Starting phenix.real_space_refine on Sun Aug 24 20:59:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fou_29354/08_2025/8fou_29354.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fou_29354/08_2025/8fou_29354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fou_29354/08_2025/8fou_29354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fou_29354/08_2025/8fou_29354.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fou_29354/08_2025/8fou_29354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fou_29354/08_2025/8fou_29354.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 14424 2.51 5 N 3864 2.21 5 O 4824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.02s 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: 23280 Number of models: 1 Model: "" Number of chains: 1 Chain: "I" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 970 Classifications: {'peptide': 127} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 119} Restraints were copied for chains: A, B, C, D, E, F, G, H, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Time building chain proxies: 2.10, per 1000 atoms: 0.09 Number of scatterers: 23280 At special positions: 0 Unit cell: (100.86, 100.86, 159.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 4824 8.00 N 3864 7.00 C 14424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5760 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 72 sheets defined 8.7% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'I' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY I 53 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 80 Processing helix chain 'A' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY A 53 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'B' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY B 53 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'C' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY C 53 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'D' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY D 53 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'E' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY E 53 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 80 Processing helix chain 'F' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY F 53 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 80 Processing helix chain 'G' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY G 53 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 80 Processing helix chain 'H' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY H 53 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 80 Processing helix chain 'J' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY J 53 " --> pdb=" O LEU J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 80 Processing helix chain 'K' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY K 53 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 80 Processing helix chain 'L' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY L 53 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 80 Processing helix chain 'M' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY M 53 " --> pdb=" O LEU M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 80 Processing helix chain 'N' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY N 53 " --> pdb=" O LEU N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 80 Processing helix chain 'O' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY O 53 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 80 Processing helix chain 'P' and resid 50 through 54 removed outlier: 4.279A pdb=" N GLY P 53 " --> pdb=" O LEU P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 80 Processing helix chain 'Q' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY Q 53 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 80 Processing helix chain 'R' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY R 53 " --> pdb=" O LEU R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 80 Processing helix chain 'S' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY S 53 " --> pdb=" O LEU S 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 80 Processing helix chain 'T' and resid 50 through 54 removed outlier: 4.278A pdb=" N GLY T 53 " --> pdb=" O LEU T 50 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 80 Processing helix chain 'U' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY U 53 " --> pdb=" O LEU U 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 80 Processing helix chain 'V' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY V 53 " --> pdb=" O LEU V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 75 through 80 Processing helix chain 'W' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY W 53 " --> pdb=" O LEU W 50 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 80 Processing helix chain 'X' and resid 50 through 54 removed outlier: 4.277A pdb=" N GLY X 53 " --> pdb=" O LEU X 50 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 80 Processing sheet with id=1, first strand: chain 'I' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE I 14 " --> pdb=" O PRO I 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER I 29 " --> pdb=" O ILE I 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE I 12 " --> pdb=" O SER I 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU I 90 " --> pdb=" O LYS I 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE I 12 " --> pdb=" O GLN I 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN I 88 " --> pdb=" O ILE I 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE I 14 " --> pdb=" O ASP I 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP I 86 " --> pdb=" O ILE I 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE I 16 " --> pdb=" O GLN I 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN I 84 " --> pdb=" O PHE I 16 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'I' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA I 121 " --> pdb=" O ALA I 62 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'I' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER I 58 " --> pdb=" O THR I 46 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE A 14 " --> pdb=" O PRO A 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER A 29 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE A 12 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU A 90 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE A 12 " --> pdb=" O GLN A 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN A 88 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE A 14 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP A 86 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE A 16 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN A 84 " --> pdb=" O PHE A 16 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA A 121 " --> pdb=" O ALA A 62 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER A 58 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE B 14 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER B 29 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 12 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU B 90 " --> pdb=" O LYS B 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE B 12 " --> pdb=" O GLN B 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN B 88 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE B 14 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP B 86 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE B 16 " --> pdb=" O GLN B 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN B 84 " --> pdb=" O PHE B 16 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA B 121 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER B 58 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'C' and resid 24 through 30 removed outlier: 5.971A pdb=" N ILE C 14 " --> pdb=" O PRO C 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER C 29 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE C 12 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU C 90 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE C 12 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN C 88 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE C 14 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP C 86 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE C 16 " --> pdb=" O GLN C 84 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN C 84 " --> pdb=" O PHE C 16 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'C' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA C 121 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'C' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER C 58 " --> pdb=" O THR C 46 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'D' and resid 24 through 30 removed outlier: 5.969A pdb=" N ILE D 14 " --> pdb=" O PRO D 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER D 29 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE D 12 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU D 90 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE D 12 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN D 88 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE D 14 " --> pdb=" O ASP D 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP D 86 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE D 16 " --> pdb=" O GLN D 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN D 84 " --> pdb=" O PHE D 16 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'D' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA D 121 " --> pdb=" O ALA D 62 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'D' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER D 58 " --> pdb=" O THR D 46 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'E' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE E 14 " --> pdb=" O PRO E 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER E 29 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE E 12 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU E 90 " --> pdb=" O LYS E 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE E 12 " --> pdb=" O GLN E 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN E 88 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE E 14 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP E 86 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE E 16 " --> pdb=" O GLN E 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN E 84 " --> pdb=" O PHE E 16 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'E' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA E 121 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'E' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER E 58 " --> pdb=" O THR E 46 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'F' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE F 14 " --> pdb=" O PRO F 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER F 29 " --> pdb=" O ILE F 12 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE F 12 " --> pdb=" O SER F 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU F 90 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE F 12 " --> pdb=" O GLN F 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN F 88 " --> pdb=" O ILE F 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE F 14 " --> pdb=" O ASP F 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP F 86 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE F 16 " --> pdb=" O GLN F 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN F 84 " --> pdb=" O PHE F 16 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'F' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA F 121 " --> pdb=" O ALA F 62 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER F 58 " --> pdb=" O THR F 46 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'G' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE G 14 " --> pdb=" O PRO G 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER G 29 " --> pdb=" O ILE G 12 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE G 12 " --> pdb=" O SER G 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU G 90 " --> pdb=" O LYS G 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE G 12 " --> pdb=" O GLN G 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN G 88 " --> pdb=" O ILE G 12 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE G 14 " --> pdb=" O ASP G 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP G 86 " --> pdb=" O ILE G 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE G 16 " --> pdb=" O GLN G 84 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN G 84 " --> pdb=" O PHE G 16 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'G' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA G 121 " --> pdb=" O ALA G 62 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER G 58 " --> pdb=" O THR G 46 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'H' and resid 24 through 30 removed outlier: 5.971A pdb=" N ILE H 14 " --> pdb=" O PRO H 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER H 29 " --> pdb=" O ILE H 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE H 12 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU H 90 " --> pdb=" O LYS H 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE H 12 " --> pdb=" O GLN H 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN H 88 " --> pdb=" O ILE H 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE H 14 " --> pdb=" O ASP H 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP H 86 " --> pdb=" O ILE H 14 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE H 16 " --> pdb=" O GLN H 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN H 84 " --> pdb=" O PHE H 16 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'H' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA H 121 " --> pdb=" O ALA H 62 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'H' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER H 58 " --> pdb=" O THR H 46 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'J' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE J 14 " --> pdb=" O PRO J 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER J 29 " --> pdb=" O ILE J 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE J 12 " --> pdb=" O SER J 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU J 90 " --> pdb=" O LYS J 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE J 12 " --> pdb=" O GLN J 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN J 88 " --> pdb=" O ILE J 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE J 14 " --> pdb=" O ASP J 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP J 86 " --> pdb=" O ILE J 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE J 16 " --> pdb=" O GLN J 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN J 84 " --> pdb=" O PHE J 16 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'J' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA J 121 " --> pdb=" O ALA J 62 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'J' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER J 58 " --> pdb=" O THR J 46 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'K' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE K 14 " --> pdb=" O PRO K 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER K 29 " --> pdb=" O ILE K 12 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE K 12 " --> pdb=" O SER K 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU K 90 " --> pdb=" O LYS K 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE K 12 " --> pdb=" O GLN K 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN K 88 " --> pdb=" O ILE K 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE K 14 " --> pdb=" O ASP K 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP K 86 " --> pdb=" O ILE K 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE K 16 " --> pdb=" O GLN K 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN K 84 " --> pdb=" O PHE K 16 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'K' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA K 121 " --> pdb=" O ALA K 62 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'K' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER K 58 " --> pdb=" O THR K 46 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'L' and resid 24 through 30 removed outlier: 5.969A pdb=" N ILE L 14 " --> pdb=" O PRO L 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER L 29 " --> pdb=" O ILE L 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE L 12 " --> pdb=" O SER L 29 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU L 90 " --> pdb=" O LYS L 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE L 12 " --> pdb=" O GLN L 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN L 88 " --> pdb=" O ILE L 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE L 14 " --> pdb=" O ASP L 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP L 86 " --> pdb=" O ILE L 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE L 16 " --> pdb=" O GLN L 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN L 84 " --> pdb=" O PHE L 16 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'L' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA L 121 " --> pdb=" O ALA L 62 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'L' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER L 58 " --> pdb=" O THR L 46 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'M' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE M 14 " --> pdb=" O PRO M 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER M 29 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE M 12 " --> pdb=" O SER M 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU M 90 " --> pdb=" O LYS M 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE M 12 " --> pdb=" O GLN M 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN M 88 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE M 14 " --> pdb=" O ASP M 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP M 86 " --> pdb=" O ILE M 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE M 16 " --> pdb=" O GLN M 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN M 84 " --> pdb=" O PHE M 16 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'M' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA M 121 " --> pdb=" O ALA M 62 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'M' and resid 45 through 46 removed outlier: 3.562A pdb=" N SER M 58 " --> pdb=" O THR M 46 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'N' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE N 14 " --> pdb=" O PRO N 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER N 29 " --> pdb=" O ILE N 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE N 12 " --> pdb=" O SER N 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU N 90 " --> pdb=" O LYS N 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE N 12 " --> pdb=" O GLN N 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN N 88 " --> pdb=" O ILE N 12 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE N 14 " --> pdb=" O ASP N 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP N 86 " --> pdb=" O ILE N 14 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE N 16 " --> pdb=" O GLN N 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN N 84 " --> pdb=" O PHE N 16 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'N' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA N 121 " --> pdb=" O ALA N 62 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'N' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER N 58 " --> pdb=" O THR N 46 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'O' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE O 14 " --> pdb=" O PRO O 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER O 29 " --> pdb=" O ILE O 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE O 12 " --> pdb=" O SER O 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU O 90 " --> pdb=" O LYS O 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE O 12 " --> pdb=" O GLN O 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN O 88 " --> pdb=" O ILE O 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE O 14 " --> pdb=" O ASP O 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP O 86 " --> pdb=" O ILE O 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE O 16 " --> pdb=" O GLN O 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN O 84 " --> pdb=" O PHE O 16 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'O' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA O 121 " --> pdb=" O ALA O 62 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'O' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER O 58 " --> pdb=" O THR O 46 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'P' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE P 14 " --> pdb=" O PRO P 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER P 29 " --> pdb=" O ILE P 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE P 12 " --> pdb=" O SER P 29 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU P 90 " --> pdb=" O LYS P 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE P 12 " --> pdb=" O GLN P 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN P 88 " --> pdb=" O ILE P 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE P 14 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP P 86 " --> pdb=" O ILE P 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE P 16 " --> pdb=" O GLN P 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN P 84 " --> pdb=" O PHE P 16 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'P' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA P 121 " --> pdb=" O ALA P 62 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'P' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER P 58 " --> pdb=" O THR P 46 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'Q' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE Q 14 " --> pdb=" O PRO Q 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER Q 29 " --> pdb=" O ILE Q 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE Q 12 " --> pdb=" O SER Q 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU Q 90 " --> pdb=" O LYS Q 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE Q 12 " --> pdb=" O GLN Q 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN Q 88 " --> pdb=" O ILE Q 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE Q 14 " --> pdb=" O ASP Q 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP Q 86 " --> pdb=" O ILE Q 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE Q 16 " --> pdb=" O GLN Q 84 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN Q 84 " --> pdb=" O PHE Q 16 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'Q' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA Q 121 " --> pdb=" O ALA Q 62 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'Q' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER Q 58 " --> pdb=" O THR Q 46 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'R' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE R 14 " --> pdb=" O PRO R 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER R 29 " --> pdb=" O ILE R 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE R 12 " --> pdb=" O SER R 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU R 90 " --> pdb=" O LYS R 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE R 12 " --> pdb=" O GLN R 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN R 88 " --> pdb=" O ILE R 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE R 14 " --> pdb=" O ASP R 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP R 86 " --> pdb=" O ILE R 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE R 16 " --> pdb=" O GLN R 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN R 84 " --> pdb=" O PHE R 16 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'R' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA R 121 " --> pdb=" O ALA R 62 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'R' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER R 58 " --> pdb=" O THR R 46 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'S' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE S 14 " --> pdb=" O PRO S 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER S 29 " --> pdb=" O ILE S 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE S 12 " --> pdb=" O SER S 29 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU S 90 " --> pdb=" O LYS S 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE S 12 " --> pdb=" O GLN S 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN S 88 " --> pdb=" O ILE S 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE S 14 " --> pdb=" O ASP S 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP S 86 " --> pdb=" O ILE S 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE S 16 " --> pdb=" O GLN S 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN S 84 " --> pdb=" O PHE S 16 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'S' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA S 121 " --> pdb=" O ALA S 62 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'S' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER S 58 " --> pdb=" O THR S 46 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'T' and resid 24 through 30 removed outlier: 5.971A pdb=" N ILE T 14 " --> pdb=" O PRO T 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER T 29 " --> pdb=" O ILE T 12 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE T 12 " --> pdb=" O SER T 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU T 90 " --> pdb=" O LYS T 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE T 12 " --> pdb=" O GLN T 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN T 88 " --> pdb=" O ILE T 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE T 14 " --> pdb=" O ASP T 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP T 86 " --> pdb=" O ILE T 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE T 16 " --> pdb=" O GLN T 84 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN T 84 " --> pdb=" O PHE T 16 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'T' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA T 121 " --> pdb=" O ALA T 62 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'T' and resid 45 through 46 removed outlier: 3.562A pdb=" N SER T 58 " --> pdb=" O THR T 46 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'U' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE U 14 " --> pdb=" O PRO U 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER U 29 " --> pdb=" O ILE U 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE U 12 " --> pdb=" O SER U 29 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU U 90 " --> pdb=" O LYS U 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE U 12 " --> pdb=" O GLN U 88 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN U 88 " --> pdb=" O ILE U 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE U 14 " --> pdb=" O ASP U 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP U 86 " --> pdb=" O ILE U 14 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE U 16 " --> pdb=" O GLN U 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN U 84 " --> pdb=" O PHE U 16 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'U' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA U 121 " --> pdb=" O ALA U 62 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'U' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER U 58 " --> pdb=" O THR U 46 " (cutoff:3.500A) Processing sheet with id=64, first strand: chain 'V' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE V 14 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER V 29 " --> pdb=" O ILE V 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE V 12 " --> pdb=" O SER V 29 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU V 90 " --> pdb=" O LYS V 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE V 12 " --> pdb=" O GLN V 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN V 88 " --> pdb=" O ILE V 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE V 14 " --> pdb=" O ASP V 86 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ASP V 86 " --> pdb=" O ILE V 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE V 16 " --> pdb=" O GLN V 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN V 84 " --> pdb=" O PHE V 16 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'V' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA V 121 " --> pdb=" O ALA V 62 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'V' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER V 58 " --> pdb=" O THR V 46 " (cutoff:3.500A) Processing sheet with id=67, first strand: chain 'W' and resid 24 through 30 removed outlier: 5.970A pdb=" N ILE W 14 " --> pdb=" O PRO W 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER W 29 " --> pdb=" O ILE W 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE W 12 " --> pdb=" O SER W 29 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU W 90 " --> pdb=" O LYS W 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE W 12 " --> pdb=" O GLN W 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN W 88 " --> pdb=" O ILE W 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE W 14 " --> pdb=" O ASP W 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP W 86 " --> pdb=" O ILE W 14 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE W 16 " --> pdb=" O GLN W 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN W 84 " --> pdb=" O PHE W 16 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'W' and resid 39 through 40 removed outlier: 3.696A pdb=" N ALA W 121 " --> pdb=" O ALA W 62 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain 'W' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER W 58 " --> pdb=" O THR W 46 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'X' and resid 24 through 30 removed outlier: 5.969A pdb=" N ILE X 14 " --> pdb=" O PRO X 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER X 29 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE X 12 " --> pdb=" O SER X 29 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU X 90 " --> pdb=" O LYS X 10 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE X 12 " --> pdb=" O GLN X 88 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN X 88 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE X 14 " --> pdb=" O ASP X 86 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP X 86 " --> pdb=" O ILE X 14 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE X 16 " --> pdb=" O GLN X 84 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN X 84 " --> pdb=" O PHE X 16 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'X' and resid 39 through 40 removed outlier: 3.695A pdb=" N ALA X 121 " --> pdb=" O ALA X 62 " (cutoff:3.500A) Processing sheet with id=72, first strand: chain 'X' and resid 45 through 46 removed outlier: 3.561A pdb=" N SER X 58 " --> pdb=" O THR X 46 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1008 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: 3.94 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7944 1.34 - 1.46: 2937 1.46 - 1.57: 12519 1.57 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 23640 Sorted by residual: bond pdb=" N ASN T 52 " pdb=" CA ASN T 52 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.95e+00 bond pdb=" N ASN J 52 " pdb=" CA ASN J 52 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.94e+00 bond pdb=" N ASN V 52 " pdb=" CA ASN V 52 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.94e+00 bond pdb=" N ASN K 52 " pdb=" CA ASN K 52 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.93e+00 bond pdb=" N ASN E 52 " pdb=" CA ASN E 52 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.91e+00 ... (remaining 23635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 31488 1.62 - 3.24: 720 3.24 - 4.85: 24 4.85 - 6.47: 48 6.47 - 8.09: 24 Bond angle restraints: 32304 Sorted by residual: angle pdb=" N ASN W 4 " pdb=" CA ASN W 4 " pdb=" C ASN W 4 " ideal model delta sigma weight residual 114.64 106.55 8.09 1.52e+00 4.33e-01 2.83e+01 angle pdb=" N ASN R 4 " pdb=" CA ASN R 4 " pdb=" C ASN R 4 " ideal model delta sigma weight residual 114.64 106.55 8.09 1.52e+00 4.33e-01 2.83e+01 angle pdb=" N ASN V 4 " pdb=" CA ASN V 4 " pdb=" C ASN V 4 " ideal model delta sigma weight residual 114.64 106.56 8.08 1.52e+00 4.33e-01 2.83e+01 angle pdb=" N ASN T 4 " pdb=" CA ASN T 4 " pdb=" C ASN T 4 " ideal model delta sigma weight residual 114.64 106.56 8.08 1.52e+00 4.33e-01 2.82e+01 angle pdb=" N ASN Q 4 " pdb=" CA ASN Q 4 " pdb=" C ASN Q 4 " ideal model delta sigma weight residual 114.64 106.56 8.08 1.52e+00 4.33e-01 2.82e+01 ... (remaining 32299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12733 17.94 - 35.88: 1283 35.88 - 53.82: 288 53.82 - 71.77: 48 71.77 - 89.71: 72 Dihedral angle restraints: 14424 sinusoidal: 5568 harmonic: 8856 Sorted by residual: dihedral pdb=" CB GLU E 108 " pdb=" CG GLU E 108 " pdb=" CD GLU E 108 " pdb=" OE1 GLU E 108 " ideal model delta sinusoidal sigma weight residual 0.00 89.71 -89.71 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU C 108 " pdb=" CG GLU C 108 " pdb=" CD GLU C 108 " pdb=" OE1 GLU C 108 " ideal model delta sinusoidal sigma weight residual 0.00 89.70 -89.70 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU K 108 " pdb=" CG GLU K 108 " pdb=" CD GLU K 108 " pdb=" OE1 GLU K 108 " ideal model delta sinusoidal sigma weight residual 0.00 89.70 -89.70 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 14421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2551 0.033 - 0.066: 793 0.066 - 0.099: 339 0.099 - 0.133: 205 0.133 - 0.166: 24 Chirality restraints: 3912 Sorted by residual: chirality pdb=" CA ASN H 52 " pdb=" N ASN H 52 " pdb=" C ASN H 52 " pdb=" CB ASN H 52 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ASN U 52 " pdb=" N ASN U 52 " pdb=" C ASN U 52 " pdb=" CB ASN U 52 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ASN G 52 " pdb=" N ASN G 52 " pdb=" C ASN G 52 " pdb=" CB ASN G 52 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 ... (remaining 3909 not shown) Planarity restraints: 4272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN L 4 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C ASN L 4 " -0.040 2.00e-02 2.50e+03 pdb=" O ASN L 4 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS L 5 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN S 4 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C ASN S 4 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN S 4 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS S 5 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN M 4 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C ASN M 4 " -0.040 2.00e-02 2.50e+03 pdb=" O ASN M 4 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS M 5 " 0.013 2.00e-02 2.50e+03 ... (remaining 4269 not shown) Histogram of nonbonded interaction distances: 0.88 - 1.69: 108 1.69 - 2.49: 282 2.49 - 3.29: 25363 3.29 - 4.10: 58280 4.10 - 4.90: 110976 Warning: very small nonbonded interaction distances. Nonbonded interactions: 195009 Sorted by model distance: nonbonded pdb=" CD GLN F 84 " pdb=" CB CYS J 3 " model vdw 0.884 2.936 nonbonded pdb=" CD GLN I 84 " pdb=" CB CYS E 3 " model vdw 0.884 2.936 nonbonded pdb=" CD GLN O 84 " pdb=" CB CYS R 3 " model vdw 0.884 2.936 nonbonded pdb=" CD GLN B 84 " pdb=" CB CYS D 3 " model vdw 0.884 2.936 nonbonded pdb=" CB CYS I 3 " pdb=" CD GLN X 84 " model vdw 0.884 2.936 ... (remaining 195004 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: 0.09 Found NCS groups: ncs_group { reference = chain 'I' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 19.040 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.016 0.587 23658 Z= 1.624 Angle : 0.602 8.089 32304 Z= 0.351 Chirality : 0.045 0.166 3912 Planarity : 0.004 0.028 4272 Dihedral : 16.429 89.706 8664 Min Nonbonded Distance : 0.884 Molprobity Statistics. All-atom Clashscore : 25.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -2.68 (0.15), residues: 3000 helix: None (None), residues: 0 sheet: -2.83 (0.11), residues: 1608 loop : -0.04 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 70 TYR 0.004 0.001 TYR F 40 PHE 0.006 0.001 PHE Q 16 TRP 0.002 0.000 TRP E 45 HIS 0.001 0.000 HIS Q 30 Details of bonding type rmsd covalent geometry : bond 0.00307 (23640) covalent geometry : angle 0.60230 (32304) hydrogen bonds : bond 0.21902 ( 504) hydrogen bonds : angle 11.51871 ( 1008) Misc. bond : bond 0.58661 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 530 time to evaluate : 0.886 Fit side-chains REVERT: A 125 ASP cc_start: 0.7920 (t0) cc_final: 0.7603 (m-30) REVERT: B 5 LYS cc_start: 0.7549 (pttm) cc_final: 0.7237 (ptpt) REVERT: B 125 ASP cc_start: 0.7748 (t0) cc_final: 0.7407 (m-30) REVERT: C 27 PRO cc_start: 0.8643 (Cg_endo) cc_final: 0.8417 (Cg_exo) REVERT: C 93 ASP cc_start: 0.8117 (p0) cc_final: 0.7884 (p0) REVERT: C 125 ASP cc_start: 0.7710 (t0) cc_final: 0.7374 (m-30) REVERT: D 125 ASP cc_start: 0.7808 (t0) cc_final: 0.7466 (m-30) REVERT: E 5 LYS cc_start: 0.7557 (pttm) cc_final: 0.7119 (ptpt) REVERT: E 125 ASP cc_start: 0.7816 (t0) cc_final: 0.7257 (m-30) REVERT: G 36 THR cc_start: 0.8606 (p) cc_final: 0.8382 (p) REVERT: G 46 THR cc_start: 0.8798 (m) cc_final: 0.8361 (p) REVERT: G 125 ASP cc_start: 0.7800 (t0) cc_final: 0.7443 (m-30) REVERT: H 125 ASP cc_start: 0.7846 (t0) cc_final: 0.7457 (m-30) REVERT: J 79 TYR cc_start: 0.9225 (m-80) cc_final: 0.8954 (m-80) REVERT: J 125 ASP cc_start: 0.7819 (t0) cc_final: 0.7367 (m-30) REVERT: K 93 ASP cc_start: 0.8391 (p0) cc_final: 0.7872 (p0) REVERT: K 101 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8274 (mt-10) REVERT: L 79 TYR cc_start: 0.9271 (m-80) cc_final: 0.9015 (m-80) REVERT: L 125 ASP cc_start: 0.7733 (t0) cc_final: 0.7353 (m-30) REVERT: M 125 ASP cc_start: 0.7920 (t0) cc_final: 0.7600 (m-30) REVERT: N 5 LYS cc_start: 0.7547 (pttm) cc_final: 0.7227 (ptpt) REVERT: N 125 ASP cc_start: 0.7759 (t0) cc_final: 0.7410 (m-30) REVERT: P 27 PRO cc_start: 0.8652 (Cg_endo) cc_final: 0.8423 (Cg_exo) REVERT: P 93 ASP cc_start: 0.8113 (p0) cc_final: 0.7880 (p0) REVERT: P 125 ASP cc_start: 0.7705 (t0) cc_final: 0.7362 (m-30) REVERT: Q 125 ASP cc_start: 0.7805 (t0) cc_final: 0.7461 (m-30) REVERT: R 5 LYS cc_start: 0.7567 (pttm) cc_final: 0.7120 (ptpt) REVERT: R 125 ASP cc_start: 0.7815 (t0) cc_final: 0.7249 (m-30) REVERT: T 46 THR cc_start: 0.8796 (m) cc_final: 0.8349 (p) REVERT: T 125 ASP cc_start: 0.7785 (t0) cc_final: 0.7418 (m-30) REVERT: U 125 ASP cc_start: 0.7843 (t0) cc_final: 0.7458 (m-30) REVERT: V 79 TYR cc_start: 0.9225 (m-80) cc_final: 0.8958 (m-80) REVERT: V 125 ASP cc_start: 0.7819 (t0) cc_final: 0.7374 (m-30) REVERT: W 93 ASP cc_start: 0.8383 (p0) cc_final: 0.7866 (p0) REVERT: W 101 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8264 (mt-10) REVERT: X 79 TYR cc_start: 0.9259 (m-80) cc_final: 0.9004 (m-80) REVERT: X 125 ASP cc_start: 0.7736 (t0) cc_final: 0.7358 (m-30) outliers start: 0 outliers final: 0 residues processed: 530 average time/residue: 0.1219 time to fit residues: 106.0053 Evaluate side-chains 462 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 462 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 0.0970 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 4 ASN ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN M 4 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 4 ASN ** U 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 4 ASN ** W 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 4 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.143381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.133255 restraints weight = 30437.083| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.65 r_work: 0.3584 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23658 Z= 0.149 Angle : 0.551 6.840 32304 Z= 0.295 Chirality : 0.046 0.167 3912 Planarity : 0.004 0.040 4272 Dihedral : 4.096 12.201 3192 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.12 % Allowed : 14.14 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -2.16 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.53 (0.12), residues: 1608 loop : 0.37 (0.19), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 70 TYR 0.018 0.001 TYR W 79 PHE 0.004 0.001 PHE M 16 TRP 0.003 0.000 TRP Q 45 HIS 0.001 0.000 HIS R 30 Details of bonding type rmsd covalent geometry : bond 0.00331 (23640) covalent geometry : angle 0.55146 (32304) hydrogen bonds : bond 0.02561 ( 504) hydrogen bonds : angle 7.20336 ( 1008) Misc. bond : bond 0.00945 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 501 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 125 ASP cc_start: 0.7771 (t0) cc_final: 0.7081 (m-30) REVERT: A 63 THR cc_start: 0.8966 (m) cc_final: 0.8615 (p) REVERT: A 125 ASP cc_start: 0.7913 (t0) cc_final: 0.7565 (m-30) REVERT: B 5 LYS cc_start: 0.7571 (pttm) cc_final: 0.7237 (ptpt) REVERT: B 125 ASP cc_start: 0.7733 (t0) cc_final: 0.7506 (m-30) REVERT: D 63 THR cc_start: 0.9016 (m) cc_final: 0.8663 (p) REVERT: D 125 ASP cc_start: 0.7675 (t0) cc_final: 0.7410 (m-30) REVERT: E 5 LYS cc_start: 0.7519 (pttm) cc_final: 0.7001 (ptpt) REVERT: E 125 ASP cc_start: 0.7825 (t0) cc_final: 0.7434 (m-30) REVERT: F 5 LYS cc_start: 0.7650 (pttm) cc_final: 0.7208 (ptpt) REVERT: F 88 GLN cc_start: 0.8333 (tm-30) cc_final: 0.7672 (tm-30) REVERT: F 125 ASP cc_start: 0.7732 (t0) cc_final: 0.7097 (m-30) REVERT: H 63 THR cc_start: 0.8982 (m) cc_final: 0.8655 (p) REVERT: H 125 ASP cc_start: 0.7819 (t0) cc_final: 0.7437 (m-30) REVERT: J 125 ASP cc_start: 0.7904 (t0) cc_final: 0.7513 (m-30) REVERT: K 5 LYS cc_start: 0.7687 (pttm) cc_final: 0.7143 (ptpt) REVERT: K 101 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8458 (mt-10) REVERT: L 79 TYR cc_start: 0.9182 (m-80) cc_final: 0.8932 (m-80) REVERT: M 63 THR cc_start: 0.8958 (m) cc_final: 0.8603 (p) REVERT: M 125 ASP cc_start: 0.7888 (t0) cc_final: 0.7549 (m-30) REVERT: N 5 LYS cc_start: 0.7529 (pttm) cc_final: 0.7185 (ptpt) REVERT: N 125 ASP cc_start: 0.7748 (t0) cc_final: 0.7519 (m-30) REVERT: O 125 ASP cc_start: 0.7733 (t0) cc_final: 0.7051 (m-30) REVERT: Q 63 THR cc_start: 0.9025 (m) cc_final: 0.8665 (p) REVERT: Q 125 ASP cc_start: 0.7725 (t0) cc_final: 0.7449 (m-30) REVERT: R 5 LYS cc_start: 0.7563 (pttm) cc_final: 0.7056 (ptpt) REVERT: R 125 ASP cc_start: 0.7814 (t0) cc_final: 0.7422 (m-30) REVERT: S 5 LYS cc_start: 0.7633 (pttm) cc_final: 0.7180 (ptpt) REVERT: S 88 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7679 (tm-30) REVERT: S 125 ASP cc_start: 0.7763 (t0) cc_final: 0.7107 (m-30) REVERT: T 125 ASP cc_start: 0.7611 (t0) cc_final: 0.7410 (m-30) REVERT: U 63 THR cc_start: 0.8972 (m) cc_final: 0.8636 (p) REVERT: U 125 ASP cc_start: 0.7824 (t0) cc_final: 0.7438 (m-30) REVERT: V 125 ASP cc_start: 0.7850 (t0) cc_final: 0.7503 (m-30) REVERT: W 5 LYS cc_start: 0.7714 (pttm) cc_final: 0.7147 (ptpt) REVERT: W 101 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8438 (mt-10) REVERT: X 79 TYR cc_start: 0.9179 (m-80) cc_final: 0.8928 (m-80) outliers start: 57 outliers final: 52 residues processed: 529 average time/residue: 0.1208 time to fit residues: 108.1385 Evaluate side-chains 479 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 427 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 97 MET Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 97 MET Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 175 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 280 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 234 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 110 optimal weight: 0.0170 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 6 GLN B 6 GLN C 4 ASN D 6 GLN E 6 GLN F 4 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN J 6 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN N 6 GLN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 4 ASN Q 6 GLN R 6 GLN S 4 ASN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 6 GLN V 6 GLN W 6 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.137237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.126745 restraints weight = 31162.893| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.69 r_work: 0.3480 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 23658 Z= 0.190 Angle : 0.553 7.444 32304 Z= 0.286 Chirality : 0.047 0.168 3912 Planarity : 0.004 0.041 4272 Dihedral : 4.223 12.699 3192 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.94 % Allowed : 17.00 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -2.24 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.59 (0.12), residues: 1608 loop : 0.31 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 70 TYR 0.021 0.002 TYR K 79 PHE 0.007 0.001 PHE A 16 TRP 0.003 0.001 TRP T 45 HIS 0.001 0.000 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00456 (23640) covalent geometry : angle 0.55292 (32304) hydrogen bonds : bond 0.02303 ( 504) hydrogen bonds : angle 6.27844 ( 1008) Misc. bond : bond 0.00704 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 503 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 63 THR cc_start: 0.9045 (m) cc_final: 0.8819 (t) REVERT: A 63 THR cc_start: 0.9020 (m) cc_final: 0.8636 (p) REVERT: A 125 ASP cc_start: 0.7869 (t0) cc_final: 0.7622 (m-30) REVERT: B 5 LYS cc_start: 0.7479 (pttm) cc_final: 0.7106 (ptpt) REVERT: B 63 THR cc_start: 0.9114 (m) cc_final: 0.8774 (p) REVERT: D 63 THR cc_start: 0.9138 (m) cc_final: 0.8663 (p) REVERT: E 5 LYS cc_start: 0.7463 (pttm) cc_final: 0.6984 (ptpt) REVERT: E 63 THR cc_start: 0.9104 (m) cc_final: 0.8848 (p) REVERT: E 125 ASP cc_start: 0.7768 (t0) cc_final: 0.7486 (m-30) REVERT: H 63 THR cc_start: 0.9001 (m) cc_final: 0.8643 (p) REVERT: H 125 ASP cc_start: 0.7808 (t0) cc_final: 0.7591 (m-30) REVERT: J 5 LYS cc_start: 0.7688 (mtmm) cc_final: 0.7117 (mtpt) REVERT: J 125 ASP cc_start: 0.7902 (t0) cc_final: 0.7622 (m-30) REVERT: K 101 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8538 (mt-10) REVERT: L 79 TYR cc_start: 0.9246 (m-80) cc_final: 0.8945 (m-80) REVERT: M 63 THR cc_start: 0.9033 (m) cc_final: 0.8653 (p) REVERT: M 125 ASP cc_start: 0.7842 (t0) cc_final: 0.7612 (m-30) REVERT: N 5 LYS cc_start: 0.7490 (pttm) cc_final: 0.7111 (ptpt) REVERT: N 63 THR cc_start: 0.9097 (m) cc_final: 0.8765 (p) REVERT: Q 63 THR cc_start: 0.9126 (m) cc_final: 0.8649 (p) REVERT: R 5 LYS cc_start: 0.7451 (pttm) cc_final: 0.6971 (ptpt) REVERT: R 63 THR cc_start: 0.9103 (m) cc_final: 0.8842 (p) REVERT: R 125 ASP cc_start: 0.7740 (t0) cc_final: 0.7454 (m-30) REVERT: U 63 THR cc_start: 0.8992 (m) cc_final: 0.8625 (p) REVERT: U 125 ASP cc_start: 0.7822 (t0) cc_final: 0.7601 (m-30) REVERT: V 5 LYS cc_start: 0.7682 (mtmm) cc_final: 0.7041 (mtpt) REVERT: V 125 ASP cc_start: 0.7902 (t0) cc_final: 0.7616 (m-30) REVERT: W 101 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8488 (mt-10) REVERT: X 79 TYR cc_start: 0.9247 (m-80) cc_final: 0.8943 (m-80) outliers start: 106 outliers final: 94 residues processed: 550 average time/residue: 0.1155 time to fit residues: 107.7169 Evaluate side-chains 547 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 453 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 51 THR Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 63 THR Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 97 MET Chi-restraints excluded: chain V residue 122 SER Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 97 MET Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 63 THR Chi-restraints excluded: chain X residue 97 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 222 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 204 optimal weight: 0.0770 chunk 125 optimal weight: 8.9990 chunk 287 optimal weight: 0.9980 chunk 253 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 219 optimal weight: 0.0370 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN C 4 ASN F 6 GLN K 6 GLN O 6 GLN P 4 ASN S 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.141994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.131631 restraints weight = 30752.985| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.68 r_work: 0.3555 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23658 Z= 0.113 Angle : 0.492 7.466 32304 Z= 0.258 Chirality : 0.045 0.166 3912 Planarity : 0.004 0.034 4272 Dihedral : 3.984 14.253 3192 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.99 % Allowed : 18.04 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.58 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.09 (0.13), residues: 1512 loop : 0.44 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 70 TYR 0.026 0.001 TYR W 40 PHE 0.003 0.000 PHE I 16 TRP 0.003 0.000 TRP E 45 HIS 0.000 0.000 HIS N 30 Details of bonding type rmsd covalent geometry : bond 0.00259 (23640) covalent geometry : angle 0.49181 (32304) hydrogen bonds : bond 0.02089 ( 504) hydrogen bonds : angle 5.78970 ( 1008) Misc. bond : bond 0.00544 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 500 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 125 ASP cc_start: 0.7839 (t0) cc_final: 0.7244 (m-30) REVERT: A 63 THR cc_start: 0.8894 (m) cc_final: 0.8575 (p) REVERT: A 125 ASP cc_start: 0.7708 (t0) cc_final: 0.7488 (m-30) REVERT: B 63 THR cc_start: 0.9058 (m) cc_final: 0.8808 (p) REVERT: D 63 THR cc_start: 0.9046 (m) cc_final: 0.8595 (p) REVERT: E 63 THR cc_start: 0.9112 (m) cc_final: 0.8843 (p) REVERT: E 125 ASP cc_start: 0.7680 (t0) cc_final: 0.7442 (m-30) REVERT: F 125 ASP cc_start: 0.7689 (t0) cc_final: 0.7117 (m-30) REVERT: H 63 THR cc_start: 0.8931 (m) cc_final: 0.8626 (p) REVERT: H 125 ASP cc_start: 0.7804 (t0) cc_final: 0.7549 (m-30) REVERT: J 125 ASP cc_start: 0.7792 (t0) cc_final: 0.7563 (m-30) REVERT: K 101 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8532 (mt-10) REVERT: K 120 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8596 (m) REVERT: L 79 TYR cc_start: 0.9173 (m-80) cc_final: 0.8964 (m-80) REVERT: M 63 THR cc_start: 0.8898 (m) cc_final: 0.8551 (p) REVERT: M 125 ASP cc_start: 0.7743 (t0) cc_final: 0.7503 (m-30) REVERT: N 63 THR cc_start: 0.9041 (m) cc_final: 0.8789 (p) REVERT: O 125 ASP cc_start: 0.7807 (t0) cc_final: 0.7209 (m-30) REVERT: Q 63 THR cc_start: 0.9043 (m) cc_final: 0.8588 (p) REVERT: R 63 THR cc_start: 0.9097 (m) cc_final: 0.8847 (p) REVERT: R 125 ASP cc_start: 0.7671 (t0) cc_final: 0.7434 (m-30) REVERT: S 125 ASP cc_start: 0.7695 (t0) cc_final: 0.7128 (m-30) REVERT: U 63 THR cc_start: 0.8930 (m) cc_final: 0.8624 (p) REVERT: U 125 ASP cc_start: 0.7778 (t0) cc_final: 0.7557 (m-30) REVERT: V 5 LYS cc_start: 0.7531 (mtmm) cc_final: 0.6984 (mtpt) REVERT: V 120 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8610 (m) REVERT: V 125 ASP cc_start: 0.7796 (t0) cc_final: 0.7570 (m-30) REVERT: W 101 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8492 (mt-10) REVERT: W 120 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8587 (m) REVERT: X 79 TYR cc_start: 0.9174 (m-80) cc_final: 0.8968 (m-80) outliers start: 134 outliers final: 92 residues processed: 578 average time/residue: 0.1176 time to fit residues: 116.0247 Evaluate side-chains 555 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 460 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 CYS Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 3 CYS Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain E residue 3 CYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain F residue 3 CYS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 3 CYS Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain J residue 3 CYS Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 3 CYS Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain M residue 3 CYS Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain N residue 3 CYS Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain O residue 3 CYS Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain Q residue 3 CYS Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain R residue 3 CYS Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain S residue 3 CYS Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain U residue 3 CYS Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain V residue 3 CYS Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 97 MET Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 122 SER Chi-restraints excluded: chain W residue 3 CYS Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 97 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 218 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 213 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 chunk 202 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 238 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 252 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 4 ASN J 4 ASN P 4 ASN V 4 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.141504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.131270 restraints weight = 30630.650| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.67 r_work: 0.3557 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23658 Z= 0.128 Angle : 0.501 7.477 32304 Z= 0.263 Chirality : 0.046 0.166 3912 Planarity : 0.004 0.032 4272 Dihedral : 3.918 12.553 3192 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.91 % Allowed : 18.53 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.51 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.05 (0.13), residues: 1512 loop : 0.50 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 70 TYR 0.017 0.001 TYR K 40 PHE 0.004 0.001 PHE H 16 TRP 0.003 0.001 TRP P 45 HIS 0.001 0.000 HIS J 30 Details of bonding type rmsd covalent geometry : bond 0.00300 (23640) covalent geometry : angle 0.50121 (32304) hydrogen bonds : bond 0.01897 ( 504) hydrogen bonds : angle 5.60818 ( 1008) Misc. bond : bond 0.00511 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 451 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8813 (m) cc_final: 0.8520 (p) REVERT: B 63 THR cc_start: 0.9008 (m) cc_final: 0.8795 (p) REVERT: D 63 THR cc_start: 0.8991 (m) cc_final: 0.8541 (p) REVERT: E 125 ASP cc_start: 0.7687 (t0) cc_final: 0.7474 (m-30) REVERT: F 96 VAL cc_start: 0.8709 (t) cc_final: 0.8496 (t) REVERT: H 63 THR cc_start: 0.8887 (m) cc_final: 0.8586 (p) REVERT: H 125 ASP cc_start: 0.7816 (t0) cc_final: 0.7560 (m-30) REVERT: K 120 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8624 (m) REVERT: L 79 TYR cc_start: 0.9172 (m-80) cc_final: 0.8963 (m-80) REVERT: M 125 ASP cc_start: 0.7695 (t0) cc_final: 0.7492 (m-30) REVERT: Q 63 THR cc_start: 0.9019 (m) cc_final: 0.8554 (p) REVERT: S 96 VAL cc_start: 0.8687 (t) cc_final: 0.8480 (t) REVERT: U 63 THR cc_start: 0.8890 (m) cc_final: 0.8586 (p) REVERT: U 125 ASP cc_start: 0.7811 (t0) cc_final: 0.7570 (m-30) REVERT: W 120 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8611 (m) REVERT: X 79 TYR cc_start: 0.9166 (m-80) cc_final: 0.8964 (m-80) outliers start: 132 outliers final: 111 residues processed: 512 average time/residue: 0.1341 time to fit residues: 118.8399 Evaluate side-chains 536 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 423 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 CYS Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 3 CYS Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 3 CYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 3 CYS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 3 CYS Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain J residue 3 CYS Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 3 CYS Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain M residue 3 CYS Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain N residue 3 CYS Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain O residue 3 CYS Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain Q residue 3 CYS Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain R residue 3 CYS Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain S residue 3 CYS Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 117 MET Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain T residue 122 SER Chi-restraints excluded: chain U residue 3 CYS Chi-restraints excluded: chain U residue 4 ASN Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 97 MET Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain V residue 3 CYS Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 97 MET Chi-restraints excluded: chain V residue 122 SER Chi-restraints excluded: chain W residue 3 CYS Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 97 MET Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 97 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 92 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 211 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 279 optimal weight: 4.9990 chunk 274 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 4 ASN E 4 ASN J 4 ASN L 4 ASN P 4 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.138616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.127876 restraints weight = 30452.546| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.73 r_work: 0.3489 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23658 Z= 0.206 Angle : 0.572 7.754 32304 Z= 0.291 Chirality : 0.048 0.175 3912 Planarity : 0.005 0.044 4272 Dihedral : 4.173 12.648 3192 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.51 % Allowed : 19.64 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.80 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.24 (0.13), residues: 1512 loop : 0.31 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 70 TYR 0.024 0.002 TYR W 79 PHE 0.006 0.001 PHE T 16 TRP 0.004 0.001 TRP C 45 HIS 0.002 0.001 HIS E 30 Details of bonding type rmsd covalent geometry : bond 0.00497 (23640) covalent geometry : angle 0.57181 (32304) hydrogen bonds : bond 0.02050 ( 504) hydrogen bonds : angle 5.55551 ( 1008) Misc. bond : bond 0.00475 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 447 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 125 ASP cc_start: 0.7890 (t0) cc_final: 0.7301 (m-30) REVERT: A 63 THR cc_start: 0.8964 (m) cc_final: 0.8600 (p) REVERT: B 63 THR cc_start: 0.9079 (m) cc_final: 0.8853 (p) REVERT: D 63 THR cc_start: 0.9076 (m) cc_final: 0.8576 (p) REVERT: E 63 THR cc_start: 0.9144 (m) cc_final: 0.8864 (p) REVERT: E 125 ASP cc_start: 0.7913 (t0) cc_final: 0.7593 (m-30) REVERT: F 40 TYR cc_start: 0.8234 (m-80) cc_final: 0.7945 (m-10) REVERT: F 125 ASP cc_start: 0.7901 (t0) cc_final: 0.7293 (m-30) REVERT: H 63 THR cc_start: 0.8967 (m) cc_final: 0.8618 (p) REVERT: L 79 TYR cc_start: 0.9240 (m-80) cc_final: 0.9007 (m-80) REVERT: M 125 ASP cc_start: 0.7881 (t0) cc_final: 0.7660 (m-30) REVERT: N 63 THR cc_start: 0.9074 (m) cc_final: 0.8845 (p) REVERT: O 125 ASP cc_start: 0.7849 (t0) cc_final: 0.7283 (m-30) REVERT: Q 63 THR cc_start: 0.9083 (m) cc_final: 0.8584 (p) REVERT: R 63 THR cc_start: 0.9118 (m) cc_final: 0.8846 (p) REVERT: S 40 TYR cc_start: 0.8226 (m-80) cc_final: 0.7927 (m-10) REVERT: S 125 ASP cc_start: 0.7860 (t0) cc_final: 0.7276 (m-30) REVERT: U 63 THR cc_start: 0.8955 (m) cc_final: 0.8638 (p) REVERT: X 79 TYR cc_start: 0.9246 (m-80) cc_final: 0.9015 (m-80) outliers start: 148 outliers final: 131 residues processed: 518 average time/residue: 0.1234 time to fit residues: 111.4797 Evaluate side-chains 559 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 428 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 CYS Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 3 CYS Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 3 CYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 3 CYS Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain H residue 3 CYS Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain J residue 3 CYS Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 3 CYS Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain M residue 3 CYS Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain N residue 3 CYS Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain O residue 3 CYS Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 3 CYS Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain R residue 3 CYS Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain S residue 3 CYS Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain T residue 122 SER Chi-restraints excluded: chain U residue 3 CYS Chi-restraints excluded: chain U residue 4 ASN Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 97 MET Chi-restraints excluded: chain V residue 3 CYS Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 97 MET Chi-restraints excluded: chain V residue 122 SER Chi-restraints excluded: chain W residue 3 CYS Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 72 LEU Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 97 MET Chi-restraints excluded: chain X residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 237 optimal weight: 1.9990 chunk 282 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 133 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 222 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 203 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 4 ASN ** H 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN P 4 ASN ** U 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 4 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.142156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.131437 restraints weight = 30075.139| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.73 r_work: 0.3537 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23658 Z= 0.134 Angle : 0.526 7.924 32304 Z= 0.274 Chirality : 0.046 0.171 3912 Planarity : 0.004 0.037 4272 Dihedral : 3.994 19.751 3192 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.80 % Allowed : 21.43 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.54 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.08 (0.13), residues: 1512 loop : 0.50 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 70 TYR 0.029 0.002 TYR I 40 PHE 0.004 0.001 PHE P 16 TRP 0.004 0.001 TRP E 45 HIS 0.001 0.000 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00317 (23640) covalent geometry : angle 0.52623 (32304) hydrogen bonds : bond 0.01943 ( 504) hydrogen bonds : angle 5.34706 ( 1008) Misc. bond : bond 0.00487 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 441 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 5 LYS cc_start: 0.7416 (pttm) cc_final: 0.7036 (ptpt) REVERT: I 125 ASP cc_start: 0.7953 (t0) cc_final: 0.7377 (m-30) REVERT: A 63 THR cc_start: 0.8812 (m) cc_final: 0.8520 (p) REVERT: C 79 TYR cc_start: 0.9110 (m-80) cc_final: 0.8770 (m-80) REVERT: D 63 THR cc_start: 0.9010 (m) cc_final: 0.8541 (p) REVERT: E 79 TYR cc_start: 0.9087 (m-80) cc_final: 0.8796 (m-80) REVERT: E 125 ASP cc_start: 0.7895 (t0) cc_final: 0.7603 (m-30) REVERT: F 5 LYS cc_start: 0.7543 (pttm) cc_final: 0.7150 (ptpt) REVERT: F 40 TYR cc_start: 0.8091 (m-80) cc_final: 0.7872 (m-10) REVERT: F 125 ASP cc_start: 0.7770 (t0) cc_final: 0.7145 (m-30) REVERT: H 63 THR cc_start: 0.8918 (m) cc_final: 0.8585 (p) REVERT: K 5 LYS cc_start: 0.7611 (pttm) cc_final: 0.7140 (ptpt) REVERT: L 79 TYR cc_start: 0.9191 (m-80) cc_final: 0.8909 (m-80) REVERT: M 125 ASP cc_start: 0.7805 (t0) cc_final: 0.7577 (m-30) REVERT: N 63 THR cc_start: 0.9030 (m) cc_final: 0.8810 (p) REVERT: O 5 LYS cc_start: 0.7401 (pttm) cc_final: 0.7046 (ptpt) REVERT: O 125 ASP cc_start: 0.7906 (t0) cc_final: 0.7342 (m-30) REVERT: P 79 TYR cc_start: 0.9115 (m-80) cc_final: 0.8765 (m-80) REVERT: Q 63 THR cc_start: 0.9032 (m) cc_final: 0.8569 (p) REVERT: R 79 TYR cc_start: 0.9084 (m-80) cc_final: 0.8794 (m-80) REVERT: S 5 LYS cc_start: 0.7483 (pttm) cc_final: 0.7094 (ptpt) REVERT: S 40 TYR cc_start: 0.8080 (m-80) cc_final: 0.7849 (m-10) REVERT: S 125 ASP cc_start: 0.7734 (t0) cc_final: 0.7136 (m-30) REVERT: W 5 LYS cc_start: 0.7586 (pttm) cc_final: 0.7128 (ptpt) REVERT: W 79 TYR cc_start: 0.8968 (m-80) cc_final: 0.8759 (m-80) REVERT: W 120 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8611 (m) REVERT: X 79 TYR cc_start: 0.9187 (m-80) cc_final: 0.8914 (m-80) outliers start: 129 outliers final: 116 residues processed: 502 average time/residue: 0.1181 time to fit residues: 103.1527 Evaluate side-chains 533 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 416 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 CYS Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 3 CYS Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 3 CYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 3 CYS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 3 CYS Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain J residue 3 CYS Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 3 CYS Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain M residue 3 CYS Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 3 CYS Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain O residue 3 CYS Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 3 CYS Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain R residue 3 CYS Chi-restraints excluded: chain R residue 4 ASN Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain S residue 3 CYS Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain T residue 122 SER Chi-restraints excluded: chain U residue 3 CYS Chi-restraints excluded: chain U residue 4 ASN Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 97 MET Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain V residue 3 CYS Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 97 MET Chi-restraints excluded: chain V residue 122 SER Chi-restraints excluded: chain W residue 3 CYS Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 120 VAL Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 97 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 141 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 chunk 199 optimal weight: 0.1980 chunk 77 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 259 optimal weight: 0.0060 chunk 86 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN ** U 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 4 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.145171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134567 restraints weight = 29673.590| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.71 r_work: 0.3576 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23658 Z= 0.114 Angle : 0.504 7.906 32304 Z= 0.267 Chirality : 0.046 0.176 3912 Planarity : 0.004 0.037 4272 Dihedral : 3.809 17.017 3192 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.72 % Allowed : 22.21 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.23 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -1.87 (0.13), residues: 1512 loop : 0.71 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 70 TYR 0.020 0.001 TYR I 40 PHE 0.004 0.000 PHE S 16 TRP 0.005 0.001 TRP J 45 HIS 0.001 0.000 HIS K 30 Details of bonding type rmsd covalent geometry : bond 0.00258 (23640) covalent geometry : angle 0.50388 (32304) hydrogen bonds : bond 0.01903 ( 504) hydrogen bonds : angle 5.23191 ( 1008) Misc. bond : bond 0.00489 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 439 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 5 LYS cc_start: 0.7311 (pttm) cc_final: 0.6925 (ptpt) REVERT: I 125 ASP cc_start: 0.7880 (t0) cc_final: 0.7336 (m-30) REVERT: D 63 THR cc_start: 0.8950 (m) cc_final: 0.8510 (p) REVERT: E 125 ASP cc_start: 0.7907 (t0) cc_final: 0.7626 (m-30) REVERT: F 5 LYS cc_start: 0.7396 (pttm) cc_final: 0.7055 (ptpt) REVERT: F 125 ASP cc_start: 0.7809 (t0) cc_final: 0.7163 (m-30) REVERT: K 5 LYS cc_start: 0.7411 (pttm) cc_final: 0.7004 (ptpt) REVERT: L 79 TYR cc_start: 0.9124 (m-80) cc_final: 0.8785 (m-80) REVERT: M 125 ASP cc_start: 0.7763 (t0) cc_final: 0.7543 (m-30) REVERT: O 5 LYS cc_start: 0.7270 (pttm) cc_final: 0.7044 (ptpt) REVERT: O 125 ASP cc_start: 0.7834 (t0) cc_final: 0.7297 (m-30) REVERT: Q 63 THR cc_start: 0.8959 (m) cc_final: 0.8502 (p) REVERT: S 5 LYS cc_start: 0.7372 (pttm) cc_final: 0.7013 (ptpt) REVERT: S 96 VAL cc_start: 0.8669 (t) cc_final: 0.8466 (t) REVERT: S 125 ASP cc_start: 0.7792 (t0) cc_final: 0.7169 (m-30) REVERT: W 5 LYS cc_start: 0.7419 (pttm) cc_final: 0.6936 (ptpt) REVERT: W 79 TYR cc_start: 0.8947 (m-80) cc_final: 0.8709 (m-80) REVERT: X 79 TYR cc_start: 0.9131 (m-80) cc_final: 0.8797 (m-80) outliers start: 127 outliers final: 114 residues processed: 503 average time/residue: 0.1177 time to fit residues: 102.5548 Evaluate side-chains 521 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 407 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 CYS Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 3 CYS Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 3 CYS Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 3 CYS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 3 CYS Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain J residue 3 CYS Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 3 CYS Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain M residue 3 CYS Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 3 CYS Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain O residue 3 CYS Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain Q residue 3 CYS Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain R residue 3 CYS Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain S residue 3 CYS Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain T residue 122 SER Chi-restraints excluded: chain U residue 3 CYS Chi-restraints excluded: chain U residue 4 ASN Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 97 MET Chi-restraints excluded: chain V residue 3 CYS Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 97 MET Chi-restraints excluded: chain V residue 122 SER Chi-restraints excluded: chain W residue 3 CYS Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 97 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 61 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 4 ASN G 4 ASN ** H 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 ASN L 4 ASN P 4 ASN T 4 ASN V 42 ASN X 4 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.140582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129817 restraints weight = 30353.570| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.74 r_work: 0.3512 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23658 Z= 0.170 Angle : 0.556 8.056 32304 Z= 0.290 Chirality : 0.047 0.178 3912 Planarity : 0.004 0.045 4272 Dihedral : 3.992 16.456 3192 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.21 % Allowed : 22.10 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.40 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -1.98 (0.13), residues: 1512 loop : 0.59 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 70 TYR 0.025 0.002 TYR I 40 PHE 0.006 0.001 PHE G 16 TRP 0.007 0.001 TRP P 45 HIS 0.002 0.001 HIS K 30 Details of bonding type rmsd covalent geometry : bond 0.00403 (23640) covalent geometry : angle 0.55623 (32304) hydrogen bonds : bond 0.01976 ( 504) hydrogen bonds : angle 5.30170 ( 1008) Misc. bond : bond 0.00471 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 428 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 5 LYS cc_start: 0.7391 (pttm) cc_final: 0.7003 (ptpt) REVERT: I 125 ASP cc_start: 0.7971 (t0) cc_final: 0.7437 (m-30) REVERT: D 63 THR cc_start: 0.9040 (m) cc_final: 0.8542 (p) REVERT: E 63 THR cc_start: 0.9175 (m) cc_final: 0.8894 (p) REVERT: E 125 ASP cc_start: 0.7939 (t0) cc_final: 0.7593 (m-30) REVERT: F 5 LYS cc_start: 0.7487 (pttm) cc_final: 0.7126 (ptpt) REVERT: J 63 THR cc_start: 0.9153 (m) cc_final: 0.8940 (p) REVERT: K 5 LYS cc_start: 0.7586 (pttm) cc_final: 0.7117 (ptpt) REVERT: K 125 ASP cc_start: 0.7841 (t0) cc_final: 0.7245 (m-30) REVERT: L 79 TYR cc_start: 0.9214 (m-80) cc_final: 0.8877 (m-80) REVERT: M 79 TYR cc_start: 0.9021 (m-80) cc_final: 0.8757 (m-80) REVERT: M 125 ASP cc_start: 0.7895 (t0) cc_final: 0.7645 (m-30) REVERT: N 63 THR cc_start: 0.9055 (m) cc_final: 0.8834 (p) REVERT: O 5 LYS cc_start: 0.7429 (pttm) cc_final: 0.7048 (ptpt) REVERT: O 125 ASP cc_start: 0.7910 (t0) cc_final: 0.7394 (m-30) REVERT: Q 63 THR cc_start: 0.9060 (m) cc_final: 0.8565 (p) REVERT: S 5 LYS cc_start: 0.7471 (pttm) cc_final: 0.7086 (ptpt) REVERT: W 5 LYS cc_start: 0.7569 (pttm) cc_final: 0.7091 (ptpt) REVERT: W 79 TYR cc_start: 0.9028 (m-80) cc_final: 0.8828 (m-80) REVERT: W 125 ASP cc_start: 0.7804 (t0) cc_final: 0.7220 (m-30) REVERT: X 79 TYR cc_start: 0.9223 (m-80) cc_final: 0.8894 (m-80) outliers start: 140 outliers final: 131 residues processed: 496 average time/residue: 0.1284 time to fit residues: 110.5605 Evaluate side-chains 555 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 424 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 CYS Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 122 SER Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 3 CYS Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 3 CYS Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 3 CYS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain H residue 3 CYS Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain J residue 3 CYS Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 3 CYS Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 108 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 3 CYS Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 3 CYS Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain O residue 3 CYS Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain O residue 122 SER Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 3 CYS Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain R residue 3 CYS Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain S residue 3 CYS Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 117 MET Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain T residue 122 SER Chi-restraints excluded: chain U residue 3 CYS Chi-restraints excluded: chain U residue 4 ASN Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 97 MET Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain V residue 3 CYS Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 97 MET Chi-restraints excluded: chain V residue 122 SER Chi-restraints excluded: chain W residue 3 CYS Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 97 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 129 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 chunk 167 optimal weight: 0.9990 chunk 284 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 214 optimal weight: 0.9990 chunk 286 optimal weight: 3.9990 chunk 266 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 4 ASN ** H 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN T 4 ASN ** U 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 4 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.143585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.132808 restraints weight = 30037.915| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.74 r_work: 0.3557 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23658 Z= 0.128 Angle : 0.537 8.008 32304 Z= 0.283 Chirality : 0.046 0.174 3912 Planarity : 0.004 0.043 4272 Dihedral : 3.930 22.042 3192 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.80 % Allowed : 22.88 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -1.86 (0.13), residues: 1512 loop : 0.71 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 70 TYR 0.029 0.002 TYR I 40 PHE 0.004 0.001 PHE P 16 TRP 0.006 0.001 TRP P 45 HIS 0.001 0.000 HIS K 30 Details of bonding type rmsd covalent geometry : bond 0.00294 (23640) covalent geometry : angle 0.53656 (32304) hydrogen bonds : bond 0.01940 ( 504) hydrogen bonds : angle 5.24371 ( 1008) Misc. bond : bond 0.00471 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6000 Ramachandran restraints generated. 3000 Oldfield, 0 Emsley, 3000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 409 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 5 LYS cc_start: 0.7283 (pttm) cc_final: 0.6993 (ptpt) REVERT: I 125 ASP cc_start: 0.8024 (t0) cc_final: 0.7522 (m-30) REVERT: D 63 THR cc_start: 0.8975 (m) cc_final: 0.8524 (p) REVERT: E 125 ASP cc_start: 0.7901 (t0) cc_final: 0.7626 (m-30) REVERT: F 5 LYS cc_start: 0.7397 (pttm) cc_final: 0.7141 (ptpt) REVERT: F 125 ASP cc_start: 0.7806 (t0) cc_final: 0.7271 (m-30) REVERT: K 5 LYS cc_start: 0.7433 (pttm) cc_final: 0.7077 (ptpt) REVERT: K 125 ASP cc_start: 0.7684 (t0) cc_final: 0.7140 (m-30) REVERT: L 79 TYR cc_start: 0.9154 (m-80) cc_final: 0.8837 (m-80) REVERT: M 79 TYR cc_start: 0.8975 (m-80) cc_final: 0.8681 (m-80) REVERT: M 125 ASP cc_start: 0.7815 (t0) cc_final: 0.7615 (m-30) REVERT: O 5 LYS cc_start: 0.7339 (pttm) cc_final: 0.7050 (ptpt) REVERT: O 125 ASP cc_start: 0.7987 (t0) cc_final: 0.7498 (m-30) REVERT: Q 63 THR cc_start: 0.8998 (m) cc_final: 0.8535 (p) REVERT: S 5 LYS cc_start: 0.7396 (pttm) cc_final: 0.7114 (ptpt) REVERT: S 125 ASP cc_start: 0.7837 (t0) cc_final: 0.7308 (m-30) REVERT: W 5 LYS cc_start: 0.7423 (pttm) cc_final: 0.6996 (ptpt) REVERT: W 79 TYR cc_start: 0.8966 (m-80) cc_final: 0.8678 (m-80) REVERT: W 125 ASP cc_start: 0.7670 (t0) cc_final: 0.7130 (m-30) REVERT: X 79 TYR cc_start: 0.9154 (m-80) cc_final: 0.8844 (m-80) outliers start: 129 outliers final: 125 residues processed: 477 average time/residue: 0.1261 time to fit residues: 104.2187 Evaluate side-chains 528 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 403 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 3 CYS Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain A residue 3 CYS Chi-restraints excluded: chain A residue 4 ASN Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain B residue 3 CYS Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 3 CYS Chi-restraints excluded: chain D residue 4 ASN Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain E residue 3 CYS Chi-restraints excluded: chain E residue 4 ASN Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 97 MET Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain F residue 3 CYS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 3 CYS Chi-restraints excluded: chain H residue 4 ASN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain J residue 3 CYS Chi-restraints excluded: chain J residue 4 ASN Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain K residue 3 CYS Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 96 VAL Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain M residue 3 CYS Chi-restraints excluded: chain M residue 4 ASN Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 3 CYS Chi-restraints excluded: chain N residue 4 ASN Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 97 MET Chi-restraints excluded: chain N residue 122 SER Chi-restraints excluded: chain O residue 3 CYS Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 97 MET Chi-restraints excluded: chain Q residue 3 CYS Chi-restraints excluded: chain Q residue 4 ASN Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 122 SER Chi-restraints excluded: chain R residue 3 CYS Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 MET Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain S residue 3 CYS Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 93 ASP Chi-restraints excluded: chain S residue 97 MET Chi-restraints excluded: chain S residue 117 MET Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 97 MET Chi-restraints excluded: chain T residue 122 SER Chi-restraints excluded: chain U residue 3 CYS Chi-restraints excluded: chain U residue 4 ASN Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 97 MET Chi-restraints excluded: chain U residue 117 MET Chi-restraints excluded: chain V residue 3 CYS Chi-restraints excluded: chain V residue 4 ASN Chi-restraints excluded: chain V residue 28 ILE Chi-restraints excluded: chain V residue 93 ASP Chi-restraints excluded: chain V residue 97 MET Chi-restraints excluded: chain V residue 122 SER Chi-restraints excluded: chain W residue 3 CYS Chi-restraints excluded: chain W residue 93 ASP Chi-restraints excluded: chain W residue 96 VAL Chi-restraints excluded: chain W residue 108 GLU Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 97 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 241 optimal weight: 4.9990 chunk 270 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 chunk 178 optimal weight: 0.1980 chunk 4 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 276 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 4 ASN G 4 ASN ** H 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 4 ASN ** U 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.145525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134817 restraints weight = 29850.307| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.74 r_work: 0.3583 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23658 Z= 0.119 Angle : 0.519 7.877 32304 Z= 0.277 Chirality : 0.046 0.174 3912 Planarity : 0.004 0.043 4272 Dihedral : 3.810 18.371 3192 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.87 % Allowed : 23.21 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -1.05 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -1.75 (0.13), residues: 1512 loop : 0.82 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 70 TYR 0.024 0.001 TYR I 40 PHE 0.005 0.000 PHE K 16 TRP 0.006 0.001 TRP P 45 HIS 0.001 0.000 HIS K 30 Details of bonding type rmsd covalent geometry : bond 0.00268 (23640) covalent geometry : angle 0.51943 (32304) hydrogen bonds : bond 0.01916 ( 504) hydrogen bonds : angle 5.18402 ( 1008) Misc. bond : bond 0.00472 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4560.85 seconds wall clock time: 79 minutes 38.52 seconds (4778.52 seconds total)