Starting phenix.real_space_refine on Tue Nov 19 03:32:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fj5_29215/11_2024/8fj5_29215.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fj5_29215/11_2024/8fj5_29215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fj5_29215/11_2024/8fj5_29215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fj5_29215/11_2024/8fj5_29215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fj5_29215/11_2024/8fj5_29215.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fj5_29215/11_2024/8fj5_29215.cif" } resolution = 2.9 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.077 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 20 5.16 5 C 11740 2.51 5 N 2980 2.21 5 O 4240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18980 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, T Time building chain proxies: 5.15, per 1000 atoms: 0.27 Number of scatterers: 18980 At special positions: 0 Unit cell: (97.44, 98.56, 202.72, 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 20 16.00 O 4240 8.00 N 2980 7.00 C 11740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.87 Conformation dependent library (CDL) restraints added in 2.6 seconds 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4720 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 60 sheets defined 26.4% alpha, 45.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.38 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 removed outlier: 3.610A pdb=" N ILE A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP A 96 " --> pdb=" O TRP A 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.747A pdb=" N ASP B 96 " --> pdb=" O TRP B 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 removed outlier: 3.747A pdb=" N ASP C 96 " --> pdb=" O TRP C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 96 removed outlier: 3.747A pdb=" N ASP D 96 " --> pdb=" O TRP D 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 96 removed outlier: 3.747A pdb=" N ASP E 96 " --> pdb=" O TRP E 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP F 96 " --> pdb=" O TRP F 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP G 96 " --> pdb=" O TRP G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP H 96 " --> pdb=" O TRP H 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE I 28 " --> pdb=" O ALA I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP I 96 " --> pdb=" O TRP I 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE J 28 " --> pdb=" O ALA J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP J 96 " --> pdb=" O TRP J 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE K 28 " --> pdb=" O ALA K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 96 removed outlier: 3.747A pdb=" N ASP K 96 " --> pdb=" O TRP K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE L 28 " --> pdb=" O ALA L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP L 96 " --> pdb=" O TRP L 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE M 28 " --> pdb=" O ALA M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 96 removed outlier: 3.747A pdb=" N ASP M 96 " --> pdb=" O TRP M 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE N 28 " --> pdb=" O ALA N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP N 96 " --> pdb=" O TRP N 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP O 96 " --> pdb=" O TRP O 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP P 96 " --> pdb=" O TRP P 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE Q 28 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP Q 96 " --> pdb=" O TRP Q 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP R 96 " --> pdb=" O TRP R 92 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE S 28 " --> pdb=" O ALA S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP S 96 " --> pdb=" O TRP S 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE T 28 " --> pdb=" O ALA T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP T 96 " --> pdb=" O TRP T 92 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 58 removed outlier: 6.759A pdb=" N SER A 52 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 63 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 58 removed outlier: 6.759A pdb=" N SER A 52 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 63 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR A 65 " --> pdb=" O TRP I 141 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP I 141 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR A 67 " --> pdb=" O GLN I 139 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN I 139 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU A 69 " --> pdb=" O THR I 137 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR I 137 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL I 125 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER I 140 " --> pdb=" O VAL I 123 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL I 123 " --> pdb=" O SER I 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL A 123 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER A 140 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 125 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 137 " --> pdb=" O GLU N 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU N 69 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN A 139 " --> pdb=" O THR N 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR N 67 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP A 141 " --> pdb=" O THR N 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR N 65 " --> pdb=" O TRP A 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN N 63 " --> pdb=" O THR N 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER N 52 " --> pdb=" O GLU N 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL A 123 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER A 140 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 125 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 137 " --> pdb=" O GLU N 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU N 69 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN A 139 " --> pdb=" O THR N 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR N 67 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP A 141 " --> pdb=" O THR N 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR N 65 " --> pdb=" O TRP A 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 58 removed outlier: 6.759A pdb=" N SER B 52 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 63 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 75 Processing sheet with id=AA8, first strand: chain 'B' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL B 123 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER B 140 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 125 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 137 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU E 69 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN B 139 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR E 67 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP B 141 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR E 65 " --> pdb=" O TRP B 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN E 63 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER E 52 " --> pdb=" O GLU E 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL B 123 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER B 140 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 125 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 137 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU E 69 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN B 139 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR E 67 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP B 141 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR E 65 " --> pdb=" O TRP B 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 51 through 58 removed outlier: 6.758A pdb=" N SER C 52 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 63 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 74 through 75 Processing sheet with id=AB3, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.461A pdb=" N VAL C 123 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER C 140 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 125 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 137 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU F 69 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN C 139 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR F 67 " --> pdb=" O GLN C 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP C 141 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR F 65 " --> pdb=" O TRP C 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN F 63 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER F 52 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.461A pdb=" N VAL C 123 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER C 140 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 125 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 137 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU F 69 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN C 139 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR F 67 " --> pdb=" O GLN C 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP C 141 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR F 65 " --> pdb=" O TRP C 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 51 through 58 removed outlier: 6.760A pdb=" N SER D 52 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN D 63 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 74 through 75 Processing sheet with id=AB7, first strand: chain 'D' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL D 123 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER D 140 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL D 125 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR D 137 " --> pdb=" O GLU G 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU G 69 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN D 139 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR G 67 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP D 141 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR G 65 " --> pdb=" O TRP D 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN G 63 " --> pdb=" O THR G 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER G 52 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL D 123 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER D 140 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL D 125 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR D 137 " --> pdb=" O GLU G 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU G 69 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN D 139 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR G 67 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP D 141 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR G 65 " --> pdb=" O TRP D 141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 74 through 75 Processing sheet with id=AC1, first strand: chain 'E' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL E 123 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER E 140 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL E 125 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR E 137 " --> pdb=" O GLU H 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU H 69 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN E 139 " --> pdb=" O THR H 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR H 67 " --> pdb=" O GLN E 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP E 141 " --> pdb=" O THR H 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR H 65 " --> pdb=" O TRP E 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN H 63 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER H 52 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL E 123 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER E 140 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL E 125 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR E 137 " --> pdb=" O GLU H 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU H 69 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN E 139 " --> pdb=" O THR H 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR H 67 " --> pdb=" O GLN E 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP E 141 " --> pdb=" O THR H 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR H 65 " --> pdb=" O TRP E 141 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 74 through 75 Processing sheet with id=AC4, first strand: chain 'F' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL F 123 " --> pdb=" O SER F 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER F 140 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL F 125 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR F 137 " --> pdb=" O GLU I 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU I 69 " --> pdb=" O THR F 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN F 139 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR I 67 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP F 141 " --> pdb=" O THR I 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR I 65 " --> pdb=" O TRP F 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN I 63 " --> pdb=" O THR I 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER I 52 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL F 123 " --> pdb=" O SER F 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER F 140 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL F 125 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR F 137 " --> pdb=" O GLU I 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU I 69 " --> pdb=" O THR F 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN F 139 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR I 67 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP F 141 " --> pdb=" O THR I 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR I 65 " --> pdb=" O TRP F 141 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 74 through 75 Processing sheet with id=AC7, first strand: chain 'G' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL G 123 " --> pdb=" O SER G 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER G 140 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL G 125 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR G 137 " --> pdb=" O GLU J 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU J 69 " --> pdb=" O THR G 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN G 139 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR J 67 " --> pdb=" O GLN G 139 " (cutoff:3.500A) removed outlier: 15.522A pdb=" N TRP G 141 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR J 65 " --> pdb=" O TRP G 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN J 63 " --> pdb=" O THR J 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER J 52 " --> pdb=" O GLU J 69 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL G 123 " --> pdb=" O SER G 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER G 140 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL G 125 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR G 137 " --> pdb=" O GLU J 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU J 69 " --> pdb=" O THR G 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN G 139 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR J 67 " --> pdb=" O GLN G 139 " (cutoff:3.500A) removed outlier: 15.522A pdb=" N TRP G 141 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR J 65 " --> pdb=" O TRP G 141 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 74 through 75 Processing sheet with id=AD1, first strand: chain 'H' and resid 79 through 82 removed outlier: 6.461A pdb=" N VAL H 123 " --> pdb=" O SER H 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER H 140 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL H 125 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR H 137 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU K 69 " --> pdb=" O THR H 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN H 139 " --> pdb=" O THR K 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR K 67 " --> pdb=" O GLN H 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP H 141 " --> pdb=" O THR K 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR K 65 " --> pdb=" O TRP H 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN K 63 " --> pdb=" O THR K 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER K 52 " --> pdb=" O GLU K 69 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 79 through 82 removed outlier: 6.461A pdb=" N VAL H 123 " --> pdb=" O SER H 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER H 140 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL H 125 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR H 137 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU K 69 " --> pdb=" O THR H 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN H 139 " --> pdb=" O THR K 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR K 67 " --> pdb=" O GLN H 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP H 141 " --> pdb=" O THR K 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR K 65 " --> pdb=" O TRP H 141 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 74 through 75 Processing sheet with id=AD4, first strand: chain 'J' and resid 74 through 75 Processing sheet with id=AD5, first strand: chain 'J' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL J 123 " --> pdb=" O SER J 140 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER J 140 " --> pdb=" O VAL J 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL J 125 " --> pdb=" O LEU J 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR J 137 " --> pdb=" O GLU L 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU L 69 " --> pdb=" O THR J 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN J 139 " --> pdb=" O THR L 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR L 67 " --> pdb=" O GLN J 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP J 141 " --> pdb=" O THR L 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR L 65 " --> pdb=" O TRP J 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN L 63 " --> pdb=" O THR L 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER L 52 " --> pdb=" O GLU L 69 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL J 123 " --> pdb=" O SER J 140 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER J 140 " --> pdb=" O VAL J 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL J 125 " --> pdb=" O LEU J 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR J 137 " --> pdb=" O GLU L 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU L 69 " --> pdb=" O THR J 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN J 139 " --> pdb=" O THR L 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR L 67 " --> pdb=" O GLN J 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP J 141 " --> pdb=" O THR L 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR L 65 " --> pdb=" O TRP J 141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 74 through 75 Processing sheet with id=AD8, first strand: chain 'K' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL K 123 " --> pdb=" O SER K 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER K 140 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL K 125 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR K 137 " --> pdb=" O GLU M 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU M 69 " --> pdb=" O THR K 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN K 139 " --> pdb=" O THR M 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR M 67 " --> pdb=" O GLN K 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP K 141 " --> pdb=" O THR M 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR M 65 " --> pdb=" O TRP K 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN M 63 " --> pdb=" O THR M 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER M 52 " --> pdb=" O GLU M 69 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL K 123 " --> pdb=" O SER K 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER K 140 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL K 125 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR K 137 " --> pdb=" O GLU M 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU M 69 " --> pdb=" O THR K 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN K 139 " --> pdb=" O THR M 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR M 67 " --> pdb=" O GLN K 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP K 141 " --> pdb=" O THR M 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR M 65 " --> pdb=" O TRP K 141 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 74 through 75 Processing sheet with id=AE2, first strand: chain 'L' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL L 123 " --> pdb=" O SER L 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER L 140 " --> pdb=" O VAL L 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL L 125 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR L 137 " --> pdb=" O GLU O 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU O 69 " --> pdb=" O THR L 137 " (cutoff:3.500A) removed outlier: 13.550A pdb=" N GLN L 139 " --> pdb=" O THR O 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR O 67 " --> pdb=" O GLN L 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP L 141 " --> pdb=" O THR O 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR O 65 " --> pdb=" O TRP L 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN O 63 " --> pdb=" O THR O 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER O 52 " --> pdb=" O GLU O 69 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL L 123 " --> pdb=" O SER L 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER L 140 " --> pdb=" O VAL L 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL L 125 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR L 137 " --> pdb=" O GLU O 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU O 69 " --> pdb=" O THR L 137 " (cutoff:3.500A) removed outlier: 13.550A pdb=" N GLN L 139 " --> pdb=" O THR O 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR O 67 " --> pdb=" O GLN L 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP L 141 " --> pdb=" O THR O 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR O 65 " --> pdb=" O TRP L 141 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 74 through 75 Processing sheet with id=AE5, first strand: chain 'M' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL M 123 " --> pdb=" O SER M 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER M 140 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL M 125 " --> pdb=" O LEU M 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR M 137 " --> pdb=" O GLU P 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU P 69 " --> pdb=" O THR M 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN M 139 " --> pdb=" O THR P 67 " (cutoff:3.500A) removed outlier: 14.234A pdb=" N THR P 67 " --> pdb=" O GLN M 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP M 141 " --> pdb=" O THR P 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR P 65 " --> pdb=" O TRP M 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN P 63 " --> pdb=" O THR P 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER P 52 " --> pdb=" O GLU P 69 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL M 123 " --> pdb=" O SER M 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER M 140 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL M 125 " --> pdb=" O LEU M 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR M 137 " --> pdb=" O GLU P 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU P 69 " --> pdb=" O THR M 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN M 139 " --> pdb=" O THR P 67 " (cutoff:3.500A) removed outlier: 14.234A pdb=" N THR P 67 " --> pdb=" O GLN M 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP M 141 " --> pdb=" O THR P 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR P 65 " --> pdb=" O TRP M 141 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 74 through 75 Processing sheet with id=AE8, first strand: chain 'N' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL N 123 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER N 140 " --> pdb=" O VAL N 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL N 125 " --> pdb=" O LEU N 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR N 137 " --> pdb=" O GLU Q 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU Q 69 " --> pdb=" O THR N 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN N 139 " --> pdb=" O THR Q 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR Q 67 " --> pdb=" O GLN N 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP N 141 " --> pdb=" O THR Q 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR Q 65 " --> pdb=" O TRP N 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN Q 63 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER Q 52 " --> pdb=" O GLU Q 69 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL N 123 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER N 140 " --> pdb=" O VAL N 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL N 125 " --> pdb=" O LEU N 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR N 137 " --> pdb=" O GLU Q 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU Q 69 " --> pdb=" O THR N 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN N 139 " --> pdb=" O THR Q 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR Q 67 " --> pdb=" O GLN N 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP N 141 " --> pdb=" O THR Q 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR Q 65 " --> pdb=" O TRP N 141 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 74 through 75 Processing sheet with id=AF2, first strand: chain 'O' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL O 123 " --> pdb=" O SER O 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER O 140 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL O 125 " --> pdb=" O LEU O 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR O 137 " --> pdb=" O GLU R 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU R 69 " --> pdb=" O THR O 137 " (cutoff:3.500A) removed outlier: 13.550A pdb=" N GLN O 139 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR R 67 " --> pdb=" O GLN O 139 " (cutoff:3.500A) removed outlier: 15.520A pdb=" N TRP O 141 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR R 65 " --> pdb=" O TRP O 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN R 63 " --> pdb=" O THR R 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER R 52 " --> pdb=" O GLU R 69 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL O 123 " --> pdb=" O SER O 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER O 140 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL O 125 " --> pdb=" O LEU O 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR O 137 " --> pdb=" O GLU R 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU R 69 " --> pdb=" O THR O 137 " (cutoff:3.500A) removed outlier: 13.550A pdb=" N GLN O 139 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR R 67 " --> pdb=" O GLN O 139 " (cutoff:3.500A) removed outlier: 15.520A pdb=" N TRP O 141 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR R 65 " --> pdb=" O TRP O 141 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 74 through 75 Processing sheet with id=AF5, first strand: chain 'P' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL P 123 " --> pdb=" O SER P 140 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER P 140 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL P 125 " --> pdb=" O LEU P 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR P 137 " --> pdb=" O GLU S 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU S 69 " --> pdb=" O THR P 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN P 139 " --> pdb=" O THR S 67 " (cutoff:3.500A) removed outlier: 14.234A pdb=" N THR S 67 " --> pdb=" O GLN P 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP P 141 " --> pdb=" O THR S 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR S 65 " --> pdb=" O TRP P 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN S 63 " --> pdb=" O THR S 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER S 52 " --> pdb=" O GLU S 69 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL P 123 " --> pdb=" O SER P 140 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER P 140 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL P 125 " --> pdb=" O LEU P 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR P 137 " --> pdb=" O GLU S 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU S 69 " --> pdb=" O THR P 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN P 139 " --> pdb=" O THR S 67 " (cutoff:3.500A) removed outlier: 14.234A pdb=" N THR S 67 " --> pdb=" O GLN P 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP P 141 " --> pdb=" O THR S 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR S 65 " --> pdb=" O TRP P 141 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 74 through 75 Processing sheet with id=AF8, first strand: chain 'Q' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL Q 123 " --> pdb=" O SER Q 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER Q 140 " --> pdb=" O VAL Q 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL Q 125 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR Q 137 " --> pdb=" O GLU T 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU T 69 " --> pdb=" O THR Q 137 " (cutoff:3.500A) removed outlier: 13.548A pdb=" N GLN Q 139 " --> pdb=" O THR T 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR T 67 " --> pdb=" O GLN Q 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP Q 141 " --> pdb=" O THR T 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR T 65 " --> pdb=" O TRP Q 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN T 63 " --> pdb=" O THR T 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER T 52 " --> pdb=" O GLU T 69 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL Q 123 " --> pdb=" O SER Q 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER Q 140 " --> pdb=" O VAL Q 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL Q 125 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR Q 137 " --> pdb=" O GLU T 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU T 69 " --> pdb=" O THR Q 137 " (cutoff:3.500A) removed outlier: 13.548A pdb=" N GLN Q 139 " --> pdb=" O THR T 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR T 67 " --> pdb=" O GLN Q 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP Q 141 " --> pdb=" O THR T 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR T 65 " --> pdb=" O TRP Q 141 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'R' and resid 74 through 75 Processing sheet with id=AG2, first strand: chain 'R' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL R 123 " --> pdb=" O SER R 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER R 140 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL R 125 " --> pdb=" O LEU R 138 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 74 through 75 Processing sheet with id=AG4, first strand: chain 'S' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL S 123 " --> pdb=" O SER S 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER S 140 " --> pdb=" O VAL S 123 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL S 125 " --> pdb=" O LEU S 138 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 74 through 75 Processing sheet with id=AG6, first strand: chain 'T' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL T 123 " --> pdb=" O SER T 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER T 140 " --> pdb=" O VAL T 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL T 125 " --> pdb=" O LEU T 138 " (cutoff:3.500A) 1065 hydrogen bonds defined for protein. 3135 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: 6.81 Time building geometry restraints manager: 5.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6260 1.34 - 1.46: 3763 1.46 - 1.57: 9217 1.57 - 1.69: 0 1.69 - 1.80: 40 Bond restraints: 19280 Sorted by residual: bond pdb=" CG1 ILE K 33 " pdb=" CD1 ILE K 33 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.28e+00 bond pdb=" CG1 ILE M 33 " pdb=" CD1 ILE M 33 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.27e+00 bond pdb=" CG1 ILE H 33 " pdb=" CD1 ILE H 33 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.26e+00 bond pdb=" CG1 ILE E 33 " pdb=" CD1 ILE E 33 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.25e+00 bond pdb=" CG1 ILE P 33 " pdb=" CD1 ILE P 33 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.25e+00 ... (remaining 19275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 24609 1.08 - 2.15: 1492 2.15 - 3.23: 219 3.23 - 4.31: 59 4.31 - 5.38: 41 Bond angle restraints: 26420 Sorted by residual: angle pdb=" N GLU M 46 " pdb=" CA GLU M 46 " pdb=" C GLU M 46 " ideal model delta sigma weight residual 110.91 114.58 -3.67 1.17e+00 7.31e-01 9.85e+00 angle pdb=" N GLU R 46 " pdb=" CA GLU R 46 " pdb=" C GLU R 46 " ideal model delta sigma weight residual 110.91 114.57 -3.66 1.17e+00 7.31e-01 9.78e+00 angle pdb=" N GLU I 46 " pdb=" CA GLU I 46 " pdb=" C GLU I 46 " ideal model delta sigma weight residual 110.91 114.56 -3.65 1.17e+00 7.31e-01 9.74e+00 angle pdb=" N GLU Q 46 " pdb=" CA GLU Q 46 " pdb=" C GLU Q 46 " ideal model delta sigma weight residual 110.91 114.56 -3.65 1.17e+00 7.31e-01 9.72e+00 angle pdb=" N GLU H 46 " pdb=" CA GLU H 46 " pdb=" C GLU H 46 " ideal model delta sigma weight residual 110.91 114.56 -3.65 1.17e+00 7.31e-01 9.71e+00 ... (remaining 26415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.68: 9840 12.68 - 25.37: 780 25.37 - 38.05: 280 38.05 - 50.73: 100 50.73 - 63.42: 20 Dihedral angle restraints: 11020 sinusoidal: 3620 harmonic: 7400 Sorted by residual: dihedral pdb=" CA GLY G 97 " pdb=" C GLY G 97 " pdb=" N SER G 98 " pdb=" CA SER G 98 " ideal model delta harmonic sigma weight residual -180.00 -162.61 -17.39 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA GLY F 97 " pdb=" C GLY F 97 " pdb=" N SER F 98 " pdb=" CA SER F 98 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA GLY D 97 " pdb=" C GLY D 97 " pdb=" N SER D 98 " pdb=" CA SER D 98 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 11017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1739 0.028 - 0.056: 1006 0.056 - 0.084: 349 0.084 - 0.112: 126 0.112 - 0.140: 100 Chirality restraints: 3320 Sorted by residual: chirality pdb=" CA SER C 14 " pdb=" N SER C 14 " pdb=" C SER C 14 " pdb=" CB SER C 14 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA SER E 14 " pdb=" N SER E 14 " pdb=" C SER E 14 " pdb=" CB SER E 14 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA SER I 14 " pdb=" N SER I 14 " pdb=" C SER I 14 " pdb=" CB SER I 14 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 3317 not shown) Planarity restraints: 3360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 33 " 0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C ILE C 33 " -0.023 2.00e-02 2.50e+03 pdb=" O ILE C 33 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY C 34 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 33 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C ILE R 33 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE R 33 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY R 34 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE O 33 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.73e+00 pdb=" C ILE O 33 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE O 33 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY O 34 " -0.008 2.00e-02 2.50e+03 ... (remaining 3357 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 7417 2.89 - 3.39: 16953 3.39 - 3.90: 30518 3.90 - 4.40: 35604 4.40 - 4.90: 60971 Nonbonded interactions: 151463 Sorted by model distance: nonbonded pdb=" O VAL R 44 " pdb=" OG SER R 45 " model vdw 2.391 3.040 nonbonded pdb=" O VAL F 44 " pdb=" OG SER F 45 " model vdw 2.392 3.040 nonbonded pdb=" O VAL S 44 " pdb=" OG SER S 45 " model vdw 2.392 3.040 nonbonded pdb=" O VAL I 44 " pdb=" OG SER I 45 " model vdw 2.392 3.040 nonbonded pdb=" O VAL H 44 " pdb=" OG SER H 45 " model vdw 2.392 3.040 ... (remaining 151458 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 2.120 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: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 38.780 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19280 Z= 0.280 Angle : 0.621 5.383 26420 Z= 0.369 Chirality : 0.044 0.140 3320 Planarity : 0.003 0.027 3360 Dihedral : 11.786 63.417 6300 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.51 (0.16), residues: 2620 helix: 3.65 (0.15), residues: 600 sheet: 1.16 (0.17), residues: 1000 loop : -0.86 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 92 HIS 0.001 0.000 HIS T 68 PHE 0.008 0.001 PHE R 55 TYR 0.005 0.001 TYR D 143 ARG 0.000 0.000 ARG N 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 2.130 Fit side-chains REVERT: C 50 GLN cc_start: 0.8543 (mt0) cc_final: 0.8309 (mt0) REVERT: C 90 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8543 (mtmt) REVERT: D 40 LEU cc_start: 0.8692 (tt) cc_final: 0.8440 (tp) REVERT: D 116 SER cc_start: 0.8724 (p) cc_final: 0.8374 (m) REVERT: D 130 ASP cc_start: 0.7967 (m-30) cc_final: 0.7714 (m-30) REVERT: F 33 ILE cc_start: 0.8440 (mt) cc_final: 0.8203 (tp) REVERT: F 40 LEU cc_start: 0.8378 (tt) cc_final: 0.8136 (tp) REVERT: F 59 ASN cc_start: 0.8877 (t0) cc_final: 0.7943 (t0) REVERT: G 59 ASN cc_start: 0.8913 (t0) cc_final: 0.8376 (t0) REVERT: G 130 ASP cc_start: 0.7888 (m-30) cc_final: 0.7682 (m-30) REVERT: H 22 MET cc_start: 0.8432 (mmp) cc_final: 0.8041 (mmp) REVERT: H 33 ILE cc_start: 0.8602 (mt) cc_final: 0.8382 (tp) REVERT: H 59 ASN cc_start: 0.8898 (t0) cc_final: 0.8650 (t0) REVERT: H 88 ASP cc_start: 0.8051 (t70) cc_final: 0.7737 (t70) REVERT: I 25 ILE cc_start: 0.8651 (mt) cc_final: 0.8386 (mm) REVERT: I 75 ASP cc_start: 0.8109 (t0) cc_final: 0.7782 (t0) REVERT: J 56 ASP cc_start: 0.8224 (t70) cc_final: 0.7961 (t70) REVERT: J 94 ASP cc_start: 0.7851 (m-30) cc_final: 0.7508 (m-30) REVERT: K 121 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8372 (mt-10) REVERT: M 94 ASP cc_start: 0.8019 (m-30) cc_final: 0.7628 (m-30) REVERT: M 130 ASP cc_start: 0.7970 (m-30) cc_final: 0.7671 (m-30) REVERT: N 130 ASP cc_start: 0.8159 (m-30) cc_final: 0.7887 (m-30) REVERT: P 50 GLN cc_start: 0.8631 (mt0) cc_final: 0.8328 (mt0) REVERT: P 56 ASP cc_start: 0.8055 (t70) cc_final: 0.7826 (t70) REVERT: Q 50 GLN cc_start: 0.8578 (mt0) cc_final: 0.8330 (mt0) REVERT: Q 56 ASP cc_start: 0.8022 (t70) cc_final: 0.7779 (t70) REVERT: Q 59 ASN cc_start: 0.8924 (t0) cc_final: 0.8512 (t0) REVERT: S 54 ASP cc_start: 0.8114 (t70) cc_final: 0.7873 (t0) REVERT: S 130 ASP cc_start: 0.7737 (m-30) cc_final: 0.7434 (m-30) REVERT: T 94 ASP cc_start: 0.8128 (m-30) cc_final: 0.7792 (m-30) REVERT: T 121 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8288 (mt-10) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.9376 time to fit residues: 420.5697 Evaluate side-chains 307 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 203 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 236 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN E 50 GLN G 50 GLN I 50 GLN J 50 GLN L 50 GLN N 50 GLN P 50 GLN S 50 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19280 Z= 0.182 Angle : 0.487 7.624 26420 Z= 0.272 Chirality : 0.043 0.145 3320 Planarity : 0.003 0.023 3360 Dihedral : 4.790 16.361 2700 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.87 % Allowed : 3.94 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.68 (0.16), residues: 2620 helix: 3.12 (0.18), residues: 700 sheet: 1.70 (0.17), residues: 960 loop : -1.17 (0.15), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 92 HIS 0.004 0.002 HIS Q 68 PHE 0.009 0.001 PHE K 55 TYR 0.008 0.001 TYR M 143 ARG 0.001 0.000 ARG F 124 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 313 time to evaluate : 2.027 Fit side-chains REVERT: D 116 SER cc_start: 0.8695 (p) cc_final: 0.8302 (m) REVERT: E 94 ASP cc_start: 0.7522 (m-30) cc_final: 0.7213 (m-30) REVERT: E 101 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7247 (tp30) REVERT: F 56 ASP cc_start: 0.8159 (t0) cc_final: 0.7843 (t70) REVERT: F 59 ASN cc_start: 0.8887 (t0) cc_final: 0.8538 (t0) REVERT: F 87 ASP cc_start: 0.7947 (m-30) cc_final: 0.7739 (m-30) REVERT: G 59 ASN cc_start: 0.8875 (t0) cc_final: 0.8484 (t0) REVERT: H 101 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7538 (mt-10) REVERT: H 143 TYR cc_start: 0.8390 (t80) cc_final: 0.8125 (t80) REVERT: I 25 ILE cc_start: 0.8739 (mt) cc_final: 0.8428 (mm) REVERT: K 121 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8289 (mt-10) REVERT: M 130 ASP cc_start: 0.7804 (m-30) cc_final: 0.7526 (m-30) REVERT: N 130 ASP cc_start: 0.8148 (m-30) cc_final: 0.7876 (m-30) REVERT: O 90 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8458 (mtpt) REVERT: P 50 GLN cc_start: 0.8537 (mt0) cc_final: 0.8274 (mt0) REVERT: P 56 ASP cc_start: 0.8036 (t70) cc_final: 0.7747 (t70) REVERT: Q 50 GLN cc_start: 0.8503 (mt0) cc_final: 0.8271 (mt0) REVERT: Q 59 ASN cc_start: 0.8897 (t0) cc_final: 0.8524 (t0) REVERT: Q 101 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: S 54 ASP cc_start: 0.8116 (t70) cc_final: 0.7904 (t0) REVERT: S 101 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7108 (tp30) REVERT: S 130 ASP cc_start: 0.7728 (m-30) cc_final: 0.7413 (m-30) REVERT: T 121 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8284 (mt-10) outliers start: 19 outliers final: 12 residues processed: 320 average time/residue: 1.0192 time to fit residues: 378.7476 Evaluate side-chains 300 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 285 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 101 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 236 optimal weight: 3.9990 chunk 255 optimal weight: 0.9980 chunk 210 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN D 50 GLN F 50 GLN H 50 GLN L 50 GLN N 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19280 Z= 0.194 Angle : 0.483 6.467 26420 Z= 0.269 Chirality : 0.043 0.148 3320 Planarity : 0.003 0.023 3360 Dihedral : 4.773 16.168 2700 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.15 % Allowed : 6.51 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.63 (0.16), residues: 2620 helix: 2.92 (0.18), residues: 720 sheet: 1.74 (0.17), residues: 960 loop : -1.24 (0.16), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 92 HIS 0.005 0.002 HIS E 68 PHE 0.012 0.001 PHE K 55 TYR 0.008 0.001 TYR P 143 ARG 0.001 0.000 ARG P 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 285 time to evaluate : 2.180 Fit side-chains REVERT: B 50 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8352 (mt0) REVERT: D 116 SER cc_start: 0.8710 (p) cc_final: 0.8284 (m) REVERT: E 94 ASP cc_start: 0.7568 (m-30) cc_final: 0.7004 (m-30) REVERT: F 56 ASP cc_start: 0.8112 (t0) cc_final: 0.7832 (t70) REVERT: F 59 ASN cc_start: 0.8930 (t0) cc_final: 0.8644 (t0) REVERT: G 59 ASN cc_start: 0.8854 (t0) cc_final: 0.8407 (t0) REVERT: H 101 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7546 (mt-10) REVERT: H 143 TYR cc_start: 0.8419 (t80) cc_final: 0.8068 (t80) REVERT: I 25 ILE cc_start: 0.8760 (mt) cc_final: 0.8460 (mm) REVERT: I 50 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: L 88 ASP cc_start: 0.7677 (t70) cc_final: 0.7403 (t70) REVERT: M 130 ASP cc_start: 0.7804 (m-30) cc_final: 0.7510 (m-30) REVERT: N 130 ASP cc_start: 0.8163 (m-30) cc_final: 0.7895 (m-30) REVERT: P 59 ASN cc_start: 0.8926 (t0) cc_final: 0.8466 (t0) REVERT: P 77 ASP cc_start: 0.8518 (m-30) cc_final: 0.8258 (m-30) REVERT: Q 50 GLN cc_start: 0.8513 (mt0) cc_final: 0.8281 (mt0) REVERT: Q 59 ASN cc_start: 0.8898 (t0) cc_final: 0.8491 (t0) REVERT: Q 101 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7507 (tt0) REVERT: S 101 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7187 (tp30) REVERT: S 130 ASP cc_start: 0.7759 (m-30) cc_final: 0.7400 (m-30) REVERT: T 101 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7301 (mt-10) REVERT: T 121 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8315 (mt-10) outliers start: 25 outliers final: 12 residues processed: 295 average time/residue: 1.1288 time to fit residues: 384.2307 Evaluate side-chains 287 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 269 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 101 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 7.9990 chunk 177 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 237 optimal weight: 6.9990 chunk 251 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN F 50 GLN H 50 GLN P 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19280 Z= 0.175 Angle : 0.460 6.253 26420 Z= 0.256 Chirality : 0.043 0.143 3320 Planarity : 0.003 0.024 3360 Dihedral : 4.631 15.524 2700 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.19 % Allowed : 7.34 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.76 (0.16), residues: 2620 helix: 3.27 (0.18), residues: 700 sheet: 1.82 (0.17), residues: 960 loop : -1.29 (0.15), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 92 HIS 0.004 0.002 HIS E 68 PHE 0.012 0.001 PHE K 55 TYR 0.008 0.001 TYR P 143 ARG 0.001 0.000 ARG P 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 276 time to evaluate : 1.957 Fit side-chains REVERT: B 50 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8281 (mt0) REVERT: D 116 SER cc_start: 0.8661 (p) cc_final: 0.8238 (m) REVERT: E 94 ASP cc_start: 0.7582 (m-30) cc_final: 0.7047 (m-30) REVERT: E 101 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7309 (tp30) REVERT: F 59 ASN cc_start: 0.8911 (t0) cc_final: 0.8631 (t0) REVERT: G 59 ASN cc_start: 0.8848 (t0) cc_final: 0.8418 (t0) REVERT: H 101 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7578 (mt-10) REVERT: H 143 TYR cc_start: 0.8390 (t80) cc_final: 0.8102 (t80) REVERT: I 25 ILE cc_start: 0.8756 (mt) cc_final: 0.8455 (mm) REVERT: J 94 ASP cc_start: 0.7706 (m-30) cc_final: 0.7481 (t0) REVERT: L 88 ASP cc_start: 0.7732 (t70) cc_final: 0.7495 (t70) REVERT: M 130 ASP cc_start: 0.7829 (m-30) cc_final: 0.7546 (m-30) REVERT: N 130 ASP cc_start: 0.8148 (m-30) cc_final: 0.7879 (m-30) REVERT: O 25 ILE cc_start: 0.8825 (mt) cc_final: 0.8504 (mm) REVERT: P 56 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7579 (t70) REVERT: P 59 ASN cc_start: 0.8925 (t0) cc_final: 0.8465 (t0) REVERT: P 77 ASP cc_start: 0.8490 (m-30) cc_final: 0.8233 (m-30) REVERT: Q 50 GLN cc_start: 0.8503 (mt0) cc_final: 0.8270 (mt0) REVERT: Q 59 ASN cc_start: 0.8890 (t0) cc_final: 0.8536 (t0) REVERT: Q 101 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: R 101 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7239 (mm-30) REVERT: S 101 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7132 (tp30) REVERT: T 101 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: T 121 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8305 (mt-10) outliers start: 26 outliers final: 14 residues processed: 282 average time/residue: 1.1405 time to fit residues: 369.3674 Evaluate side-chains 286 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 265 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain J residue 101 GLU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain P residue 56 ASP Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 101 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: