-restraints excluded: chain 1J residue 21 VAL Chi-restraints excluded: chain 1J residue 26 ILE Chi-restraints excluded: chain 1J residue 47 LEU Chi-restraints excluded: chain 1K residue 23 MET Chi-restraints excluded: chain 1L residue 4 LEU Chi-restraints excluded: chain 1L residue 23 MET Chi-restraints excluded: chain 1L residue 26 ILE Chi-restraints excluded: chain 1L residue 49 LEU Chi-restraints excluded: chain 1L residue 53 ILE Chi-restraints excluded: chain 1M residue 11 VAL Chi-restraints excluded: chain 1M residue 47 LEU Chi-restraints excluded: chain 1O residue 31 ILE Chi-restraints excluded: chain 1P residue 52 VAL Chi-restraints excluded: chain 2A residue 4 LEU Chi-restraints excluded: chain 2A residue 23 MET Chi-restraints excluded: chain 2A residue 31 ILE Chi-restraints excluded: chain 2A residue 47 LEU Chi-restraints excluded: chain 2A residue 51 VAL Chi-restraints excluded: chain 2B residue 21 VAL Chi-restraints excluded: chain 2B residue 23 MET Chi-restraints excluded: chain 2B residue 26 ILE Chi-restraints excluded: chain 2C residue 11 VAL Chi-restraints excluded: chain 2C residue 26 ILE Chi-restraints excluded: chain 2D residue 26 ILE Chi-restraints excluded: chain 2D residue 53 ILE Chi-restraints excluded: chain 2F residue 31 ILE Chi-restraints excluded: chain 2F residue 47 LEU Chi-restraints excluded: chain 2F residue 51 VAL Chi-restraints excluded: chain 2G residue 26 ILE Chi-restraints excluded: chain 2H residue 26 ILE Chi-restraints excluded: chain 2H residue 31 ILE Chi-restraints excluded: chain 2H residue 61 THR Chi-restraints excluded: chain 2I residue 4 LEU Chi-restraints excluded: chain 2I residue 21 VAL Chi-restraints excluded: chain 2I residue 26 ILE Chi-restraints excluded: chain 2I residue 47 LEU Chi-restraints excluded: chain 2I residue 51 VAL Chi-restraints excluded: chain 2I residue 52 VAL Chi-restraints excluded: chain 2I residue 53 ILE Chi-restraints excluded: chain 2J residue 4 LEU Chi-restraints excluded: chain 2J residue 47 LEU Chi-restraints excluded: chain 2K residue 4 LEU Chi-restraints excluded: chain 2K residue 51 VAL Chi-restraints excluded: chain 2L residue 23 MET Chi-restraints excluded: chain 2L residue 57 THR Chi-restraints excluded: chain 2L residue 58 VAL Chi-restraints excluded: chain 2L residue 61 THR Chi-restraints excluded: chain 2M residue 11 VAL Chi-restraints excluded: chain 2M residue 31 ILE Chi-restraints excluded: chain 2N residue 23 MET Chi-restraints excluded: chain 2N residue 58 VAL Chi-restraints excluded: chain 2N residue 63 ILE Chi-restraints excluded: chain 2O residue 31 ILE Chi-restraints excluded: chain 2P residue 41 LYS Chi-restraints excluded: chain 3A residue 21 VAL Chi-restraints excluded: chain 3B residue 4 LEU Chi-restraints excluded: chain 3B residue 25 ILE Chi-restraints excluded: chain 3B residue 26 ILE Chi-restraints excluded: chain 3C residue 12 LYS Chi-restraints excluded: chain 3C residue 31 ILE Chi-restraints excluded: chain 3C residue 47 LEU Chi-restraints excluded: chain 3C residue 51 VAL Chi-restraints excluded: chain 3C residue 57 THR Chi-restraints excluded: chain 3D residue 50 VAL Chi-restraints excluded: chain 3E residue 11 VAL Chi-restraints excluded: chain 3E residue 26 ILE Chi-restraints excluded: chain 3E residue 46 LEU Chi-restraints excluded: chain 3F residue 11 VAL Chi-restraints excluded: chain 3F residue 26 ILE Chi-restraints excluded: chain 3F residue 43 LEU Chi-restraints excluded: chain 3F residue 51 VAL Chi-restraints excluded: chain 3G residue 11 VAL Chi-restraints excluded: chain 3G residue 23 MET Chi-restraints excluded: chain 3G residue 31 ILE Chi-restraints excluded: chain 3G residue 41 LYS Chi-restraints excluded: chain 3G residue 47 LEU Chi-restraints excluded: chain 3G residue 51 VAL Chi-restraints excluded: chain 3G residue 57 THR Chi-restraints excluded: chain 3H residue 11 VAL Chi-restraints excluded: chain 3H residue 21 VAL Chi-restraints excluded: chain 3H residue 23 MET Chi-restraints excluded: chain 3H residue 31 ILE Chi-restraints excluded: chain 3I residue 11 VAL Chi-restraints excluded: chain 3I residue 23 MET Chi-restraints excluded: chain 3I residue 52 VAL Chi-restraints excluded: chain 3I residue 58 VAL Chi-restraints excluded: chain 3J residue 4 LEU Chi-restraints excluded: chain 3J residue 11 VAL Chi-restraints excluded: chain 3K residue 4 LEU Chi-restraints excluded: chain 3K residue 23 MET Chi-restraints excluded: chain 3K residue 46 LEU Chi-restraints excluded: chain 3K residue 50 VAL Chi-restraints excluded: chain 3K residue 51 VAL Chi-restraints excluded: chain 3L residue 51 VAL Chi-restraints excluded: chain 3L residue 53 ILE Chi-restraints excluded: chain 3M residue 21 VAL Chi-restraints excluded: chain 3M residue 58 VAL Chi-restraints excluded: chain 3N residue 21 VAL Chi-restraints excluded: chain 3N residue 23 MET Chi-restraints excluded: chain 3N residue 39 ARG Chi-restraints excluded: chain 3P residue 52 VAL Chi-restraints excluded: chain 3P residue 53 ILE Chi-restraints excluded: chain 4A residue 11 VAL Chi-restraints excluded: chain 4B residue 31 ILE Chi-restraints excluded: chain 4C residue 26 ILE Chi-restraints excluded: chain 4C residue 61 THR Chi-restraints excluded: chain 4D residue 31 ILE Chi-restraints excluded: chain 4D residue 41 LYS Chi-restraints excluded: chain 4D residue 46 LEU Chi-restraints excluded: chain 4D residue 47 LEU Chi-restraints excluded: chain 4D residue 61 THR Chi-restraints excluded: chain 4E residue 23 MET Chi-restraints excluded: chain 4E residue 50 VAL Chi-restraints excluded: chain 4F residue 4 LEU Chi-restraints excluded: chain 4F residue 26 ILE Chi-restraints excluded: chain 4H residue 21 VAL Chi-restraints excluded: chain 4I residue 21 VAL Chi-restraints excluded: chain 4I residue 23 MET Chi-restraints excluded: chain 4I residue 26 ILE Chi-restraints excluded: chain 4J residue 51 VAL Chi-restraints excluded: chain 4K residue 21 VAL Chi-restraints excluded: chain 4K residue 26 ILE Chi-restraints excluded: chain 4K residue 27 ILE Chi-restraints excluded: chain 4K residue 47 LEU Chi-restraints excluded: chain 4L residue 4 LEU Chi-restraints excluded: chain 4L residue 12 LYS Chi-restraints excluded: chain 4L residue 23 MET Chi-restraints excluded: chain 4L residue 31 ILE Chi-restraints excluded: chain 4M residue 21 VAL Chi-restraints excluded: chain 4M residue 23 MET Chi-restraints excluded: chain 4N residue 23 MET Chi-restraints excluded: chain 4N residue 50 VAL Chi-restraints excluded: chain 4O residue 21 VAL Chi-restraints excluded: chain 4O residue 31 ILE Chi-restraints excluded: chain 4O residue 47 LEU Chi-restraints excluded: chain 4O residue 50 VAL Chi-restraints excluded: chain 4O residue 57 THR Chi-restraints excluded: chain 4P residue 47 LEU Chi-restraints excluded: chain 4P residue 52 VAL Chi-restraints excluded: chain 5A residue 57 THR Chi-restraints excluded: chain 5B residue 11 VAL Chi-restraints excluded: chain 5B residue 26 ILE Chi-restraints excluded: chain 5B residue 47 LEU Chi-restraints excluded: chain 5B residue 53 ILE Chi-restraints excluded: chain 5C residue 11 VAL Chi-restraints excluded: chain 5C residue 31 ILE Chi-restraints excluded: chain 5C residue 43 LEU Chi-restraints excluded: chain 5C residue 57 THR Chi-restraints excluded: chain 5C residue 61 THR Chi-restraints excluded: chain 5D residue 4 LEU Chi-restraints excluded: chain 5E residue 11 VAL Chi-restraints excluded: chain 5E residue 12 LYS Chi-restraints excluded: chain 5E residue 19 SER Chi-restraints excluded: chain 5E residue 21 VAL Chi-restraints excluded: chain 5E residue 26 ILE Chi-restraints excluded: chain 5E residue 31 ILE Chi-restraints excluded: chain 5E residue 50 VAL Chi-restraints excluded: chain 5F residue 4 LEU Chi-restraints excluded: chain 5F residue 11 VAL Chi-restraints excluded: chain 5F residue 26 ILE Chi-restraints excluded: chain 5F residue 47 LEU Chi-restraints excluded: chain 5F residue 53 ILE Chi-restraints excluded: chain 5G residue 27 ILE Chi-restraints excluded: chain 5G residue 47 LEU Chi-restraints excluded: chain 5G residue 57 THR Chi-restraints excluded: chain 5H residue 26 ILE Chi-restraints excluded: chain 5I residue 4 LEU Chi-restraints excluded: chain 5I residue 23 MET Chi-restraints excluded: chain 5I residue 31 ILE Chi-restraints excluded: chain 5I residue 53 ILE Chi-restraints excluded: chain 5I residue 61 THR Chi-restraints excluded: chain 5J residue 23 MET Chi-restraints excluded: chain 5J residue 31 ILE Chi-restraints excluded: chain 5J residue 52 VAL Chi-restraints excluded: chain 5K residue 4 LEU Chi-restraints excluded: chain 5L residue 21 VAL Chi-restraints excluded: chain 5L residue 27 ILE Chi-restraints excluded: chain 5M residue 11 VAL Chi-restraints excluded: chain 5N residue 21 VAL Chi-restraints excluded: chain 5N residue 47 LEU Chi-restraints excluded: chain 5O residue 21 VAL Chi-restraints excluded: chain 5P residue 52 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 152 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 345 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 289 optimal weight: 9.9990 chunk 300 optimal weight: 30.0000 chunk 324 optimal weight: 8.9990 chunk 467 optimal weight: 7.9990 chunk 179 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.122804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098433 restraints weight = 57782.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.102661 restraints weight = 28841.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.105481 restraints weight = 17710.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.107383 restraints weight = 12575.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.108632 restraints weight = 9900.246| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.7279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41600 Z= 0.135 Angle : 0.621 11.770 55411 Z= 0.302 Chirality : 0.038 0.204 7190 Planarity : 0.002 0.028 6070 Dihedral : 14.189 77.699 8495 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.98 % Allowed : 29.90 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.12), residues: 4880 helix: -0.26 (0.08), residues: 3280 sheet: None (None), residues: 0 loop : -1.09 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG3A 39 TYR 0.023 0.002 TYR5E 37 PHE 0.017 0.001 PHE3N 15 Details of bonding type rmsd covalent geometry : bond 0.00339 (41600) covalent geometry : angle 0.62089 (55410) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.04003 ( 2000) hydrogen bonds : angle 4.87931 ( 6000) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1917 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 1710 time to evaluate : 1.401 Fit side-chains REVERT: 1B 40 THR cc_start: 0.9161 (m) cc_final: 0.8938 (p) REVERT: 1B 46 LEU cc_start: 0.9283 (mt) cc_final: 0.9055 (mt) REVERT: 1C 22 MET cc_start: 0.8435 (tpp) cc_final: 0.8063 (tpp) REVERT: 1C 40 THR cc_start: 0.9293 (m) cc_final: 0.8866 (p) REVERT: 1E 40 THR cc_start: 0.9275 (m) cc_final: 0.8858 (p) REVERT: 1F 40 THR cc_start: 0.9223 (m) cc_final: 0.9001 (p) REVERT: 1H 40 THR cc_start: 0.9380 (m) cc_final: 0.8971 (p) REVERT: 1H 46 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9115 (mp) REVERT: 1I 40 THR cc_start: 0.9189 (m) cc_final: 0.8709 (p) REVERT: 1J 40 THR cc_start: 0.8990 (m) cc_final: 0.8404 (p) REVERT: 1K 40 THR cc_start: 0.9084 (m) cc_final: 0.8848 (p) REVERT: 1L 22 MET cc_start: 0.8438 (mmt) cc_final: 0.8083 (tpp) REVERT: 1L 40 THR cc_start: 0.9174 (m) cc_final: 0.8593 (p) REVERT: 1M 29 GLU cc_start: 0.8337 (tp30) cc_final: 0.8137 (tp30) REVERT: 1P 39 ARG cc_start: 0.6034 (mmt180) cc_final: 0.5104 (mmm160) REVERT: 2A 4 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7871 (tt) REVERT: 2A 23 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7802 (ptm) REVERT: 2A 37 TYR cc_start: 0.9347 (t80) cc_final: 0.8739 (t80) REVERT: 2B 40 THR cc_start: 0.9253 (m) cc_final: 0.8830 (p) REVERT: 2C 40 THR cc_start: 0.9291 (m) cc_final: 0.8922 (p) REVERT: 2D 26 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8764 (mt) REVERT: 2E 22 MET cc_start: 0.8505 (tpp) cc_final: 0.7925 (tpp) REVERT: 2E 40 THR cc_start: 0.9105 (m) cc_final: 0.8677 (p) REVERT: 2G 39 ARG cc_start: 0.8155 (ttp-170) cc_final: 0.7843 (ttp80) REVERT: 2H 40 THR cc_start: 0.9091 (m) cc_final: 0.8634 (p) REVERT: 2I 40 THR cc_start: 0.9040 (m) cc_final: 0.8627 (p) REVERT: 2J 40 THR cc_start: 0.9042 (m) cc_final: 0.8746 (p) REVERT: 2K 40 THR cc_start: 0.9286 (m) cc_final: 0.8917 (p) REVERT: 2K 46 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9123 (mt) REVERT: 2L 29 GLU cc_start: 0.8362 (tp30) cc_final: 0.7944 (tp30) REVERT: 2L 40 THR cc_start: 0.9285 (m) cc_final: 0.8824 (p) REVERT: 2M 40 THR cc_start: 0.9157 (m) cc_final: 0.8623 (p) REVERT: 2N 29 GLU cc_start: 0.8397 (tp30) cc_final: 0.8003 (tp30) REVERT: 2N 60 LEU cc_start: 0.9019 (mt) cc_final: 0.8811 (mt) REVERT: 3A 40 THR cc_start: 0.9154 (m) cc_final: 0.8863 (p) REVERT: 3B 40 THR cc_start: 0.9109 (m) cc_final: 0.8693 (p) REVERT: 3C 40 THR cc_start: 0.9017 (m) cc_final: 0.8678 (p) REVERT: 3D 40 THR cc_start: 0.9282 (m) cc_final: 0.8959 (p) REVERT: 3E 40 THR cc_start: 0.9140 (m) cc_final: 0.8842 (p) REVERT: 3E 41 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8371 (tttt) REVERT: 3F 40 THR cc_start: 0.9175 (m) cc_final: 0.8873 (p) REVERT: 3G 12 LYS cc_start: 0.8875 (ttmt) cc_final: 0.8586 (tttt) REVERT: 3G 41 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8455 (tttp) REVERT: 3H 46 LEU cc_start: 0.9310 (mt) cc_final: 0.9007 (mt) REVERT: 3J 39 ARG cc_start: 0.8018 (ttp80) cc_final: 0.7763 (ttp80) REVERT: 3J 40 THR cc_start: 0.9302 (m) cc_final: 0.8868 (p) REVERT: 3K 40 THR cc_start: 0.9285 (m) cc_final: 0.8917 (p) REVERT: 3L 40 THR cc_start: 0.9254 (m) cc_final: 0.8803 (p) REVERT: 3M 39 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7840 (ttp80) REVERT: 3O 47 LEU cc_start: 0.9111 (tt) cc_final: 0.8813 (tp) REVERT: 4A 40 THR cc_start: 0.9211 (m) cc_final: 0.8816 (p) REVERT: 4B 40 THR cc_start: 0.9058 (m) cc_final: 0.8805 (p) REVERT: 4C 22 MET cc_start: 0.8170 (tpp) cc_final: 0.7659 (tpp) REVERT: 4C 40 THR cc_start: 0.9225 (m) cc_final: 0.8815 (p) REVERT: 4D 10 ASP cc_start: 0.8015 (p0) cc_final: 0.7792 (p0) REVERT: 4D 40 THR cc_start: 0.9150 (m) cc_final: 0.8772 (p) REVERT: 4D 41 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8448 (tttt) REVERT: 4F 40 THR cc_start: 0.9335 (m) cc_final: 0.9066 (p) REVERT: 4H 40 THR cc_start: 0.9332 (m) cc_final: 0.9006 (p) REVERT: 4K 10 ASP cc_start: 0.7387 (p0) cc_final: 0.7134 (p0) REVERT: 4K 40 THR cc_start: 0.9229 (m) cc_final: 0.8903 (p) REVERT: 4K 60 LEU cc_start: 0.9004 (mt) cc_final: 0.8728 (mt) REVERT: 4L 40 THR cc_start: 0.9016 (m) cc_final: 0.8809 (p) REVERT: 4L 46 LEU cc_start: 0.9242 (mt) cc_final: 0.8999 (mt) REVERT: 4N 46 LEU cc_start: 0.9213 (mt) cc_final: 0.8922 (mt) REVERT: 4N 47 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8555 (mt) REVERT: 4N 60 LEU cc_start: 0.8964 (mt) cc_final: 0.8557 (mt) REVERT: 4O 37 TYR cc_start: 0.9350 (t80) cc_final: 0.9034 (t80) REVERT: 4O 46 LEU cc_start: 0.9386 (mt) cc_final: 0.9150 (mt) REVERT: 5A 47 LEU cc_start: 0.9147 (tt) cc_final: 0.8697 (mt) REVERT: 5C 36 MET cc_start: 0.8381 (mtp) cc_final: 0.8112 (mtp) REVERT: 5C 40 THR cc_start: 0.9186 (m) cc_final: 0.8646 (p) REVERT: 5D 22 MET cc_start: 0.8154 (mmp) cc_final: 0.7941 (mmp) REVERT: 5D 40 THR cc_start: 0.9170 (m) cc_final: 0.8791 (p) REVERT: 5E 40 THR cc_start: 0.9205 (m) cc_final: 0.8599 (p) REVERT: 5F 40 THR cc_start: 0.9136 (m) cc_final: 0.8844 (p) REVERT: 5G 40 THR cc_start: 0.9209 (m) cc_final: 0.8878 (p) REVERT: 5G 47 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8720 (mt) REVERT: 5H 40 THR cc_start: 0.9172 (m) cc_final: 0.8550 (p) REVERT: 5I 4 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7917 (tt) REVERT: 5I 40 THR cc_start: 0.9223 (m) cc_final: 0.8755 (p) REVERT: 5J 36 MET cc_start: 0.8124 (mtm) cc_final: 0.7917 (mtm) REVERT: 5J 40 THR cc_start: 0.9212 (m) cc_final: 0.8832 (p) REVERT: 5K 40 THR cc_start: 0.9255 (m) cc_final: 0.8963 (p) REVERT: 5L 23 MET cc_start: 0.7846 (ttm) cc_final: 0.7366 (ttm) REVERT: 5O 29 GLU cc_start: 0.8283 (tp30) cc_final: 0.7982 (tp30) REVERT: 5P 46 LEU cc_start: 0.9432 (mt) cc_final: 0.9133 (mt) outliers start: 207 outliers final: 174 residues processed: 1787 average time/residue: 0.2161 time to fit residues: 643.2391 Evaluate side-chains 1843 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 1658 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 23 MET Chi-restraints excluded: chain 1A residue 57 THR Chi-restraints excluded: chain 1B residue 26 ILE Chi-restraints excluded: chain 1C residue 21 VAL Chi-restraints excluded: chain 1C residue 23 MET Chi-restraints excluded: chain 1C residue 26 ILE Chi-restraints excluded: chain 1C residue 53 ILE Chi-restraints excluded: chain 1D residue 11 VAL Chi-restraints excluded: chain 1D residue 21 VAL Chi-restraints excluded: chain 1D residue 26 ILE Chi-restraints excluded: chain 1D residue 31 ILE Chi-restraints excluded: chain 1D residue 47 LEU Chi-restraints excluded: chain 1D residue 51 VAL Chi-restraints excluded: chain 1E residue 21 VAL Chi-restraints excluded: chain 1E residue 26 ILE Chi-restraints excluded: chain 1E residue 31 ILE Chi-restraints excluded: chain 1F residue 26 ILE Chi-restraints excluded: chain 1G residue 25 ILE Chi-restraints excluded: chain 1G residue 26 ILE Chi-restraints excluded: chain 1G residue 47 LEU Chi-restraints excluded: chain 1G residue 51 VAL Chi-restraints excluded: chain 1H residue 23 MET Chi-restraints excluded: chain 1H residue 26 ILE Chi-restraints excluded: chain 1H residue 46 LEU Chi-restraints excluded: chain 1H residue 47 LEU Chi-restraints excluded: chain 1I residue 23 MET Chi-restraints excluded: chain 1I residue 26 ILE Chi-restraints excluded: chain 1I residue 31 ILE Chi-restraints excluded: chain 1J residue 21 VAL Chi-restraints excluded: chain 1J residue 26 ILE Chi-restraints excluded: chain 1J residue 47 LEU Chi-restraints excluded: chain 1K residue 23 MET Chi-restraints excluded: chain 1L residue 26 ILE Chi-restraints excluded: chain 1L residue 49 LEU Chi-restraints excluded: chain 1L residue 53 ILE Chi-restraints excluded: chain 1M residue 11 VAL Chi-restraints excluded: chain 1M residue 47 LEU Chi-restraints excluded: chain 1O residue 23 MET Chi-restraints excluded: chain 1P residue 52 VAL Chi-restraints excluded: chain 2A residue 4 LEU Chi-restraints excluded: chain 2A residue 12 LYS Chi-restraints excluded: chain 2A residue 23 MET Chi-restraints excluded: chain 2A residue 51 VAL Chi-restraints excluded: chain 2B residue 23 MET Chi-restraints excluded: chain 2B residue 26 ILE Chi-restraints excluded: chain 2B residue 47 LEU Chi-restraints excluded: chain 2C residue 26 ILE Chi-restraints excluded: chain 2D residue 26 ILE Chi-restraints excluded: chain 2D residue 53 ILE Chi-restraints excluded: chain 2F residue 4 LEU Chi-restraints excluded: chain 2F residue 47 LEU Chi-restraints excluded: chain 2F residue 51 VAL Chi-restraints excluded: chain 2G residue 26 ILE Chi-restraints excluded: chain 2H residue 26 ILE Chi-restraints excluded: chain 2H residue 31 ILE Chi-restraints excluded: chain 2H residue 61 THR Chi-restraints excluded: chain 2I residue 26 ILE Chi-restraints excluded: chain 2I residue 47 LEU Chi-restraints excluded: chain 2I residue 51 VAL Chi-restraints excluded: chain 2I residue 52 VAL Chi-restraints excluded: chain 2J residue 4 LEU Chi-restraints excluded: chain 2J residue 47 LEU Chi-restraints excluded: chain 2K residue 4 LEU Chi-restraints excluded: chain 2K residue 46 LEU Chi-restraints excluded: chain 2K residue 51 VAL Chi-restraints excluded: chain 2L residue 52 VAL Chi-restraints excluded: chain 2L residue 58 VAL Chi-restraints excluded: chain 2M residue 11 VAL Chi-restraints excluded: chain 2N residue 23 MET Chi-restraints excluded: chain 2N residue 50 VAL Chi-restraints excluded: chain 2N residue 58 VAL Chi-restraints excluded: chain 2P residue 41 LYS Chi-restraints excluded: chain 3A residue 4 LEU Chi-restraints excluded: chain 3A residue 21 VAL Chi-restraints excluded: chain 3B residue 4 LEU Chi-restraints excluded: chain 3B residue 25 ILE Chi-restraints excluded: chain 3B residue 26 ILE Chi-restraints excluded: chain 3C residue 12 LYS Chi-restraints excluded: chain 3C residue 31 ILE Chi-restraints excluded: chain 3C residue 51 VAL Chi-restraints excluded: chain 3D residue 50 VAL Chi-restraints excluded: chain 3E residue 23 MET Chi-restraints excluded: chain 3E residue 26 ILE Chi-restraints excluded: chain 3E residue 41 LYS Chi-restraints excluded: chain 3E residue 46 LEU Chi-restraints excluded: chain 3F residue 11 VAL Chi-restraints excluded: chain 3F residue 26 ILE Chi-restraints excluded: chain 3G residue 23 MET Chi-restraints excluded: chain 3G residue 31 ILE Chi-restraints excluded: chain 3G residue 41 LYS Chi-restraints excluded: chain 3G residue 47 LEU Chi-restraints excluded: chain 3G residue 51 VAL Chi-restraints excluded: chain 3H residue 21 VAL Chi-restraints excluded: chain 3H residue 23 MET Chi-restraints excluded: chain 3I residue 11 VAL Chi-restraints excluded: chain 3I residue 52 VAL Chi-restraints excluded: chain 3I residue 58 VAL Chi-restraints excluded: chain 3J residue 11 VAL Chi-restraints excluded: chain 3K residue 4 LEU Chi-restraints excluded: chain 3K residue 23 MET Chi-restraints excluded: chain 3K residue 46 LEU Chi-restraints excluded: chain 3K residue 50 VAL Chi-restraints excluded: chain 3K residue 53 ILE Chi-restraints excluded: chain 3L residue 51 VAL Chi-restraints excluded: chain 3L residue 53 ILE Chi-restraints excluded: chain 3M residue 21 VAL Chi-restraints excluded: chain 3M residue 58 VAL Chi-restraints excluded: chain 3N residue 21 VAL Chi-restraints excluded: chain 3N residue 23 MET Chi-restraints excluded: chain 3N residue 46 LEU Chi-restraints excluded: chain 3O residue 50 VAL Chi-restraints excluded: chain 3P residue 52 VAL Chi-restraints excluded: chain 3P residue 53 ILE Chi-restraints excluded: chain 4A residue 11 VAL Chi-restraints excluded: chain 4B residue 31 ILE Chi-restraints excluded: chain 4C residue 26 ILE Chi-restraints excluded: chain 4D residue 31 ILE Chi-restraints excluded: chain 4D residue 41 LYS Chi-restraints excluded: chain 4D residue 46 LEU Chi-restraints excluded: chain 4D residue 47 LEU Chi-restraints excluded: chain 4E residue 23 MET Chi-restraints excluded: chain 4E residue 50 VAL Chi-restraints excluded: chain 4F residue 4 LEU Chi-restraints excluded: chain 4F residue 26 ILE Chi-restraints excluded: chain 4G residue 31 ILE Chi-restraints excluded: chain 4H residue 21 VAL Chi-restraints excluded: chain 4I residue 21 VAL Chi-restraints excluded: chain 4I residue 23 MET Chi-restraints excluded: chain 4I residue 26 ILE Chi-restraints excluded: chain 4J residue 51 VAL Chi-restraints excluded: chain 4K residue 21 VAL Chi-restraints excluded: chain 4K residue 26 ILE Chi-restraints excluded: chain 4L residue 23 MET Chi-restraints excluded: chain 4L residue 31 ILE Chi-restraints excluded: chain 4M residue 21 VAL Chi-restraints excluded: chain 4M residue 31 ILE Chi-restraints excluded: chain 4N residue 23 MET Chi-restraints excluded: chain 4N residue 47 LEU Chi-restraints excluded: chain 4N residue 50 VAL Chi-restraints excluded: chain 4O residue 21 VAL Chi-restraints excluded: chain 4O residue 31 ILE Chi-restraints excluded: chain 4O residue 47 LEU Chi-restraints excluded: chain 4O residue 50 VAL Chi-restraints excluded: chain 4O residue 57 THR Chi-restraints excluded: chain 4P residue 41 LYS Chi-restraints excluded: chain 4P residue 47 LEU Chi-restraints excluded: chain 4P residue 52 VAL Chi-restraints excluded: chain 5B residue 11 VAL Chi-restraints excluded: chain 5B residue 26 ILE Chi-restraints excluded: chain 5B residue 45 ILE Chi-restraints excluded: chain 5B residue 47 LEU Chi-restraints excluded: chain 5C residue 11 VAL Chi-restraints excluded: chain 5C residue 23 MET Chi-restraints excluded: chain 5C residue 31 ILE Chi-restraints excluded: chain 5C residue 43 LEU Chi-restraints excluded: chain 5D residue 4 LEU Chi-restraints excluded: chain 5E residue 12 LYS Chi-restraints excluded: chain 5E residue 19 SER Chi-restraints excluded: chain 5E residue 21 VAL Chi-restraints excluded: chain 5E residue 26 ILE Chi-restraints excluded: chain 5E residue 31 ILE Chi-restraints excluded: chain 5F residue 4 LEU Chi-restraints excluded: chain 5F residue 11 VAL Chi-restraints excluded: chain 5F residue 26 ILE Chi-restraints excluded: chain 5F residue 53 ILE Chi-restraints excluded: chain 5G residue 27 ILE Chi-restraints excluded: chain 5G residue 31 ILE Chi-restraints excluded: chain 5G residue 47 LEU Chi-restraints excluded: chain 5G residue 57 THR Chi-restraints excluded: chain 5H residue 26 ILE Chi-restraints excluded: chain 5H residue 46 LEU Chi-restraints excluded: chain 5I residue 4 LEU Chi-restraints excluded: chain 5I residue 23 MET Chi-restraints excluded: chain 5I residue 31 ILE Chi-restraints excluded: chain 5I residue 53 ILE Chi-restraints excluded: chain 5I residue 61 THR Chi-restraints excluded: chain 5J residue 4 LEU Chi-restraints excluded: chain 5J residue 31 ILE Chi-restraints excluded: chain 5J residue 50 VAL Chi-restraints excluded: chain 5K residue 4 LEU Chi-restraints excluded: chain 5K residue 31 ILE Chi-restraints excluded: chain 5L residue 21 VAL Chi-restraints excluded: chain 5N residue 47 LEU Chi-restraints excluded: chain 5O residue 21 VAL Chi-restraints excluded: chain 5P residue 52 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 326 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 406 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 chunk 293 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 392 optimal weight: 0.8980 chunk 384 optimal weight: 20.0000 chunk 256 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.095484 restraints weight = 58429.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.099636 restraints weight = 29342.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.102430 restraints weight = 18112.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.104303 restraints weight = 12906.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105466 restraints weight = 10178.974| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.7305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 41600 Z= 0.175 Angle : 0.665 11.407 55411 Z= 0.323 Chirality : 0.039 0.196 7190 Planarity : 0.002 0.035 6070 Dihedral : 14.473 76.136 8495 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 5.19 % Allowed : 30.62 % Favored : 64.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.12), residues: 4880 helix: -0.34 (0.08), residues: 3280 sheet: None (None), residues: 0 loop : -1.09 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG1I 39 TYR 0.026 0.002 TYR5E 37 PHE 0.019 0.001 PHE3N 15 Details of bonding type rmsd covalent geometry : bond 0.00446 (41600) covalent geometry : angle 0.66471 (55410) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.04424 ( 2000) hydrogen bonds : angle 4.97413 ( 6000) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1882 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 1666 time to evaluate : 1.321 Fit side-chains REVERT: 1A 40 THR cc_start: 0.9195 (m) cc_final: 0.8789 (p) REVERT: 1B 40 THR cc_start: 0.9194 (m) cc_final: 0.8968 (p) REVERT: 1C 22 MET cc_start: 0.8461 (tpp) cc_final: 0.8042 (tpp) REVERT: 1C 40 THR cc_start: 0.9330 (m) cc_final: 0.8973 (p) REVERT: 1E 37 TYR cc_start: 0.9377 (t80) cc_final: 0.9083 (t80) REVERT: 1E 40 THR cc_start: 0.9259 (m) cc_final: 0.8865 (p) REVERT: 1F 22 MET cc_start: 0.8180 (tpp) cc_final: 0.7582 (tpp) REVERT: 1H 40 THR cc_start: 0.9374 (m) cc_final: 0.8935 (p) REVERT: 1I 40 THR cc_start: 0.9199 (m) cc_final: 0.8776 (p) REVERT: 1I 46 LEU cc_start: 0.9502 (mt) cc_final: 0.9264 (mp) REVERT: 1J 40 THR cc_start: 0.9034 (m) cc_final: 0.8471 (p) REVERT: 1K 40 THR cc_start: 0.9120 (m) cc_final: 0.8838 (p) REVERT: 1L 22 MET cc_start: 0.8461 (mmt) cc_final: 0.8034 (tpp) REVERT: 1L 40 THR cc_start: 0.9214 (m) cc_final: 0.8651 (p) REVERT: 1P 39 ARG cc_start: 0.6139 (mmt180) cc_final: 0.5172 (mmm160) REVERT: 2A 37 TYR cc_start: 0.9379 (t80) cc_final: 0.8767 (t80) REVERT: 2B 37 TYR cc_start: 0.9128 (t80) cc_final: 0.8869 (t80) REVERT: 2B 40 THR cc_start: 0.9281 (m) cc_final: 0.8851 (p) REVERT: 2C 40 THR cc_start: 0.9314 (m) cc_final: 0.8987 (p) REVERT: 2D 26 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8708 (mt) REVERT: 2E 22 MET cc_start: 0.8488 (tpp) cc_final: 0.7925 (tpp) REVERT: 2E 40 THR cc_start: 0.9129 (m) cc_final: 0.8722 (p) REVERT: 2G 39 ARG cc_start: 0.8194 (ttp-170) cc_final: 0.7922 (ttp80) REVERT: 2H 40 THR cc_start: 0.9157 (m) cc_final: 0.8725 (p) REVERT: 2I 40 THR cc_start: 0.9055 (m) cc_final: 0.8646 (p) REVERT: 2J 40 THR cc_start: 0.9091 (m) cc_final: 0.8790 (p) REVERT: 2K 37 TYR cc_start: 0.9375 (t80) cc_final: 0.8825 (t80) REVERT: 2K 40 THR cc_start: 0.9296 (m) cc_final: 0.8930 (p) REVERT: 2L 29 GLU cc_start: 0.8364 (tp30) cc_final: 0.7891 (tp30) REVERT: 2L 40 THR cc_start: 0.9306 (m) cc_final: 0.8883 (p) REVERT: 2M 40 THR cc_start: 0.9197 (m) cc_final: 0.8665 (p) REVERT: 2N 29 GLU cc_start: 0.8446 (tp30) cc_final: 0.8099 (tp30) REVERT: 2N 60 LEU cc_start: 0.8981 (mt) cc_final: 0.8753 (mt) REVERT: 2O 46 LEU cc_start: 0.9484 (mt) cc_final: 0.9071 (mt) REVERT: 2P 47 LEU cc_start: 0.9045 (tt) cc_final: 0.8694 (tp) REVERT: 3A 40 THR cc_start: 0.9174 (m) cc_final: 0.8873 (p) REVERT: 3B 40 THR cc_start: 0.9164 (m) cc_final: 0.8719 (p) REVERT: 3C 40 THR cc_start: 0.9107 (m) cc_final: 0.8752 (p) REVERT: 3D 40 THR cc_start: 0.9287 (m) cc_final: 0.8946 (p) REVERT: 3E 40 THR cc_start: 0.9161 (m) cc_final: 0.8865 (p) REVERT: 3E 41 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8363 (tttt) REVERT: 3F 40 THR cc_start: 0.9211 (m) cc_final: 0.8974 (p) REVERT: 3G 12 LYS cc_start: 0.8879 (ttmt) cc_final: 0.8588 (tttt) REVERT: 3G 41 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8455 (tttp) REVERT: 3H 46 LEU cc_start: 0.9407 (mt) cc_final: 0.9164 (mt) REVERT: 3J 39 ARG cc_start: 0.8056 (ttp80) cc_final: 0.7787 (ttp80) REVERT: 3J 40 THR cc_start: 0.9294 (m) cc_final: 0.8843 (p) REVERT: 3K 40 THR cc_start: 0.9297 (m) cc_final: 0.8943 (p) REVERT: 3L 40 THR cc_start: 0.9293 (m) cc_final: 0.8837 (p) REVERT: 3M 37 TYR cc_start: 0.9187 (t80) cc_final: 0.8902 (t80) REVERT: 3M 39 ARG cc_start: 0.8282 (ttp80) cc_final: 0.8000 (ttp80) REVERT: 3O 47 LEU cc_start: 0.9138 (tt) cc_final: 0.8838 (tp) REVERT: 4A 40 THR cc_start: 0.9256 (m) cc_final: 0.8848 (p) REVERT: 4B 40 THR cc_start: 0.9120 (m) cc_final: 0.8847 (p) REVERT: 4C 22 MET cc_start: 0.8166 (tpp) cc_final: 0.7658 (tpp) REVERT: 4C 40 THR cc_start: 0.9264 (m) cc_final: 0.8860 (p) REVERT: 4D 40 THR cc_start: 0.9192 (m) cc_final: 0.8800 (p) REVERT: 4D 41 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8416 (tttt) REVERT: 4F 40 THR cc_start: 0.9343 (m) cc_final: 0.9076 (p) REVERT: 4H 40 THR cc_start: 0.9326 (m) cc_final: 0.8985 (p) REVERT: 4K 40 THR cc_start: 0.9223 (m) cc_final: 0.8905 (p) REVERT: 4K 60 LEU cc_start: 0.9016 (mt) cc_final: 0.8732 (mt) REVERT: 4L 40 THR cc_start: 0.9028 (m) cc_final: 0.8805 (p) REVERT: 4L 46 LEU cc_start: 0.9274 (mt) cc_final: 0.9051 (mt) REVERT: 4N 46 LEU cc_start: 0.9346 (mt) cc_final: 0.9003 (mt) REVERT: 4N 47 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8619 (mt) REVERT: 4N 60 LEU cc_start: 0.8971 (mt) cc_final: 0.8583 (mt) REVERT: 4O 37 TYR cc_start: 0.9400 (t80) cc_final: 0.9077 (t80) REVERT: 4O 46 LEU cc_start: 0.9430 (mt) cc_final: 0.9199 (mt) REVERT: 5A 47 LEU cc_start: 0.9136 (tt) cc_final: 0.8715 (mt) REVERT: 5C 36 MET cc_start: 0.8420 (mtp) cc_final: 0.8160 (mtp) REVERT: 5C 40 THR cc_start: 0.9167 (m) cc_final: 0.8651 (p) REVERT: 5D 40 THR cc_start: 0.9231 (m) cc_final: 0.8843 (p) REVERT: 5E 40 THR cc_start: 0.9245 (m) cc_final: 0.8650 (p) REVERT: 5F 40 THR cc_start: 0.9164 (m) cc_final: 0.8885 (p) REVERT: 5G 40 THR cc_start: 0.9216 (m) cc_final: 0.8902 (p) REVERT: 5H 40 THR cc_start: 0.9239 (m) cc_final: 0.8720 (p) REVERT: 5I 4 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7982 (tt) REVERT: 5I 40 THR cc_start: 0.9226 (m) cc_final: 0.8716 (p) REVERT: 5J 36 MET cc_start: 0.8179 (mtm) cc_final: 0.7965 (mtm) REVERT: 5J 40 THR cc_start: 0.9219 (m) cc_final: 0.8852 (p) REVERT: 5K 40 THR cc_start: 0.9218 (m) cc_final: 0.8910 (p) REVERT: 5L 23 MET cc_start: 0.7850 (ttm) cc_final: 0.7419 (ttm) REVERT: 5M 60 LEU cc_start: 0.9096 (mt) cc_final: 0.8788 (mt) REVERT: 5O 29 GLU cc_start: 0.8333 (tp30) cc_final: 0.7999 (tp30) REVERT: 5P 46 LEU cc_start: 0.9437 (mt) cc_final: 0.9175 (mt) outliers start: 216 outliers final: 197 residues processed: 1751 average time/residue: 0.2143 time to fit residues: 622.4969 Evaluate side-chains 1840 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 1637 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 23 MET Chi-restraints excluded: chain 1A residue 51 VAL Chi-restraints excluded: chain 1A residue 57 THR Chi-restraints excluded: chain 1B residue 23 MET Chi-restraints excluded: chain 1B residue 25 ILE Chi-restraints excluded: chain 1B residue 26 ILE Chi-restraints excluded: chain 1C residue 21 VAL Chi-restraints excluded: chain 1C residue 23 MET Chi-restraints excluded: chain 1C residue 26 ILE Chi-restraints excluded: chain 1C residue 53 ILE Chi-restraints excluded: chain 1D residue 11 VAL Chi-restraints excluded: chain 1D residue 26 ILE Chi-restraints excluded: chain 1D residue 31 ILE Chi-restraints excluded: chain 1D residue 47 LEU Chi-restraints excluded: chain 1D residue 51 VAL Chi-restraints excluded: chain 1E residue 21 VAL Chi-restraints excluded: chain 1E residue 26 ILE Chi-restraints excluded: chain 1E residue 31 ILE Chi-restraints excluded: chain 1F residue 26 ILE Chi-restraints excluded: chain 1F residue 47 LEU Chi-restraints excluded: chain 1G residue 25 ILE Chi-restraints excluded: chain 1G residue 26 ILE Chi-restraints excluded: chain 1G residue 47 LEU Chi-restraints excluded: chain 1G residue 51 VAL Chi-restraints excluded: chain 1G residue 52 VAL Chi-restraints excluded: chain 1H residue 23 MET Chi-restraints excluded: chain 1H residue 26 ILE Chi-restraints excluded: chain 1H residue 47 LEU Chi-restraints excluded: chain 1I residue 23 MET Chi-restraints excluded: chain 1I residue 26 ILE Chi-restraints excluded: chain 1I residue 31 ILE Chi-restraints excluded: chain 1I residue 47 LEU Chi-restraints excluded: chain 1J residue 21 VAL Chi-restraints excluded: chain 1J residue 47 LEU Chi-restraints excluded: chain 1K residue 23 MET Chi-restraints excluded: chain 1L residue 26 ILE Chi-restraints excluded: chain 1L residue 49 LEU Chi-restraints excluded: chain 1L residue 53 ILE Chi-restraints excluded: chain 1M residue 11 VAL Chi-restraints excluded: chain 1M residue 47 LEU Chi-restraints excluded: chain 1N residue 11 VAL Chi-restraints excluded: chain 1O residue 23 MET Chi-restraints excluded: chain 1O residue 31 ILE Chi-restraints excluded: chain 1P residue 52 VAL Chi-restraints excluded: chain 2A residue 12 LYS Chi-restraints excluded: chain 2A residue 23 MET Chi-restraints excluded: chain 2A residue 51 VAL Chi-restraints excluded: chain 2B residue 23 MET Chi-restraints excluded: chain 2B residue 24 CYS Chi-restraints excluded: chain 2B residue 26 ILE Chi-restraints excluded: chain 2B residue 47 LEU Chi-restraints excluded: chain 2C residue 11 VAL Chi-restraints excluded: chain 2C residue 26 ILE Chi-restraints excluded: chain 2D residue 26 ILE Chi-restraints excluded: chain 2D residue 51 VAL Chi-restraints excluded: chain 2D residue 53 ILE Chi-restraints excluded: chain 2F residue 47 LEU Chi-restraints excluded: chain 2F residue 51 VAL Chi-restraints excluded: chain 2G residue 26 ILE Chi-restraints excluded: chain 2H residue 26 ILE Chi-restraints excluded: chain 2H residue 31 ILE Chi-restraints excluded: chain 2H residue 61 THR Chi-restraints excluded: chain 2I residue 4 LEU Chi-restraints excluded: chain 2I residue 26 ILE Chi-restraints excluded: chain 2I residue 47 LEU Chi-restraints excluded: chain 2I residue 51 VAL Chi-restraints excluded: chain 2I residue 52 VAL Chi-restraints excluded: chain 2J residue 4 LEU Chi-restraints excluded: chain 2J residue 47 LEU Chi-restraints excluded: chain 2K residue 4 LEU Chi-restraints excluded: chain 2L residue 52 VAL Chi-restraints excluded: chain 2L residue 57 THR Chi-restraints excluded: chain 2L residue 58 VAL Chi-restraints excluded: chain 2M residue 11 VAL Chi-restraints excluded: chain 2M residue 31 ILE Chi-restraints excluded: chain 2N residue 23 MET Chi-restraints excluded: chain 2N residue 50 VAL Chi-restraints excluded: chain 2N residue 58 VAL Chi-restraints excluded: chain 2N residue 63 ILE Chi-restraints excluded: chain 2P residue 41 LYS Chi-restraints excluded: chain 2P residue 53 ILE Chi-restraints excluded: chain 3A residue 4 LEU Chi-restraints excluded: chain 3A residue 21 VAL Chi-restraints excluded: chain 3B residue 4 LEU Chi-restraints excluded: chain 3B residue 25 ILE Chi-restraints excluded: chain 3B residue 26 ILE Chi-restraints excluded: chain 3C residue 12 LYS Chi-restraints excluded: chain 3C residue 31 ILE Chi-restraints excluded: chain 3C residue 51 VAL Chi-restraints excluded: chain 3C residue 57 THR Chi-restraints excluded: chain 3D residue 50 VAL Chi-restraints excluded: chain 3E residue 11 VAL Chi-restraints excluded: chain 3E residue 23 MET Chi-restraints excluded: chain 3E residue 26 ILE Chi-restraints excluded: chain 3E residue 41 LYS Chi-restraints excluded: chain 3E residue 46 LEU Chi-restraints excluded: chain 3F residue 11 VAL Chi-restraints excluded: chain 3F residue 26 ILE Chi-restraints excluded: chain 3G residue 23 MET Chi-restraints excluded: chain 3G residue 31 ILE Chi-restraints excluded: chain 3G residue 41 LYS Chi-restraints excluded: chain 3G residue 47 LEU Chi-restraints excluded: chain 3G residue 51 VAL Chi-restraints excluded: chain 3G residue 57 THR Chi-restraints excluded: chain 3H residue 11 VAL Chi-restraints excluded: chain 3H residue 21 VAL Chi-restraints excluded: chain 3H residue 23 MET Chi-restraints excluded: chain 3I residue 11 VAL Chi-restraints excluded: chain 3I residue 52 VAL Chi-restraints excluded: chain 3I residue 58 VAL Chi-restraints excluded: chain 3J residue 11 VAL Chi-restraints excluded: chain 3K residue 4 LEU Chi-restraints excluded: chain 3K residue 23 MET Chi-restraints excluded: chain 3K residue 46 LEU Chi-restraints excluded: chain 3K residue 50 VAL Chi-restraints excluded: chain 3K residue 51 VAL Chi-restraints excluded: chain 3L residue 23 MET Chi-restraints excluded: chain 3L residue 31 ILE Chi-restraints excluded: chain 3L residue 51 VAL Chi-restraints excluded: chain 3L residue 53 ILE Chi-restraints excluded: chain 3M residue 21 VAL Chi-restraints excluded: chain 3M residue 58 VAL Chi-restraints excluded: chain 3N residue 21 VAL Chi-restraints excluded: chain 3N residue 46 LEU Chi-restraints excluded: chain 3O residue 50 VAL Chi-restraints excluded: chain 3P residue 53 ILE Chi-restraints excluded: chain 4A residue 11 VAL Chi-restraints excluded: chain 4B residue 31 ILE Chi-restraints excluded: chain 4C residue 26 ILE Chi-restraints excluded: chain 4D residue 31 ILE Chi-restraints excluded: chain 4D residue 41 LYS Chi-restraints excluded: chain 4D residue 46 LEU Chi-restraints excluded: chain 4D residue 47 LEU Chi-restraints excluded: chain 4E residue 23 MET Chi-restraints excluded: chain 4E residue 50 VAL Chi-restraints excluded: chain 4F residue 4 LEU Chi-restraints excluded: chain 4F residue 26 ILE Chi-restraints excluded: chain 4G residue 31 ILE Chi-restraints excluded: chain 4H residue 21 VAL Chi-restraints excluded: chain 4I residue 21 VAL Chi-restraints excluded: chain 4I residue 23 MET Chi-restraints excluded: chain 4I residue 26 ILE Chi-restraints excluded: chain 4J residue 51 VAL Chi-restraints excluded: chain 4K residue 21 VAL Chi-restraints excluded: chain 4K residue 26 ILE Chi-restraints excluded: chain 4K residue 27 ILE Chi-restraints excluded: chain 4L residue 4 LEU Chi-restraints excluded: chain 4L residue 23 MET Chi-restraints excluded: chain 4L residue 31 ILE Chi-restraints excluded: chain 4M residue 21 VAL Chi-restraints excluded: chain 4M residue 31 ILE Chi-restraints excluded: chain 4N residue 23 MET Chi-restraints excluded: chain 4N residue 47 LEU Chi-restraints excluded: chain 4O residue 21 VAL Chi-restraints excluded: chain 4O residue 31 ILE Chi-restraints excluded: chain 4O residue 47 LEU Chi-restraints excluded: chain 4O residue 50 VAL Chi-restraints excluded: chain 4O residue 57 THR Chi-restraints excluded: chain 4P residue 41 LYS Chi-restraints excluded: chain 4P residue 47 LEU Chi-restraints excluded: chain 4P residue 52 VAL Chi-restraints excluded: chain 5A residue 57 THR Chi-restraints excluded: chain 5B residue 11 VAL Chi-restraints excluded: chain 5B residue 26 ILE Chi-restraints excluded: chain 5B residue 45 ILE Chi-restraints excluded: chain 5B residue 47 LEU Chi-restraints excluded: chain 5B residue 57 THR Chi-restraints excluded: chain 5C residue 11 VAL Chi-restraints excluded: chain 5C residue 31 ILE Chi-restraints excluded: chain 5D residue 4 LEU Chi-restraints excluded: chain 5E residue 11 VAL Chi-restraints excluded: chain 5E residue 12 LYS Chi-restraints excluded: chain 5E residue 19 SER Chi-restraints excluded: chain 5E residue 21 VAL Chi-restraints excluded: chain 5E residue 23 MET Chi-restraints excluded: chain 5E residue 26 ILE Chi-restraints excluded: chain 5E residue 31 ILE Chi-restraints excluded: chain 5E residue 43 LEU Chi-restraints excluded: chain 5F residue 4 LEU Chi-restraints excluded: chain 5F residue 11 VAL Chi-restraints excluded: chain 5F residue 26 ILE Chi-restraints excluded: chain 5F residue 53 ILE Chi-restraints excluded: chain 5G residue 27 ILE Chi-restraints excluded: chain 5G residue 31 ILE Chi-restraints excluded: chain 5G residue 47 LEU Chi-restraints excluded: chain 5G residue 57 THR Chi-restraints excluded: chain 5H residue 26 ILE Chi-restraints excluded: chain 5H residue 46 LEU Chi-restraints excluded: chain 5I residue 4 LEU Chi-restraints excluded: chain 5I residue 23 MET Chi-restraints excluded: chain 5I residue 31 ILE Chi-restraints excluded: chain 5I residue 53 ILE Chi-restraints excluded: chain 5I residue 61 THR Chi-restraints excluded: chain 5J residue 4 LEU Chi-restraints excluded: chain 5J residue 31 ILE Chi-restraints excluded: chain 5J residue 50 VAL Chi-restraints excluded: chain 5K residue 4 LEU Chi-restraints excluded: chain 5K residue 31 ILE Chi-restraints excluded: chain 5L residue 21 VAL Chi-restraints excluded: chain 5N residue 41 LYS Chi-restraints excluded: chain 5N residue 47 LEU Chi-restraints excluded: chain 5O residue 21 VAL Chi-restraints excluded: chain 5P residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 449 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 323 optimal weight: 4.9990 chunk 405 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 388 optimal weight: 9.9990 chunk 413 optimal weight: 9.9990 chunk 298 optimal weight: 1.9990 chunk 275 optimal weight: 8.9990 chunk 444 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.124309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.099735 restraints weight = 57683.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.103991 restraints weight = 28941.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.106829 restraints weight = 17816.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.108735 restraints weight = 12687.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109841 restraints weight = 10034.966| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.7525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41600 Z= 0.127 Angle : 0.639 12.907 55411 Z= 0.309 Chirality : 0.038 0.195 7190 Planarity : 0.002 0.029 6070 Dihedral : 13.779 75.869 8495 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.23 % Allowed : 32.31 % Favored : 63.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.12), residues: 4880 helix: -0.07 (0.09), residues: 3280 sheet: None (None), residues: 0 loop : -1.03 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG2E 39 TYR 0.028 0.002 TYR5E 37 PHE 0.021 0.001 PHE2D 15 Details of bonding type rmsd covalent geometry : bond 0.00321 (41600) covalent geometry : angle 0.63870 (55410) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.03873 ( 2000) hydrogen bonds : angle 4.81459 ( 6000) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1899 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 1723 time to evaluate : 1.522 Fit side-chains REVERT: 1B 40 THR cc_start: 0.9144 (m) cc_final: 0.8926 (p) REVERT: 1B 46 LEU cc_start: 0.9256 (mt) cc_final: 0.9031 (mt) REVERT: 1C 22 MET cc_start: 0.8438 (tpp) cc_final: 0.8172 (tpp) REVERT: 1C 40 THR cc_start: 0.9271 (m) cc_final: 0.8955 (p) REVERT: 1E 40 THR cc_start: 0.9250 (m) cc_final: 0.8848 (p) REVERT: 1H 40 THR cc_start: 0.9351 (m) cc_final: 0.8825 (p) REVERT: 1I 40 THR cc_start: 0.9188 (m) cc_final: 0.8785 (p) REVERT: 1J 40 THR cc_start: 0.8936 (m) cc_final: 0.8385 (p) REVERT: 1K 40 THR cc_start: 0.9062 (m) cc_final: 0.8830 (p) REVERT: 1L 22 MET cc_start: 0.8448 (mmt) cc_final: 0.8042 (tpp) REVERT: 1L 40 THR cc_start: 0.9159 (m) cc_final: 0.8596 (p) REVERT: 1P 39 ARG cc_start: 0.5938 (mmt180) cc_final: 0.5035 (mmm160) REVERT: 2A 23 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7774 (ptm) REVERT: 2A 37 TYR cc_start: 0.9320 (t80) cc_final: 0.8787 (t80) REVERT: 2B 40 THR cc_start: 0.9245 (m) cc_final: 0.8826 (p) REVERT: 2C 40 THR cc_start: 0.9264 (m) cc_final: 0.8909 (p) REVERT: 2D 26 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8820 (mt) REVERT: 2E 22 MET cc_start: 0.8463 (tpp) cc_final: 0.7877 (tpp) REVERT: 2E 40 THR cc_start: 0.9107 (m) cc_final: 0.8705 (p) REVERT: 2H 40 THR cc_start: 0.9067 (m) cc_final: 0.8581 (p) REVERT: 2I 40 THR cc_start: 0.8989 (m) cc_final: 0.8622 (p) REVERT: 2J 40 THR cc_start: 0.9029 (m) cc_final: 0.8742 (p) REVERT: 2K 40 THR cc_start: 0.9246 (m) cc_final: 0.8927 (p) REVERT: 2L 29 GLU cc_start: 0.8426 (tp30) cc_final: 0.8085 (tp30) REVERT: 2L 40 THR cc_start: 0.9262 (m) cc_final: 0.8820 (p) REVERT: 2M 40 THR cc_start: 0.9106 (m) cc_final: 0.8574 (p) REVERT: 2N 29 GLU cc_start: 0.8412 (tp30) cc_final: 0.8023 (tp30) REVERT: 2O 46 LEU cc_start: 0.9421 (mt) cc_final: 0.8962 (mt) REVERT: 3A 40 THR cc_start: 0.9135 (m) cc_final: 0.8849 (p) REVERT: 3B 40 THR cc_start: 0.9086 (m) cc_final: 0.8651 (p) REVERT: 3C 40 THR cc_start: 0.9071 (m) cc_final: 0.8651 (p) REVERT: 3D 40 THR cc_start: 0.9222 (m) cc_final: 0.8908 (p) REVERT: 3E 40 THR cc_start: 0.9120 (m) cc_final: 0.8855 (p) REVERT: 3E 41 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8341 (tttt) REVERT: 3F 40 THR cc_start: 0.9174 (m) cc_final: 0.8965 (p) REVERT: 3G 12 LYS cc_start: 0.8872 (ttmt) cc_final: 0.8591 (tttt) REVERT: 3G 41 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8427 (tttp) REVERT: 3H 46 LEU cc_start: 0.9348 (mt) cc_final: 0.9019 (mt) REVERT: 3J 39 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7735 (ttp80) REVERT: 3J 40 THR cc_start: 0.9284 (m) cc_final: 0.8898 (p) REVERT: 3K 40 THR cc_start: 0.9263 (m) cc_final: 0.8911 (p) REVERT: 3L 29 GLU cc_start: 0.8459 (tp30) cc_final: 0.7907 (tp30) REVERT: 3L 40 THR cc_start: 0.9234 (m) cc_final: 0.8809 (p) REVERT: 3M 37 TYR cc_start: 0.9118 (t80) cc_final: 0.8856 (t80) REVERT: 3M 39 ARG cc_start: 0.8033 (ttp80) cc_final: 0.7799 (ttp80) REVERT: 3O 47 LEU cc_start: 0.9129 (tt) cc_final: 0.8864 (tp) REVERT: 4A 40 THR cc_start: 0.9180 (m) cc_final: 0.8799 (p) REVERT: 4B 40 THR cc_start: 0.9111 (m) cc_final: 0.8848 (p) REVERT: 4C 22 MET cc_start: 0.8131 (tpp) cc_final: 0.7867 (tpp) REVERT: 4C 40 THR cc_start: 0.9173 (m) cc_final: 0.8765 (p) REVERT: 4D 40 THR cc_start: 0.9112 (m) cc_final: 0.8737 (p) REVERT: 4D 41 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8519 (tttt) REVERT: 4E 37 TYR cc_start: 0.9225 (t80) cc_final: 0.9024 (t80) REVERT: 4F 40 THR cc_start: 0.9290 (m) cc_final: 0.8997 (p) REVERT: 4H 40 THR cc_start: 0.9307 (m) cc_final: 0.8990 (p) REVERT: 4K 10 ASP cc_start: 0.7216 (p0) cc_final: 0.6972 (p0) REVERT: 4K 40 THR cc_start: 0.9190 (m) cc_final: 0.8885 (p) REVERT: 4K 60 LEU cc_start: 0.8975 (mt) cc_final: 0.8721 (mt) REVERT: 4L 40 THR cc_start: 0.8989 (m) cc_final: 0.8785 (p) REVERT: 4L 46 LEU cc_start: 0.9224 (mt) cc_final: 0.8973 (mt) REVERT: 4N 27 ILE cc_start: 0.9199 (tt) cc_final: 0.8938 (pt) REVERT: 4N 46 LEU cc_start: 0.9200 (mt) cc_final: 0.8922 (mt) REVERT: 4N 47 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8552 (mt) REVERT: 4N 60 LEU cc_start: 0.8904 (mt) cc_final: 0.8488 (mt) REVERT: 5A 47 LEU cc_start: 0.9123 (tt) cc_final: 0.8669 (mt) REVERT: 5C 40 THR cc_start: 0.9117 (m) cc_final: 0.8566 (p) REVERT: 5D 40 THR cc_start: 0.9192 (m) cc_final: 0.8797 (p) REVERT: 5E 40 THR cc_start: 0.9194 (m) cc_final: 0.8643 (p) REVERT: 5F 40 THR cc_start: 0.9106 (m) cc_final: 0.8807 (p) REVERT: 5G 40 THR cc_start: 0.9238 (m) cc_final: 0.8924 (p) REVERT: 5G 47 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8682 (mt) REVERT: 5H 40 THR cc_start: 0.9157 (m) cc_final: 0.8572 (p) REVERT: 5I 4 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7887 (tt) REVERT: 5I 40 THR cc_start: 0.9172 (m) cc_final: 0.8696 (p) REVERT: 5J 36 MET cc_start: 0.8032 (mtm) cc_final: 0.7793 (mtm) REVERT: 5J 40 THR cc_start: 0.9192 (m) cc_final: 0.8828 (p) REVERT: 5K 40 THR cc_start: 0.9100 (m) cc_final: 0.8809 (p) REVERT: 5L 23 MET cc_start: 0.7725 (ttm) cc_final: 0.7324 (ttm) REVERT: 5M 60 LEU cc_start: 0.9072 (mt) cc_final: 0.8797 (mt) REVERT: 5N 12 LYS cc_start: 0.8480 (ttmm) cc_final: 0.8224 (ttmt) REVERT: 5O 29 GLU cc_start: 0.8236 (tp30) cc_final: 0.7968 (tp30) REVERT: 5P 46 LEU cc_start: 0.9400 (mt) cc_final: 0.9115 (mt) outliers start: 176 outliers final: 153 residues processed: 1777 average time/residue: 0.2235 time to fit residues: 659.0159 Evaluate side-chains 1835 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 1674 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1B residue 23 MET Chi-restraints excluded: chain 1B residue 25 ILE Chi-restraints excluded: chain 1B residue 26 ILE Chi-restraints excluded: chain 1C residue 21 VAL Chi-restraints excluded: chain 1C residue 23 MET Chi-restraints excluded: chain 1C residue 26 ILE Chi-restraints excluded: chain 1C residue 53 ILE Chi-restraints excluded: chain 1D residue 11 VAL Chi-restraints excluded: chain 1D residue 26 ILE Chi-restraints excluded: chain 1D residue 31 ILE Chi-restraints excluded: chain 1D residue 51 VAL Chi-restraints excluded: chain 1E residue 26 ILE Chi-restraints excluded: chain 1E residue 31 ILE Chi-restraints excluded: chain 1F residue 26 ILE Chi-restraints excluded: chain 1G residue 25 ILE Chi-restraints excluded: chain 1G residue 26 ILE Chi-restraints excluded: chain 1G residue 47 LEU Chi-restraints excluded: chain 1G residue 51 VAL Chi-restraints excluded: chain 1H residue 23 MET Chi-restraints excluded: chain 1H residue 26 ILE Chi-restraints excluded: chain 1H residue 47 LEU Chi-restraints excluded: chain 1I residue 23 MET Chi-restraints excluded: chain 1I residue 26 ILE Chi-restraints excluded: chain 1I residue 31 ILE Chi-restraints excluded: chain 1J residue 21 VAL Chi-restraints excluded: chain 1J residue 46 LEU Chi-restraints excluded: chain 1K residue 23 MET Chi-restraints excluded: chain 1L residue 26 ILE Chi-restraints excluded: chain 1L residue 49 LEU Chi-restraints excluded: chain 1L residue 53 ILE Chi-restraints excluded: chain 1M residue 11 VAL Chi-restraints excluded: chain 1M residue 23 MET Chi-restraints excluded: chain 1M residue 47 LEU Chi-restraints excluded: chain 1O residue 23 MET Chi-restraints excluded: chain 1P residue 52 VAL Chi-restraints excluded: chain 2A residue 12 LYS Chi-restraints excluded: chain 2A residue 23 MET Chi-restraints excluded: chain 2B residue 23 MET Chi-restraints excluded: chain 2B residue 24 CYS Chi-restraints excluded: chain 2B residue 26 ILE Chi-restraints excluded: chain 2B residue 47 LEU Chi-restraints excluded: chain 2C residue 26 ILE Chi-restraints excluded: chain 2D residue 26 ILE Chi-restraints excluded: chain 2D residue 53 ILE Chi-restraints excluded: chain 2F residue 46 LEU Chi-restraints excluded: chain 2F residue 47 LEU Chi-restraints excluded: chain 2F residue 51 VAL Chi-restraints excluded: chain 2G residue 26 ILE Chi-restraints excluded: chain 2H residue 26 ILE Chi-restraints excluded: chain 2H residue 61 THR Chi-restraints excluded: chain 2I residue 4 LEU Chi-restraints excluded: chain 2I residue 26 ILE Chi-restraints excluded: chain 2I residue 47 LEU Chi-restraints excluded: chain 2I residue 51 VAL Chi-restraints excluded: chain 2I residue 52 VAL Chi-restraints excluded: chain 2J residue 47 LEU Chi-restraints excluded: chain 2K residue 4 LEU Chi-restraints excluded: chain 2L residue 52 VAL Chi-restraints excluded: chain 2L residue 58 VAL Chi-restraints excluded: chain 2M residue 11 VAL Chi-restraints excluded: chain 2N residue 23 MET Chi-restraints excluded: chain 2N residue 50 VAL Chi-restraints excluded: chain 2N residue 63 ILE Chi-restraints excluded: chain 2O residue 60 LEU Chi-restraints excluded: chain 2P residue 41 LYS Chi-restraints excluded: chain 2P residue 53 ILE Chi-restraints excluded: chain 3A residue 4 LEU Chi-restraints excluded: chain 3A residue 21 VAL Chi-restraints excluded: chain 3B residue 4 LEU Chi-restraints excluded: chain 3B residue 25 ILE Chi-restraints excluded: chain 3B residue 26 ILE Chi-restraints excluded: chain 3C residue 12 LYS Chi-restraints excluded: chain 3C residue 31 ILE Chi-restraints excluded: chain 3C residue 51 VAL Chi-restraints excluded: chain 3D residue 50 VAL Chi-restraints excluded: chain 3E residue 26 ILE Chi-restraints excluded: chain 3E residue 41 LYS Chi-restraints excluded: chain 3F residue 26 ILE Chi-restraints excluded: chain 3G residue 23 MET Chi-restraints excluded: chain 3G residue 41 LYS Chi-restraints excluded: chain 3G residue 47 LEU Chi-restraints excluded: chain 3G residue 51 VAL Chi-restraints excluded: chain 3H residue 21 VAL Chi-restraints excluded: chain 3H residue 23 MET Chi-restraints excluded: chain 3H residue 54 VAL Chi-restraints excluded: chain 3I residue 11 VAL Chi-restraints excluded: chain 3I residue 52 VAL Chi-restraints excluded: chain 3I residue 58 VAL Chi-restraints excluded: chain 3K residue 4 LEU Chi-restraints excluded: chain 3K residue 23 MET Chi-restraints excluded: chain 3K residue 46 LEU Chi-restraints excluded: chain 3K residue 50 VAL Chi-restraints excluded: chain 3L residue 51 VAL Chi-restraints excluded: chain 3L residue 53 ILE Chi-restraints excluded: chain 3M residue 21 VAL Chi-restraints excluded: chain 3M residue 58 VAL Chi-restraints excluded: chain 3N residue 21 VAL Chi-restraints excluded: chain 3N residue 46 LEU Chi-restraints excluded: chain 3O residue 50 VAL Chi-restraints excluded: chain 3O residue 60 LEU Chi-restraints excluded: chain 4B residue 31 ILE Chi-restraints excluded: chain 4C residue 26 ILE Chi-restraints excluded: chain 4D residue 31 ILE Chi-restraints excluded: chain 4D residue 41 LYS Chi-restraints excluded: chain 4D residue 46 LEU Chi-restraints excluded: chain 4D residue 47 LEU Chi-restraints excluded: chain 4E residue 23 MET Chi-restraints excluded: chain 4E residue 50 VAL Chi-restraints excluded: chain 4F residue 4 LEU Chi-restraints excluded: chain 4F residue 26 ILE Chi-restraints excluded: chain 4G residue 31 ILE Chi-restraints excluded: chain 4H residue 21 VAL Chi-restraints excluded: chain 4I residue 21 VAL Chi-restraints excluded: chain 4I residue 23 MET Chi-restraints excluded: chain 4I residue 26 ILE Chi-restraints excluded: chain 4J residue 51 VAL Chi-restraints excluded: chain 4K residue 21 VAL Chi-restraints excluded: chain 4K residue 26 ILE Chi-restraints excluded: chain 4L residue 4 LEU Chi-restraints excluded: chain 4M residue 21 VAL Chi-restraints excluded: chain 4N residue 23 MET Chi-restraints excluded: chain 4N residue 47 LEU Chi-restraints excluded: chain 4O residue 21 VAL Chi-restraints excluded: chain 4O residue 47 LEU Chi-restraints excluded: chain 4O residue 50 VAL Chi-restraints excluded: chain 4P residue 41 LYS Chi-restraints excluded: chain 4P residue 47 LEU Chi-restraints excluded: chain 5B residue 25 ILE Chi-restraints excluded: chain 5B residue 26 ILE Chi-restraints excluded: chain 5B residue 45 ILE Chi-restraints excluded: chain 5B residue 47 LEU Chi-restraints excluded: chain 5C residue 11 VAL Chi-restraints excluded: chain 5D residue 4 LEU Chi-restraints excluded: chain 5E residue 12 LYS Chi-restraints excluded: chain 5E residue 19 SER Chi-restraints excluded: chain 5E residue 21 VAL Chi-restraints excluded: chain 5E residue 26 ILE Chi-restraints excluded: chain 5E residue 31 ILE Chi-restraints excluded: chain 5F residue 4 LEU Chi-restraints excluded: chain 5F residue 11 VAL Chi-restraints excluded: chain 5F residue 26 ILE Chi-restraints excluded: chain 5F residue 53 ILE Chi-restraints excluded: chain 5G residue 23 MET Chi-restraints excluded: chain 5G residue 47 LEU Chi-restraints excluded: chain 5H residue 26 ILE Chi-restraints excluded: chain 5H residue 46 LEU Chi-restraints excluded: chain 5I residue 4 LEU Chi-restraints excluded: chain 5I residue 23 MET Chi-restraints excluded: chain 5I residue 31 ILE Chi-restraints excluded: chain 5I residue 53 ILE Chi-restraints excluded: chain 5I residue 61 THR Chi-restraints excluded: chain 5J residue 23 MET Chi-restraints excluded: chain 5J residue 31 ILE Chi-restraints excluded: chain 5J residue 50 VAL Chi-restraints excluded: chain 5K residue 4 LEU Chi-restraints excluded: chain 5K residue 31 ILE Chi-restraints excluded: chain 5L residue 21 VAL Chi-restraints excluded: chain 5N residue 41 LYS Chi-restraints excluded: chain 5N residue 47 LEU Chi-restraints excluded: chain 5O residue 21 VAL Chi-restraints excluded: chain 5P residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 16 optimal weight: 10.0000 chunk 454 optimal weight: 8.9990 chunk 476 optimal weight: 20.0000 chunk 84 optimal weight: 50.0000 chunk 437 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 339 optimal weight: 6.9990 chunk 96 optimal weight: 30.0000 chunk 430 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.118081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.093694 restraints weight = 58913.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.097827 restraints weight = 29715.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.100608 restraints weight = 18369.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.102490 restraints weight = 13081.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.103730 restraints weight = 10329.417| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.7420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 41600 Z= 0.207 Angle : 0.711 12.330 55411 Z= 0.344 Chirality : 0.040 0.218 7190 Planarity : 0.002 0.046 6070 Dihedral : 14.530 74.869 8495 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 4.62 % Allowed : 32.64 % Favored : 62.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.12), residues: 4880 helix: -0.36 (0.08), residues: 3280 sheet: None (None), residues: 0 loop : -1.08 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG3A 39 TYR 0.027 0.002 TYR5E 37 PHE 0.023 0.002 PHE4M 15 Details of bonding type rmsd covalent geometry : bond 0.00530 (41600) covalent geometry : angle 0.71147 (55410) SS BOND : angle 0.00000 ( 1) hydrogen bonds : bond 0.04642 ( 2000) hydrogen bonds : angle 5.04554 ( 6000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10337.39 seconds wall clock time: 177 minutes 21.85 seconds (10641.85 seconds total)