Starting phenix.real_space_refine on Thu Jun 19 20:03:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fou_29354/06_2025/8fou_29354.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fou_29354/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fou_29354/06_2025/8fou_29354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fou_29354/06_2025/8fou_29354.map" model { file = "/net/cci-nas-00/data/ceres_data/8fou_29354/06_2025/8fou_29354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fou_29354/06_2025/8fou_29354.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23280 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, X Time building chain proxies: 6.97, per 1000 atoms: 0.30 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: 5.29 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 3.96 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: 7.27 Time building geometry restraints manager: 6.13 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: 0.21 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' 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: 37.700 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: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 44.710 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.300 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.002 0.000 TRP E 45 HIS 0.001 0.000 HIS Q 30 PHE 0.006 0.001 PHE Q 16 TYR 0.004 0.001 TYR F 40 ARG 0.003 0.000 ARG K 70 Details of bonding type rmsd hydrogen bonds : bond 0.21902 ( 504) hydrogen bonds : angle 11.51871 ( 1008) covalent geometry : bond 0.00307 (23640) covalent geometry : angle 0.60230 (32304) 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 : 2.541 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: 0.7236 (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: 0.7883 (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: 0.7368 (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: 0.7599 (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: 0.7363 (m-30) REVERT: Q 125 ASP cc_start: 0.7805 (t0) cc_final: 0.7460 (m-30) REVERT: R 5 LYS cc_start: 0.7567 (pttm) cc_final: 0.7121 (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: 0.7867 (p0) REVERT: W 101 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8263 (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: 0.3024 time to fit residues: 259.4812 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 : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.7980 chunk 218 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 137 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 261 optimal weight: 0.6980 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.137636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.127553 restraints weight = 31027.645| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.65 r_work: 0.3495 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23658 Z= 0.222 Angle : 0.603 6.681 32304 Z= 0.319 Chirality : 0.048 0.172 3912 Planarity : 0.005 0.041 4272 Dihedral : 4.341 12.243 3192 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.16 % Allowed : 15.25 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.81 (0.11), residues: 1608 loop : 0.14 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 45 HIS 0.002 0.001 HIS N 30 PHE 0.006 0.001 PHE D 16 TYR 0.011 0.002 TYR A 79 ARG 0.004 0.001 ARG H 70 Details of bonding type rmsd hydrogen bonds : bond 0.02744 ( 504) hydrogen bonds : angle 7.15665 ( 1008) covalent geometry : bond 0.00526 (23640) covalent geometry : angle 0.60335 (32304) Misc. bond : bond 0.01034 ( 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 556 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 498 time to evaluate : 2.663 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: 0.9071 (m) cc_final: 0.8792 (t) REVERT: I 125 ASP cc_start: 0.7886 (t0) cc_final: 0.7106 (m-30) REVERT: A 63 THR cc_start: 0.9064 (m) cc_final: 0.8684 (p) REVERT: A 125 ASP cc_start: 0.7934 (t0) cc_final: 0.7555 (m-30) REVERT: B 5 LYS cc_start: 0.7554 (pttm) cc_final: 0.7227 (ptpt) REVERT: B 125 ASP cc_start: 0.7856 (t0) cc_final: 0.7575 (m-30) REVERT: D 63 THR cc_start: 0.9164 (m) cc_final: 0.8756 (p) REVERT: D 125 ASP cc_start: 0.7765 (t0) cc_final: 0.7422 (m-30) REVERT: E 5 LYS cc_start: 0.7567 (pttm) cc_final: 0.6979 (ptpt) REVERT: E 125 ASP cc_start: 0.7942 (t0) cc_final: 0.7439 (m-30) REVERT: G 125 ASP cc_start: 0.7737 (t0) cc_final: 0.7463 (m-30) REVERT: H 63 THR cc_start: 0.9124 (m) cc_final: 0.8720 (p) REVERT: H 125 ASP cc_start: 0.7842 (t0) cc_final: 0.7432 (m-30) REVERT: J 5 LYS cc_start: 0.7531 (mtmm) cc_final: 0.7003 (mtpt) REVERT: J 79 TYR cc_start: 0.9288 (m-80) cc_final: 0.9070 (m-80) REVERT: J 125 ASP cc_start: 0.8011 (t0) cc_final: 0.7545 (m-30) REVERT: K 63 THR cc_start: 0.8999 (m) cc_final: 0.8795 (t) REVERT: K 93 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7995 (p0) REVERT: K 101 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8514 (mt-10) REVERT: L 79 TYR cc_start: 0.9271 (m-80) cc_final: 0.9028 (m-80) REVERT: L 125 ASP cc_start: 0.7652 (t0) cc_final: 0.7405 (m-30) REVERT: M 63 THR cc_start: 0.9066 (m) cc_final: 0.8685 (p) REVERT: M 125 ASP cc_start: 0.7945 (t0) cc_final: 0.7560 (m-30) REVERT: N 5 LYS cc_start: 0.7529 (pttm) cc_final: 0.7184 (ptpt) REVERT: N 125 ASP cc_start: 0.7880 (t0) cc_final: 0.7586 (m-30) REVERT: O 125 ASP cc_start: 0.7891 (t0) cc_final: 0.7135 (m-30) REVERT: P 27 PRO cc_start: 0.8658 (Cg_endo) cc_final: 0.8458 (Cg_exo) REVERT: Q 63 THR cc_start: 0.9166 (m) cc_final: 0.8760 (p) REVERT: Q 125 ASP cc_start: 0.7791 (t0) cc_final: 0.7492 (m-30) REVERT: R 5 LYS cc_start: 0.7593 (pttm) cc_final: 0.7014 (ptpt) REVERT: R 125 ASP cc_start: 0.7951 (t0) cc_final: 0.7432 (m-30) REVERT: T 125 ASP cc_start: 0.7721 (t0) cc_final: 0.7448 (m-30) REVERT: U 63 THR cc_start: 0.9118 (m) cc_final: 0.8705 (p) REVERT: U 125 ASP cc_start: 0.7848 (t0) cc_final: 0.7430 (m-30) REVERT: V 5 LYS cc_start: 0.7530 (mtmm) cc_final: 0.6992 (mtpt) REVERT: V 79 TYR cc_start: 0.9293 (m-80) cc_final: 0.9080 (m-80) REVERT: V 125 ASP cc_start: 0.7942 (t0) cc_final: 0.7519 (m-30) REVERT: W 63 THR cc_start: 0.9009 (m) cc_final: 0.8806 (t) REVERT: W 93 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.8016 (p0) REVERT: W 101 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8503 (mt-10) REVERT: X 79 TYR cc_start: 0.9269 (m-80) cc_final: 0.9009 (m-80) REVERT: X 125 ASP cc_start: 0.7633 (t0) cc_final: 0.7392 (m-30) outliers start: 58 outliers final: 54 residues processed: 517 average time/residue: 0.2707 time to fit residues: 238.7297 Evaluate side-chains 498 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 442 time to evaluate : 2.548 ------------------------------------------------------------------------------- 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 B residue 122 SER Chi-restraints excluded: chain C residue 28 ILE 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 J residue 122 SER Chi-restraints excluded: chain K residue 28 ILE 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 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 N residue 122 SER 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 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 V residue 122 SER Chi-restraints excluded: chain W residue 28 ILE Chi-restraints excluded: chain W residue 93 ASP 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 262 optimal weight: 7.9990 chunk 183 optimal weight: 0.5980 chunk 219 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 287 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 4 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN 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 4 ASN ** W 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.136673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.125485 restraints weight = 30465.915| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.79 r_work: 0.3455 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 23658 Z= 0.249 Angle : 0.611 7.435 32304 Z= 0.311 Chirality : 0.048 0.175 3912 Planarity : 0.005 0.046 4272 Dihedral : 4.557 13.758 3192 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.80 % Allowed : 17.75 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.15), residues: 3000 helix: None (None), residues: 0 sheet: -2.85 (0.11), residues: 1608 loop : 0.09 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 45 HIS 0.002 0.001 HIS B 30 PHE 0.008 0.001 PHE D 16 TYR 0.020 0.002 TYR O 40 ARG 0.003 0.000 ARG C 70 Details of bonding type rmsd hydrogen bonds : bond 0.02514 ( 504) hydrogen bonds : angle 6.39173 ( 1008) covalent geometry : bond 0.00604 (23640) covalent geometry : angle 0.61075 (32304) Misc. bond : bond 0.00717 ( 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 616 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 487 time to evaluate : 2.457 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: 0.9105 (m) cc_final: 0.8688 (p) REVERT: A 125 ASP cc_start: 0.8017 (t0) cc_final: 0.7658 (m-30) REVERT: B 5 LYS cc_start: 0.7477 (pttm) cc_final: 0.6982 (ptpt) REVERT: B 63 THR cc_start: 0.9222 (m) cc_final: 0.8894 (p) REVERT: B 125 ASP cc_start: 0.8017 (t0) cc_final: 0.7748 (m-30) REVERT: D 63 THR cc_start: 0.9212 (m) cc_final: 0.8712 (p) REVERT: D 125 ASP cc_start: 0.7981 (t0) cc_final: 0.7596 (m-30) REVERT: E 5 LYS cc_start: 0.7473 (pttm) cc_final: 0.6922 (ptpt) REVERT: E 125 ASP cc_start: 0.8002 (t0) cc_final: 0.7565 (m-30) REVERT: G 125 ASP cc_start: 0.7836 (t0) cc_final: 0.7483 (m-30) REVERT: H 63 THR cc_start: 0.9174 (m) cc_final: 0.8715 (p) REVERT: H 125 ASP cc_start: 0.7885 (t0) cc_final: 0.7605 (m-30) REVERT: J 63 THR cc_start: 0.9219 (m) cc_final: 0.8882 (p) REVERT: J 125 ASP cc_start: 0.8146 (t0) cc_final: 0.7673 (m-30) REVERT: L 79 TYR cc_start: 0.9311 (m-80) cc_final: 0.9053 (m-80) REVERT: L 125 ASP cc_start: 0.7868 (t0) cc_final: 0.7497 (m-30) REVERT: M 63 THR cc_start: 0.9114 (m) cc_final: 0.8697 (p) REVERT: M 125 ASP cc_start: 0.8034 (t0) cc_final: 0.7664 (m-30) REVERT: N 5 LYS cc_start: 0.7480 (pttm) cc_final: 0.6971 (ptpt) REVERT: N 63 THR cc_start: 0.9223 (m) cc_final: 0.8895 (p) REVERT: N 125 ASP cc_start: 0.8058 (t0) cc_final: 0.7767 (m-30) REVERT: Q 63 THR cc_start: 0.9188 (m) cc_final: 0.8696 (p) REVERT: Q 125 ASP cc_start: 0.7948 (t0) cc_final: 0.7598 (m-30) REVERT: R 5 LYS cc_start: 0.7458 (pttm) cc_final: 0.6910 (ptpt) REVERT: R 125 ASP cc_start: 0.8012 (t0) cc_final: 0.7570 (m-30) REVERT: T 125 ASP cc_start: 0.7815 (t0) cc_final: 0.7457 (m-30) REVERT: U 63 THR cc_start: 0.9169 (m) cc_final: 0.8705 (p) REVERT: U 125 ASP cc_start: 0.7897 (t0) cc_final: 0.7593 (m-30) REVERT: V 63 THR cc_start: 0.9216 (m) cc_final: 0.8881 (p) REVERT: V 125 ASP cc_start: 0.8106 (t0) cc_final: 0.7658 (m-30) REVERT: W 70 ARG cc_start: 0.8732 (ttt-90) cc_final: 0.8424 (ptm160) REVERT: X 79 TYR cc_start: 0.9311 (m-80) cc_final: 0.8996 (m-80) REVERT: X 125 ASP cc_start: 0.7820 (t0) cc_final: 0.7489 (m-30) outliers start: 129 outliers final: 87 residues processed: 556 average time/residue: 0.2824 time to fit residues: 271.5768 Evaluate side-chains 540 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 453 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 72 LEU 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 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 17 THR 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 H residue 120 VAL 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 97 MET Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain L residue 28 ILE 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 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 63 THR 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 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 72 LEU 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 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 17 THR Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 122 SER Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 120 VAL Chi-restraints excluded: chain U residue 122 SER 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 97 MET Chi-restraints excluded: chain W residue 122 SER Chi-restraints excluded: chain X residue 28 ILE 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 122 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 chunk 175 optimal weight: 0.5980 chunk 201 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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** C 4 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 4 ASN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.138606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.128138 restraints weight = 30604.050| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.69 r_work: 0.3493 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2337 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= 0.178 Angle : 0.549 7.494 32304 Z= 0.281 Chirality : 0.046 0.170 3912 Planarity : 0.005 0.041 4272 Dihedral : 4.392 18.810 3192 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.65 % Allowed : 18.49 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.53 (0.12), residues: 1512 loop : 0.11 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 45 HIS 0.001 0.000 HIS B 30 PHE 0.005 0.001 PHE O 16 TYR 0.039 0.002 TYR F 40 ARG 0.003 0.000 ARG H 70 Details of bonding type rmsd hydrogen bonds : bond 0.02174 ( 504) hydrogen bonds : angle 5.89028 ( 1008) covalent geometry : bond 0.00433 (23640) covalent geometry : angle 0.54887 (32304) Misc. bond : bond 0.00489 ( 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 605 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 480 time to evaluate : 2.792 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: 0.9038 (m) cc_final: 0.8649 (p) REVERT: A 125 ASP cc_start: 0.7931 (t0) cc_final: 0.7683 (m-30) REVERT: B 5 LYS cc_start: 0.7372 (pttm) cc_final: 0.6917 (ptpt) REVERT: B 63 THR cc_start: 0.9208 (m) cc_final: 0.8929 (p) REVERT: D 63 THR cc_start: 0.9162 (m) cc_final: 0.8719 (p) REVERT: D 125 ASP cc_start: 0.7824 (t0) cc_final: 0.7597 (m-30) REVERT: E 5 LYS cc_start: 0.7343 (pttm) cc_final: 0.6872 (ptpt) REVERT: E 63 THR cc_start: 0.9234 (m) cc_final: 0.8937 (p) REVERT: E 79 TYR cc_start: 0.9170 (m-80) cc_final: 0.8938 (m-80) REVERT: E 125 ASP cc_start: 0.7886 (t0) cc_final: 0.7624 (m-30) REVERT: G 125 ASP cc_start: 0.7840 (t0) cc_final: 0.7577 (m-30) REVERT: H 63 THR cc_start: 0.9058 (m) cc_final: 0.8669 (p) REVERT: J 63 THR cc_start: 0.9162 (m) cc_final: 0.8909 (p) REVERT: J 125 ASP cc_start: 0.7965 (t0) cc_final: 0.7680 (m-30) REVERT: K 70 ARG cc_start: 0.8580 (ttt-90) cc_final: 0.8302 (ptm160) REVERT: L 79 TYR cc_start: 0.9226 (m-80) cc_final: 0.8944 (m-80) REVERT: M 63 THR cc_start: 0.9044 (m) cc_final: 0.8661 (p) REVERT: M 125 ASP cc_start: 0.7913 (t0) cc_final: 0.7674 (m-30) REVERT: N 5 LYS cc_start: 0.7379 (pttm) cc_final: 0.6923 (ptpt) REVERT: N 63 THR cc_start: 0.9194 (m) cc_final: 0.8919 (p) REVERT: Q 63 THR cc_start: 0.9152 (m) cc_final: 0.8713 (p) REVERT: R 5 LYS cc_start: 0.7325 (pttm) cc_final: 0.6872 (ptpt) REVERT: R 63 THR cc_start: 0.9221 (m) cc_final: 0.8933 (p) REVERT: R 79 TYR cc_start: 0.9150 (m-80) cc_final: 0.8890 (m-80) REVERT: R 125 ASP cc_start: 0.7885 (t0) cc_final: 0.7621 (m-30) REVERT: T 125 ASP cc_start: 0.7781 (t0) cc_final: 0.7535 (m-30) REVERT: U 63 THR cc_start: 0.9061 (m) cc_final: 0.8667 (p) REVERT: V 63 THR cc_start: 0.9168 (m) cc_final: 0.8919 (p) REVERT: V 125 ASP cc_start: 0.7970 (t0) cc_final: 0.7680 (m-30) REVERT: W 70 ARG cc_start: 0.8562 (ttt-90) cc_final: 0.8324 (ptm160) REVERT: X 79 TYR cc_start: 0.9230 (m-80) cc_final: 0.8942 (m-80) outliers start: 125 outliers final: 101 residues processed: 544 average time/residue: 0.2778 time to fit residues: 257.3951 Evaluate side-chains 542 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 441 time to evaluate : 2.792 ------------------------------------------------------------------------------- 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 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 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 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 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 120 VAL Chi-restraints excluded: chain G residue 17 THR 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 28 ILE Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 120 VAL 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 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 60 SER Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 122 SER 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 O residue 3 CYS Chi-restraints excluded: chain O residue 28 ILE Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain P residue 28 ILE 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 17 THR 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 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 120 VAL Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR 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 U residue 120 VAL Chi-restraints excluded: chain U residue 122 SER 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 60 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 120 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 272 optimal weight: 1.9990 chunk 282 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 168 optimal weight: 0.1980 chunk 124 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 203 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 6 GLN B 4 ASN C 4 ASN F 6 GLN J 4 ASN K 6 GLN L 4 ASN N 4 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 4 ASN S 6 GLN V 4 ASN W 6 GLN X 4 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.141675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.130945 restraints weight = 30075.202| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.75 r_work: 0.3528 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23658 Z= 0.132 Angle : 0.514 7.507 32304 Z= 0.268 Chirality : 0.046 0.166 3912 Planarity : 0.004 0.035 4272 Dihedral : 4.154 22.432 3192 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.87 % Allowed : 19.75 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.31 (0.13), residues: 1512 loop : 0.36 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 45 HIS 0.001 0.000 HIS B 30 PHE 0.004 0.001 PHE K 16 TYR 0.026 0.001 TYR F 40 ARG 0.007 0.000 ARG I 70 Details of bonding type rmsd hydrogen bonds : bond 0.01950 ( 504) hydrogen bonds : angle 5.57752 ( 1008) covalent geometry : bond 0.00315 (23640) covalent geometry : angle 0.51440 (32304) Misc. bond : bond 0.00482 ( 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 612 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 481 time to evaluate : 2.499 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: 0.9000 (m) cc_final: 0.8542 (p) REVERT: A 125 ASP cc_start: 0.7896 (t0) cc_final: 0.7542 (m-30) REVERT: B 5 LYS cc_start: 0.7325 (pttm) cc_final: 0.6791 (ptpt) REVERT: B 63 THR cc_start: 0.9124 (m) cc_final: 0.8783 (p) REVERT: D 63 THR cc_start: 0.9066 (m) cc_final: 0.8537 (p) REVERT: D 125 ASP cc_start: 0.7864 (t0) cc_final: 0.7497 (m-30) REVERT: E 5 LYS cc_start: 0.7376 (pttm) cc_final: 0.6880 (ptpt) REVERT: E 63 THR cc_start: 0.9207 (m) cc_final: 0.8857 (p) REVERT: E 125 ASP cc_start: 0.7946 (t0) cc_final: 0.7549 (m-30) REVERT: F 96 VAL cc_start: 0.8772 (t) cc_final: 0.8546 (t) REVERT: G 88 GLN cc_start: 0.8696 (tm-30) cc_final: 0.7951 (tm-30) REVERT: G 125 ASP cc_start: 0.7732 (t0) cc_final: 0.7371 (m-30) REVERT: H 63 THR cc_start: 0.8964 (m) cc_final: 0.8545 (p) REVERT: J 63 THR cc_start: 0.9171 (m) cc_final: 0.8854 (p) REVERT: J 125 ASP cc_start: 0.8006 (t0) cc_final: 0.7603 (m-30) REVERT: K 70 ARG cc_start: 0.8689 (ttt-90) cc_final: 0.8430 (ptm160) REVERT: K 96 VAL cc_start: 0.8828 (t) cc_final: 0.8567 (t) REVERT: K 101 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8463 (mt-10) REVERT: L 79 TYR cc_start: 0.9231 (m-80) cc_final: 0.8913 (m-80) REVERT: M 63 THR cc_start: 0.9011 (m) cc_final: 0.8562 (p) REVERT: M 125 ASP cc_start: 0.7907 (t0) cc_final: 0.7540 (m-30) REVERT: N 5 LYS cc_start: 0.7339 (pttm) cc_final: 0.6790 (ptpt) REVERT: N 63 THR cc_start: 0.9138 (m) cc_final: 0.8814 (p) REVERT: Q 63 THR cc_start: 0.9063 (m) cc_final: 0.8532 (p) REVERT: R 5 LYS cc_start: 0.7370 (pttm) cc_final: 0.6876 (ptpt) REVERT: R 63 THR cc_start: 0.9202 (m) cc_final: 0.8854 (p) REVERT: R 125 ASP cc_start: 0.7927 (t0) cc_final: 0.7530 (m-30) REVERT: S 96 VAL cc_start: 0.8765 (t) cc_final: 0.8541 (t) REVERT: T 125 ASP cc_start: 0.7723 (t0) cc_final: 0.7355 (m-30) REVERT: U 63 THR cc_start: 0.8962 (m) cc_final: 0.8539 (p) REVERT: V 63 THR cc_start: 0.9158 (m) cc_final: 0.8849 (p) REVERT: V 125 ASP cc_start: 0.7998 (t0) cc_final: 0.7602 (m-30) REVERT: W 70 ARG cc_start: 0.8685 (ttt-90) cc_final: 0.8425 (ptm160) REVERT: W 96 VAL cc_start: 0.8825 (t) cc_final: 0.8565 (t) REVERT: X 79 TYR cc_start: 0.9229 (m-80) cc_final: 0.8907 (m-80) outliers start: 131 outliers final: 109 residues processed: 547 average time/residue: 0.2620 time to fit residues: 244.4608 Evaluate side-chains 557 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 448 time to evaluate : 2.415 ------------------------------------------------------------------------------- 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 43 CYS 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 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 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 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 E residue 122 SER Chi-restraints excluded: chain F residue 3 CYS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 43 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 108 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 SER Chi-restraints excluded: chain G residue 17 THR 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 72 LEU Chi-restraints excluded: chain H residue 93 ASP 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 93 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain K residue 3 CYS 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 L residue 122 SER 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 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 43 CYS Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain P residue 28 ILE 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 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 28 ILE Chi-restraints excluded: chain S residue 43 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 108 GLU Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain S residue 122 SER Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR 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 72 LEU 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 W residue 3 CYS 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 Chi-restraints excluded: chain X residue 60 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 271 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 34 optimal weight: 0.0870 chunk 136 optimal weight: 6.9990 chunk 270 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 4 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN O 6 GLN ** Q 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 = 0.3765 r_free = 0.3765 target = 0.144405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.133990 restraints weight = 29718.848| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.69 r_work: 0.3564 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 23658 Z= 0.112 Angle : 0.498 7.361 32304 Z= 0.263 Chirality : 0.045 0.169 3912 Planarity : 0.004 0.043 4272 Dihedral : 3.961 19.157 3192 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 5.02 % Allowed : 21.76 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.12 (0.13), residues: 1512 loop : 0.50 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 45 HIS 0.001 0.000 HIS P 30 PHE 0.003 0.000 PHE S 16 TYR 0.018 0.001 TYR F 40 ARG 0.007 0.000 ARG S 70 Details of bonding type rmsd hydrogen bonds : bond 0.01849 ( 504) hydrogen bonds : angle 5.37392 ( 1008) covalent geometry : bond 0.00256 (23640) covalent geometry : angle 0.49755 (32304) Misc. bond : bond 0.00473 ( 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 613 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 478 time to evaluate : 2.731 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 96 VAL cc_start: 0.8802 (t) cc_final: 0.8559 (t) REVERT: I 125 ASP cc_start: 0.7806 (t0) cc_final: 0.7180 (m-30) REVERT: A 63 THR cc_start: 0.8903 (m) cc_final: 0.8536 (p) REVERT: A 125 ASP cc_start: 0.7762 (t0) cc_final: 0.7509 (m-30) REVERT: B 63 THR cc_start: 0.9103 (m) cc_final: 0.8803 (p) REVERT: D 63 THR cc_start: 0.8987 (m) cc_final: 0.8506 (p) REVERT: D 125 ASP cc_start: 0.7829 (t0) cc_final: 0.7551 (m-30) REVERT: E 63 THR cc_start: 0.9174 (m) cc_final: 0.8852 (p) REVERT: E 125 ASP cc_start: 0.7828 (t0) cc_final: 0.7584 (m-30) REVERT: F 96 VAL cc_start: 0.8730 (t) cc_final: 0.8516 (t) REVERT: J 63 THR cc_start: 0.9132 (m) cc_final: 0.8863 (p) REVERT: J 125 ASP cc_start: 0.7899 (t0) cc_final: 0.7606 (m-30) REVERT: K 96 VAL cc_start: 0.8794 (t) cc_final: 0.8542 (t) REVERT: L 79 TYR cc_start: 0.9178 (m-80) cc_final: 0.8888 (m-80) REVERT: M 63 THR cc_start: 0.8902 (m) cc_final: 0.8542 (p) REVERT: M 125 ASP cc_start: 0.7795 (t0) cc_final: 0.7508 (m-30) REVERT: N 63 THR cc_start: 0.9090 (m) cc_final: 0.8806 (p) REVERT: O 125 ASP cc_start: 0.7813 (t0) cc_final: 0.7214 (m-30) REVERT: Q 63 THR cc_start: 0.9006 (m) cc_final: 0.8526 (p) REVERT: R 63 THR cc_start: 0.9167 (m) cc_final: 0.8854 (p) REVERT: R 79 TYR cc_start: 0.9107 (m-80) cc_final: 0.8831 (m-80) REVERT: R 125 ASP cc_start: 0.7843 (t0) cc_final: 0.7578 (m-30) REVERT: S 96 VAL cc_start: 0.8713 (t) cc_final: 0.8501 (t) REVERT: V 63 THR cc_start: 0.9126 (m) cc_final: 0.8862 (p) REVERT: V 125 ASP cc_start: 0.7920 (t0) cc_final: 0.7620 (m-30) REVERT: W 96 VAL cc_start: 0.8794 (t) cc_final: 0.8544 (t) REVERT: X 79 TYR cc_start: 0.9179 (m-80) cc_final: 0.8887 (m-80) outliers start: 135 outliers final: 113 residues processed: 548 average time/residue: 0.2780 time to fit residues: 257.6607 Evaluate side-chains 550 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 437 time to evaluate : 2.629 ------------------------------------------------------------------------------- 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 43 CYS Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain I residue 97 MET 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 97 MET Chi-restraints excluded: chain C residue 28 ILE 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 43 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 108 GLU 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 72 LEU Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 120 VAL 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 K residue 3 CYS Chi-restraints excluded: chain K residue 108 GLU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 48 THR 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 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 97 MET 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 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 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 28 ILE Chi-restraints excluded: chain S residue 43 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 108 GLU 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 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 72 LEU Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 97 MET Chi-restraints excluded: chain U residue 120 VAL 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 97 MET 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 60 SER Chi-restraints excluded: chain X residue 97 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 250 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 167 optimal weight: 0.8980 chunk 136 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 4 ASN J 42 ASN ** M 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 4 ASN V 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.142109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.131533 restraints weight = 30243.645| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.72 r_work: 0.3535 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23658 Z= 0.140 Angle : 0.521 7.618 32304 Z= 0.273 Chirality : 0.046 0.168 3912 Planarity : 0.004 0.044 4272 Dihedral : 3.980 17.838 3192 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 5.51 % Allowed : 21.65 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.10 (0.13), residues: 1512 loop : 0.49 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 45 HIS 0.001 0.000 HIS W 30 PHE 0.004 0.001 PHE G 16 TYR 0.019 0.001 TYR S 40 ARG 0.005 0.000 ARG S 70 Details of bonding type rmsd hydrogen bonds : bond 0.01831 ( 504) hydrogen bonds : angle 5.30321 ( 1008) covalent geometry : bond 0.00328 (23640) covalent geometry : angle 0.52122 (32304) Misc. bond : bond 0.00466 ( 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 590 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 442 time to evaluate : 2.512 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: 0.8878 (m) cc_final: 0.8537 (p) REVERT: B 5 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7594 (ptpt) REVERT: B 63 THR cc_start: 0.9111 (m) cc_final: 0.8857 (p) REVERT: D 63 THR cc_start: 0.9004 (m) cc_final: 0.8529 (p) REVERT: D 125 ASP cc_start: 0.7879 (t0) cc_final: 0.7618 (m-30) REVERT: E 63 THR cc_start: 0.9146 (m) cc_final: 0.8862 (p) REVERT: E 125 ASP cc_start: 0.7836 (t0) cc_final: 0.7574 (m-30) REVERT: F 96 VAL cc_start: 0.8736 (t) cc_final: 0.8509 (t) REVERT: J 63 THR cc_start: 0.9145 (m) cc_final: 0.8899 (p) REVERT: J 125 ASP cc_start: 0.7896 (t0) cc_final: 0.7663 (m-30) REVERT: L 79 TYR cc_start: 0.9200 (m-80) cc_final: 0.8926 (m-80) REVERT: M 63 THR cc_start: 0.8882 (m) cc_final: 0.8541 (p) REVERT: M 125 ASP cc_start: 0.7803 (t0) cc_final: 0.7590 (m-30) REVERT: N 63 THR cc_start: 0.9127 (m) cc_final: 0.8871 (p) REVERT: Q 63 THR cc_start: 0.9033 (m) cc_final: 0.8562 (p) REVERT: R 63 THR cc_start: 0.9138 (m) cc_final: 0.8846 (p) REVERT: R 125 ASP cc_start: 0.7817 (t0) cc_final: 0.7554 (m-30) REVERT: S 96 VAL cc_start: 0.8717 (t) cc_final: 0.8497 (t) REVERT: V 63 THR cc_start: 0.9139 (m) cc_final: 0.8891 (p) REVERT: V 125 ASP cc_start: 0.7908 (t0) cc_final: 0.7673 (m-30) REVERT: X 79 TYR cc_start: 0.9196 (m-80) cc_final: 0.8928 (m-80) outliers start: 148 outliers final: 128 residues processed: 524 average time/residue: 0.2727 time to fit residues: 245.7978 Evaluate side-chains 559 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 430 time to evaluate : 2.565 ------------------------------------------------------------------------------- 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 43 CYS Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain I residue 97 MET 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 5 LYS 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 93 ASP 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 17 THR Chi-restraints excluded: chain F residue 43 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 108 GLU 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 72 LEU Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 120 VAL 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 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 97 MET Chi-restraints excluded: chain L residue 122 SER 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 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 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 43 CYS Chi-restraints excluded: chain O residue 60 SER 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 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 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 43 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 108 GLU 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 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 72 LEU Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 97 MET Chi-restraints excluded: chain U residue 120 VAL Chi-restraints excluded: chain U residue 122 SER 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 48 THR Chi-restraints excluded: chain W residue 97 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 124 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 273 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.140452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.129339 restraints weight = 30412.985| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.82 r_work: 0.3503 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23658 Z= 0.165 Angle : 0.550 7.903 32304 Z= 0.285 Chirality : 0.047 0.180 3912 Planarity : 0.004 0.039 4272 Dihedral : 4.106 23.378 3192 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 5.69 % Allowed : 22.17 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.17 (0.13), residues: 1512 loop : 0.45 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 45 HIS 0.001 0.000 HIS R 30 PHE 0.005 0.001 PHE C 16 TYR 0.022 0.002 TYR S 40 ARG 0.005 0.000 ARG S 70 Details of bonding type rmsd hydrogen bonds : bond 0.01872 ( 504) hydrogen bonds : angle 5.28666 ( 1008) covalent geometry : bond 0.00394 (23640) covalent geometry : angle 0.54953 (32304) Misc. bond : bond 0.00457 ( 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 596 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 443 time to evaluate : 2.503 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: 0.7470 (pttm) cc_final: 0.7015 (ptpt) REVERT: I 96 VAL cc_start: 0.8834 (t) cc_final: 0.8616 (t) REVERT: I 125 ASP cc_start: 0.8059 (t0) cc_final: 0.7342 (m-30) REVERT: A 63 THR cc_start: 0.8882 (m) cc_final: 0.8486 (p) REVERT: B 5 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7667 (ptpt) REVERT: B 63 THR cc_start: 0.9145 (m) cc_final: 0.8830 (p) REVERT: D 63 THR cc_start: 0.9018 (m) cc_final: 0.8482 (p) REVERT: D 125 ASP cc_start: 0.7975 (t0) cc_final: 0.7585 (m-30) REVERT: E 63 THR cc_start: 0.9218 (m) cc_final: 0.8860 (p) REVERT: E 79 TYR cc_start: 0.9192 (m-80) cc_final: 0.8914 (m-80) REVERT: E 125 ASP cc_start: 0.8021 (t0) cc_final: 0.7564 (m-30) REVERT: F 96 VAL cc_start: 0.8872 (t) cc_final: 0.8623 (t) REVERT: G 88 GLN cc_start: 0.8718 (tm-30) cc_final: 0.7893 (tm-30) REVERT: J 63 THR cc_start: 0.9194 (m) cc_final: 0.8881 (p) REVERT: J 125 ASP cc_start: 0.7989 (t0) cc_final: 0.7633 (m-30) REVERT: K 125 ASP cc_start: 0.7920 (t0) cc_final: 0.7196 (m-30) REVERT: L 79 TYR cc_start: 0.9265 (m-80) cc_final: 0.8963 (m-80) REVERT: M 63 THR cc_start: 0.8923 (m) cc_final: 0.8519 (p) REVERT: M 125 ASP cc_start: 0.7962 (t0) cc_final: 0.7590 (m-30) REVERT: N 63 THR cc_start: 0.9159 (m) cc_final: 0.8843 (p) REVERT: O 96 VAL cc_start: 0.8891 (t) cc_final: 0.8631 (t) REVERT: O 125 ASP cc_start: 0.7981 (t0) cc_final: 0.7280 (m-30) REVERT: Q 63 THR cc_start: 0.9055 (m) cc_final: 0.8521 (p) REVERT: R 63 THR cc_start: 0.9218 (m) cc_final: 0.8866 (p) REVERT: R 125 ASP cc_start: 0.7952 (t0) cc_final: 0.7514 (m-30) REVERT: S 96 VAL cc_start: 0.8866 (t) cc_final: 0.8645 (t) REVERT: S 125 ASP cc_start: 0.7845 (t0) cc_final: 0.7068 (m-30) REVERT: T 88 GLN cc_start: 0.8701 (tm-30) cc_final: 0.7891 (tm-30) REVERT: V 63 THR cc_start: 0.9198 (m) cc_final: 0.8889 (p) REVERT: V 125 ASP cc_start: 0.8063 (t0) cc_final: 0.7672 (m-30) REVERT: X 79 TYR cc_start: 0.9266 (m-80) cc_final: 0.8960 (m-80) outliers start: 153 outliers final: 139 residues processed: 522 average time/residue: 0.2681 time to fit residues: 240.9805 Evaluate side-chains 573 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 433 time to evaluate : 2.524 ------------------------------------------------------------------------------- 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 43 CYS Chi-restraints excluded: chain I residue 60 SER 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 5 LYS 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 93 ASP 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 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 43 CYS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 108 GLU 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 72 LEU Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 120 VAL 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 97 MET Chi-restraints excluded: chain K residue 108 GLU 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 120 VAL Chi-restraints excluded: chain L residue 122 SER 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 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 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 43 CYS Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 108 GLU 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 93 ASP 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 17 THR Chi-restraints excluded: chain S residue 43 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 108 GLU 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 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 72 LEU Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 97 MET Chi-restraints excluded: chain U residue 120 VAL Chi-restraints excluded: chain U residue 122 SER 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 97 MET 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 60 SER Chi-restraints excluded: chain X residue 97 MET Chi-restraints excluded: chain X residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 281 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 98 optimal weight: 0.0870 chunk 244 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 chunk 184 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 4 ASN G 4 ASN ** H 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN ** M 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3739 r_free = 0.3739 target = 0.142325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.131775 restraints weight = 30147.954| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.73 r_work: 0.3532 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23658 Z= 0.134 Angle : 0.532 8.041 32304 Z= 0.279 Chirality : 0.046 0.176 3912 Planarity : 0.004 0.038 4272 Dihedral : 4.025 20.798 3192 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.36 % Allowed : 22.92 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -2.07 (0.13), residues: 1512 loop : 0.57 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 45 HIS 0.001 0.000 HIS W 30 PHE 0.005 0.001 PHE W 16 TYR 0.020 0.001 TYR S 40 ARG 0.004 0.000 ARG S 70 Details of bonding type rmsd hydrogen bonds : bond 0.01855 ( 504) hydrogen bonds : angle 5.23971 ( 1008) covalent geometry : bond 0.00315 (23640) covalent geometry : angle 0.53236 (32304) Misc. bond : bond 0.00453 ( 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 571 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 427 time to evaluate : 2.734 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: 0.7397 (pttm) cc_final: 0.7007 (ptpt) REVERT: I 96 VAL cc_start: 0.8827 (t) cc_final: 0.8614 (t) REVERT: I 125 ASP cc_start: 0.7943 (t0) cc_final: 0.7328 (m-30) REVERT: A 63 THR cc_start: 0.8780 (m) cc_final: 0.8429 (p) REVERT: B 63 THR cc_start: 0.9180 (m) cc_final: 0.8884 (p) REVERT: D 63 THR cc_start: 0.8991 (m) cc_final: 0.8529 (p) REVERT: D 125 ASP cc_start: 0.7874 (t0) cc_final: 0.7673 (m-30) REVERT: E 63 THR cc_start: 0.9168 (m) cc_final: 0.8886 (p) REVERT: E 125 ASP cc_start: 0.7928 (t0) cc_final: 0.7620 (m-30) REVERT: F 125 ASP cc_start: 0.7830 (t0) cc_final: 0.7122 (m-30) REVERT: J 79 TYR cc_start: 0.9255 (m-80) cc_final: 0.9038 (m-80) REVERT: J 125 ASP cc_start: 0.7924 (t0) cc_final: 0.7675 (m-30) REVERT: K 5 LYS cc_start: 0.7549 (pttm) cc_final: 0.7089 (ptpt) REVERT: K 125 ASP cc_start: 0.7827 (t0) cc_final: 0.7234 (m-30) REVERT: L 79 TYR cc_start: 0.9204 (m-80) cc_final: 0.8852 (m-80) REVERT: M 63 THR cc_start: 0.8804 (m) cc_final: 0.8431 (p) REVERT: M 125 ASP cc_start: 0.7929 (t0) cc_final: 0.7662 (m-30) REVERT: N 63 THR cc_start: 0.9139 (m) cc_final: 0.8865 (p) REVERT: O 5 LYS cc_start: 0.7346 (pttm) cc_final: 0.6970 (ptpt) REVERT: O 125 ASP cc_start: 0.7908 (t0) cc_final: 0.7289 (m-30) REVERT: Q 63 THR cc_start: 0.9006 (m) cc_final: 0.8549 (p) REVERT: R 63 THR cc_start: 0.9175 (m) cc_final: 0.8896 (p) REVERT: R 125 ASP cc_start: 0.7912 (t0) cc_final: 0.7588 (m-30) REVERT: S 125 ASP cc_start: 0.7712 (t0) cc_final: 0.7092 (m-30) REVERT: T 88 GLN cc_start: 0.8559 (tm-30) cc_final: 0.7849 (tm-30) REVERT: V 79 TYR cc_start: 0.9261 (m-80) cc_final: 0.9043 (m-80) REVERT: V 125 ASP cc_start: 0.7991 (t0) cc_final: 0.7717 (m-30) REVERT: W 5 LYS cc_start: 0.7527 (pttm) cc_final: 0.7066 (ptpt) REVERT: X 79 TYR cc_start: 0.9208 (m-80) cc_final: 0.8917 (m-80) outliers start: 144 outliers final: 135 residues processed: 511 average time/residue: 0.2748 time to fit residues: 241.6355 Evaluate side-chains 546 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 411 time to evaluate : 2.380 ------------------------------------------------------------------------------- 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 43 CYS Chi-restraints excluded: chain I residue 60 SER 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 97 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain C residue 28 ILE 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 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 43 CYS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 97 MET Chi-restraints excluded: chain F residue 108 GLU 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 72 LEU Chi-restraints excluded: chain H residue 93 ASP Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 120 VAL 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 60 SER Chi-restraints excluded: chain K residue 93 ASP 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 120 VAL Chi-restraints excluded: chain L residue 122 SER 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 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 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 43 CYS Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain O residue 108 GLU 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 93 ASP 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 43 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 108 GLU 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 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 72 LEU Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 97 MET Chi-restraints excluded: chain U residue 120 VAL Chi-restraints excluded: chain U residue 122 SER 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 X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 60 SER Chi-restraints excluded: chain X residue 97 MET Chi-restraints excluded: chain X residue 117 MET Chi-restraints excluded: chain X residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 54 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 190 optimal weight: 0.0570 chunk 259 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 260 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 235 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 ASN ** H 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.145177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.134349 restraints weight = 30014.834| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.79 r_work: 0.3565 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23658 Z= 0.117 Angle : 0.514 8.015 32304 Z= 0.275 Chirality : 0.046 0.178 3912 Planarity : 0.004 0.038 4272 Dihedral : 3.866 20.419 3192 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.91 % Allowed : 23.70 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -1.89 (0.13), residues: 1512 loop : 0.70 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP T 45 HIS 0.001 0.000 HIS K 30 PHE 0.005 0.000 PHE W 16 TYR 0.015 0.001 TYR S 40 ARG 0.004 0.000 ARG S 70 Details of bonding type rmsd hydrogen bonds : bond 0.01847 ( 504) hydrogen bonds : angle 5.16556 ( 1008) covalent geometry : bond 0.00264 (23640) covalent geometry : angle 0.51449 (32304) Misc. bond : bond 0.00452 ( 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 565 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 433 time to evaluate : 2.770 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: 0.7262 (pttm) cc_final: 0.6841 (ptpt) REVERT: I 96 VAL cc_start: 0.8874 (t) cc_final: 0.8653 (t) REVERT: I 125 ASP cc_start: 0.7995 (t0) cc_final: 0.7259 (m-30) REVERT: B 63 THR cc_start: 0.9064 (m) cc_final: 0.8744 (p) REVERT: C 79 TYR cc_start: 0.9061 (m-80) cc_final: 0.8715 (m-80) REVERT: D 63 THR cc_start: 0.8911 (m) cc_final: 0.8404 (p) REVERT: D 125 ASP cc_start: 0.7937 (t0) cc_final: 0.7626 (m-30) REVERT: E 63 THR cc_start: 0.9172 (m) cc_final: 0.8831 (p) REVERT: E 125 ASP cc_start: 0.7975 (t0) cc_final: 0.7561 (m-30) REVERT: F 5 LYS cc_start: 0.7487 (pttm) cc_final: 0.7001 (ptpt) REVERT: F 125 ASP cc_start: 0.7757 (t0) cc_final: 0.7001 (m-30) REVERT: J 79 TYR cc_start: 0.9249 (m-80) cc_final: 0.9036 (m-80) REVERT: J 125 ASP cc_start: 0.7929 (t0) cc_final: 0.7569 (m-30) REVERT: K 5 LYS cc_start: 0.7505 (pttm) cc_final: 0.6950 (ptpt) REVERT: K 125 ASP cc_start: 0.7761 (t0) cc_final: 0.7059 (m-30) REVERT: L 79 TYR cc_start: 0.9168 (m-80) cc_final: 0.8797 (m-80) REVERT: M 125 ASP cc_start: 0.7963 (t0) cc_final: 0.7600 (m-30) REVERT: N 63 THR cc_start: 0.9077 (m) cc_final: 0.8744 (p) REVERT: O 5 LYS cc_start: 0.7265 (pttm) cc_final: 0.6806 (ptpt) REVERT: O 125 ASP cc_start: 0.7862 (t0) cc_final: 0.7126 (m-30) REVERT: P 79 TYR cc_start: 0.9067 (m-80) cc_final: 0.8723 (m-80) REVERT: Q 63 THR cc_start: 0.8939 (m) cc_final: 0.8447 (p) REVERT: R 63 THR cc_start: 0.9188 (m) cc_final: 0.8851 (p) REVERT: R 125 ASP cc_start: 0.7959 (t0) cc_final: 0.7526 (m-30) REVERT: S 5 LYS cc_start: 0.7470 (pttm) cc_final: 0.7061 (ptpt) REVERT: S 125 ASP cc_start: 0.7728 (t0) cc_final: 0.7017 (m-30) REVERT: V 79 TYR cc_start: 0.9258 (m-80) cc_final: 0.9047 (m-80) REVERT: V 125 ASP cc_start: 0.7966 (t0) cc_final: 0.7594 (m-30) REVERT: W 5 LYS cc_start: 0.7526 (pttm) cc_final: 0.6970 (ptpt) REVERT: W 70 ARG cc_start: 0.8626 (ttt-90) cc_final: 0.8163 (ptm160) REVERT: X 79 TYR cc_start: 0.9163 (m-80) cc_final: 0.8779 (m-80) outliers start: 132 outliers final: 118 residues processed: 512 average time/residue: 0.2742 time to fit residues: 240.4307 Evaluate side-chains 529 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 411 time to evaluate : 2.427 ------------------------------------------------------------------------------- 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 43 CYS Chi-restraints excluded: chain I residue 60 SER 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 3 CYS 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 97 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 93 ASP 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 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 17 THR Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 108 GLU 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 72 LEU 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 28 ILE Chi-restraints excluded: chain K residue 60 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 122 SER Chi-restraints excluded: chain M residue 3 CYS 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 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 43 CYS Chi-restraints excluded: chain O residue 60 SER 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 97 MET Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain Q residue 3 CYS 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 43 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 122 SER Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 48 THR 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 72 LEU Chi-restraints excluded: chain U residue 93 ASP Chi-restraints excluded: chain U residue 97 MET Chi-restraints excluded: chain U residue 122 SER 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 60 SER Chi-restraints excluded: chain X residue 28 ILE Chi-restraints excluded: chain X residue 48 THR Chi-restraints excluded: chain X residue 60 SER Chi-restraints excluded: chain X residue 97 MET Chi-restraints excluded: chain X residue 117 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 143 optimal weight: 1.9990 chunk 238 optimal weight: 0.0000 chunk 8 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 161 optimal weight: 9.9990 chunk 93 optimal weight: 0.0170 chunk 126 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 141 optimal weight: 0.7980 overall best weight: 0.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 4 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.146998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.136117 restraints weight = 29851.021| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.79 r_work: 0.3588 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3163 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= 0.113 Angle : 0.516 8.028 32304 Z= 0.277 Chirality : 0.046 0.175 3912 Planarity : 0.004 0.038 4272 Dihedral : 3.792 19.289 3192 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.43 % Allowed : 24.55 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.16), residues: 3000 helix: None (None), residues: 0 sheet: -1.75 (0.13), residues: 1512 loop : 0.79 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 45 HIS 0.001 0.000 HIS K 30 PHE 0.005 0.000 PHE K 16 TYR 0.013 0.001 TYR Q 40 ARG 0.003 0.000 ARG N 70 Details of bonding type rmsd hydrogen bonds : bond 0.01855 ( 504) hydrogen bonds : angle 5.15296 ( 1008) covalent geometry : bond 0.00251 (23640) covalent geometry : angle 0.51581 (32304) Misc. bond : bond 0.00450 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11390.58 seconds wall clock time: 199 minutes 47.74 seconds (11987.74 seconds total)