Starting phenix.real_space_refine on Mon May 19 10:18:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fj5_29215/05_2025/8fj5_29215.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fj5_29215/05_2025/8fj5_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/cci-nas-00/data/ceres_data/8fj5_29215/05_2025/8fj5_29215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fj5_29215/05_2025/8fj5_29215.map" model { file = "/net/cci-nas-00/data/ceres_data/8fj5_29215/05_2025/8fj5_29215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fj5_29215/05_2025/8fj5_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.05, 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: 4.68 Conformation dependent library (CDL) restraints added in 2.5 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: 2.93 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: 6.92 Time building geometry restraints manager: 5.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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: 0.21 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 '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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.840 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 38.310 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 54.050 ------------------------------------------------------------------------------- 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= 0.187 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 Details of bonding type rmsd hydrogen bonds : bond 0.17440 ( 915) hydrogen bonds : angle 5.25526 ( 3135) covalent geometry : bond 0.00424 (19280) covalent geometry : angle 0.62093 (26420) *********************** 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 : 2.061 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: 0.8723 time to fit residues: 392.0857 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 : 1.989 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.110073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.091553 restraints weight = 22516.902| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 1.55 r_work: 0.2765 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 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= 0.124 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 Details of bonding type rmsd hydrogen bonds : bond 0.06053 ( 915) hydrogen bonds : angle 3.56910 ( 3135) covalent geometry : bond 0.00271 (19280) covalent geometry : angle 0.48694 (26420) *********************** 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 : 2.040 Fit side-chains REVERT: A 56 ASP cc_start: 0.8396 (t70) cc_final: 0.8183 (t70) REVERT: D 116 SER cc_start: 0.8714 (p) cc_final: 0.8301 (m) REVERT: E 94 ASP cc_start: 0.7748 (m-30) cc_final: 0.7472 (m-30) REVERT: E 101 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7716 (tp30) REVERT: F 56 ASP cc_start: 0.8649 (t0) cc_final: 0.8384 (t70) REVERT: F 59 ASN cc_start: 0.8975 (t0) cc_final: 0.8644 (t0) REVERT: G 59 ASN cc_start: 0.8987 (t0) cc_final: 0.8621 (t0) REVERT: H 101 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7884 (mt-10) REVERT: H 143 TYR cc_start: 0.8624 (t80) cc_final: 0.8349 (t80) REVERT: I 25 ILE cc_start: 0.8848 (mt) cc_final: 0.8570 (mm) REVERT: J 56 ASP cc_start: 0.8774 (t70) cc_final: 0.8569 (t70) REVERT: K 121 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8460 (mt-10) REVERT: M 130 ASP cc_start: 0.8189 (m-30) cc_final: 0.7940 (m-30) REVERT: N 130 ASP cc_start: 0.8515 (m-30) cc_final: 0.8283 (m-30) REVERT: O 69 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8259 (tp30) REVERT: O 90 LYS cc_start: 0.8785 (mtpt) cc_final: 0.8584 (mtpt) REVERT: P 50 GLN cc_start: 0.8732 (mt0) cc_final: 0.8477 (mt0) REVERT: P 56 ASP cc_start: 0.8644 (t70) cc_final: 0.8388 (t70) REVERT: Q 50 GLN cc_start: 0.8714 (mt0) cc_final: 0.8491 (mt0) REVERT: Q 59 ASN cc_start: 0.9079 (t0) cc_final: 0.8721 (t0) REVERT: Q 101 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: S 101 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7573 (tp30) REVERT: S 130 ASP cc_start: 0.8266 (m-30) cc_final: 0.7938 (m-30) REVERT: T 121 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8446 (mt-10) outliers start: 19 outliers final: 12 residues processed: 320 average time/residue: 0.9684 time to fit residues: 360.9671 Evaluate side-chains 299 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 284 time to evaluate : 2.205 ------------------------------------------------------------------------------- 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 50 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 151 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 175 optimal weight: 0.0470 chunk 158 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 211 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.112688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.094818 restraints weight = 22235.760| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.47 r_work: 0.2796 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19280 Z= 0.103 Angle : 0.447 6.042 26420 Z= 0.248 Chirality : 0.042 0.141 3320 Planarity : 0.002 0.021 3360 Dihedral : 4.510 14.980 2700 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.96 % Allowed : 6.56 % Favored : 92.48 % 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: 1.89 (0.16), residues: 2620 helix: 3.35 (0.18), residues: 700 sheet: 1.89 (0.17), residues: 960 loop : -1.19 (0.16), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP T 92 HIS 0.003 0.002 HIS Q 68 PHE 0.009 0.001 PHE K 55 TYR 0.007 0.001 TYR P 143 ARG 0.001 0.000 ARG P 124 Details of bonding type rmsd hydrogen bonds : bond 0.05227 ( 915) hydrogen bonds : angle 3.36560 ( 3135) covalent geometry : bond 0.00218 (19280) covalent geometry : angle 0.44714 (26420) *********************** 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 308 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 287 time to evaluate : 2.192 Fit side-chains REVERT: B 50 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8578 (mt0) REVERT: D 116 SER cc_start: 0.8698 (p) cc_final: 0.8264 (m) REVERT: E 69 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8420 (mt-10) REVERT: E 94 ASP cc_start: 0.7773 (m-30) cc_final: 0.7236 (m-30) REVERT: E 101 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7680 (tp30) REVERT: F 56 ASP cc_start: 0.8614 (t0) cc_final: 0.8398 (t70) REVERT: F 59 ASN cc_start: 0.9020 (t0) cc_final: 0.8720 (t0) REVERT: G 59 ASN cc_start: 0.8964 (t0) cc_final: 0.8537 (t0) REVERT: H 143 TYR cc_start: 0.8619 (t80) cc_final: 0.8338 (t80) REVERT: I 25 ILE cc_start: 0.8877 (mt) cc_final: 0.8605 (mm) REVERT: J 94 ASP cc_start: 0.8028 (m-30) cc_final: 0.7704 (t0) REVERT: K 121 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8426 (mt-10) REVERT: L 88 ASP cc_start: 0.7735 (t70) cc_final: 0.7332 (t70) REVERT: M 130 ASP cc_start: 0.8144 (m-30) cc_final: 0.7898 (m-30) REVERT: N 130 ASP cc_start: 0.8499 (m-30) cc_final: 0.8279 (m-30) REVERT: O 69 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8270 (tp30) REVERT: P 50 GLN cc_start: 0.8693 (mt0) cc_final: 0.8442 (mt0) REVERT: P 59 ASN cc_start: 0.9042 (t0) cc_final: 0.8578 (t0) REVERT: P 77 ASP cc_start: 0.8967 (m-30) cc_final: 0.8732 (m-30) REVERT: Q 50 GLN cc_start: 0.8655 (mt0) cc_final: 0.8413 (mt0) REVERT: Q 59 ASN cc_start: 0.9083 (t0) cc_final: 0.8717 (t0) REVERT: Q 101 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: S 101 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7498 (tp30) REVERT: S 130 ASP cc_start: 0.8165 (m-30) cc_final: 0.7844 (m-30) REVERT: T 101 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: T 121 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8515 (mt-10) outliers start: 21 outliers final: 9 residues processed: 294 average time/residue: 1.0181 time to fit residues: 346.2264 Evaluate side-chains 283 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 270 time to evaluate : 2.061 ------------------------------------------------------------------------------- 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 E residue 101 GLU 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 K residue 33 ILE Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain Q 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 181 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN F 50 GLN H 50 GLN L 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.118702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.101471 restraints weight = 21597.499| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.47 r_work: 0.2778 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19280 Z= 0.107 Angle : 0.445 5.558 26420 Z= 0.247 Chirality : 0.042 0.144 3320 Planarity : 0.002 0.022 3360 Dihedral : 4.455 14.891 2700 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.15 % Allowed : 7.16 % Favored : 91.70 % 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: 1.93 (0.16), residues: 2620 helix: 3.39 (0.18), residues: 700 sheet: 1.96 (0.17), residues: 960 loop : -1.23 (0.16), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP T 92 HIS 0.004 0.002 HIS E 68 PHE 0.010 0.001 PHE K 55 TYR 0.007 0.001 TYR P 143 ARG 0.002 0.000 ARG P 124 Details of bonding type rmsd hydrogen bonds : bond 0.05349 ( 915) hydrogen bonds : angle 3.34728 ( 3135) covalent geometry : bond 0.00230 (19280) covalent geometry : angle 0.44475 (26420) *********************** 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 301 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 276 time to evaluate : 2.038 Fit side-chains REVERT: B 50 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8557 (mt0) REVERT: D 116 SER cc_start: 0.8696 (p) cc_final: 0.8247 (m) REVERT: E 69 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8428 (mt-10) REVERT: E 94 ASP cc_start: 0.7840 (m-30) cc_final: 0.7306 (m-30) REVERT: E 101 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7673 (tp30) REVERT: F 56 ASP cc_start: 0.8601 (t0) cc_final: 0.8380 (t70) REVERT: F 59 ASN cc_start: 0.9014 (t0) cc_final: 0.8731 (t0) REVERT: G 59 ASN cc_start: 0.8939 (t0) cc_final: 0.8537 (t0) REVERT: I 25 ILE cc_start: 0.8884 (mt) cc_final: 0.8590 (mm) REVERT: I 50 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: J 88 ASP cc_start: 0.7944 (t0) cc_final: 0.7676 (t70) REVERT: J 94 ASP cc_start: 0.8059 (m-30) cc_final: 0.7783 (t0) REVERT: K 121 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8408 (mt-10) REVERT: L 88 ASP cc_start: 0.7821 (t70) cc_final: 0.7493 (t70) REVERT: M 40 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7935 (tt) REVERT: M 130 ASP cc_start: 0.8170 (m-30) cc_final: 0.7910 (m-30) REVERT: O 25 ILE cc_start: 0.8925 (mt) cc_final: 0.8644 (mm) REVERT: O 69 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8253 (tp30) REVERT: P 50 GLN cc_start: 0.8699 (mt0) cc_final: 0.8440 (mt0) REVERT: P 59 ASN cc_start: 0.9053 (t0) cc_final: 0.8608 (t0) REVERT: P 77 ASP cc_start: 0.8961 (m-30) cc_final: 0.8730 (m-30) REVERT: Q 50 GLN cc_start: 0.8642 (mt0) cc_final: 0.8403 (mt0) REVERT: Q 59 ASN cc_start: 0.9068 (t0) cc_final: 0.8730 (t0) REVERT: Q 101 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: R 101 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7764 (mm-30) REVERT: S 101 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7516 (tp30) REVERT: S 130 ASP cc_start: 0.8169 (m-30) cc_final: 0.7792 (m-30) REVERT: T 101 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7837 (mt-10) outliers start: 25 outliers final: 11 residues processed: 283 average time/residue: 1.1195 time to fit residues: 364.1257 Evaluate side-chains 293 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 274 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 54 ASP 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 E residue 101 GLU Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 56 ASP 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 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 160 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 11 optimal weight: 0.0070 chunk 202 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN F 50 GLN H 50 GLN J 50 GLN L 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.113428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.096073 restraints weight = 21885.527| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 1.47 r_work: 0.2703 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19280 Z= 0.159 Angle : 0.513 6.628 26420 Z= 0.285 Chirality : 0.045 0.152 3320 Planarity : 0.003 0.024 3360 Dihedral : 4.889 16.932 2700 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.19 % Allowed : 8.21 % Favored : 90.60 % 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: 1.54 (0.16), residues: 2620 helix: 2.84 (0.18), residues: 720 sheet: 1.73 (0.17), residues: 960 loop : -1.34 (0.15), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 92 HIS 0.007 0.003 HIS E 68 PHE 0.017 0.002 PHE K 55 TYR 0.008 0.001 TYR P 143 ARG 0.002 0.000 ARG P 124 Details of bonding type rmsd hydrogen bonds : bond 0.07139 ( 915) hydrogen bonds : angle 3.69488 ( 3135) covalent geometry : bond 0.00372 (19280) covalent geometry : angle 0.51288 (26420) *********************** REFINEMENT MACRO_CYCLE 5 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 309 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 283 time to evaluate : 2.032 Fit side-chains REVERT: A 144 ASN cc_start: 0.8352 (m-40) cc_final: 0.8149 (m110) REVERT: B 50 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8519 (mt0) REVERT: D 116 SER cc_start: 0.8838 (p) cc_final: 0.8370 (m) REVERT: E 94 ASP cc_start: 0.7982 (m-30) cc_final: 0.7409 (m-30) REVERT: F 59 ASN cc_start: 0.9021 (t0) cc_final: 0.8736 (t0) REVERT: G 59 ASN cc_start: 0.8983 (t0) cc_final: 0.8602 (t0) REVERT: H 101 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: H 143 TYR cc_start: 0.8639 (t80) cc_final: 0.8159 (t80) REVERT: I 25 ILE cc_start: 0.8895 (mt) cc_final: 0.8642 (mm) REVERT: I 50 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8621 (mt0) REVERT: I 101 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7511 (mm-30) REVERT: J 88 ASP cc_start: 0.8057 (t0) cc_final: 0.7784 (t0) REVERT: J 94 ASP cc_start: 0.8089 (m-30) cc_final: 0.7784 (t0) REVERT: L 88 ASP cc_start: 0.8010 (t70) cc_final: 0.7599 (t70) REVERT: M 40 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8096 (tt) REVERT: M 130 ASP cc_start: 0.8222 (m-30) cc_final: 0.7979 (m-30) REVERT: O 25 ILE cc_start: 0.8926 (mt) cc_final: 0.8644 (mm) REVERT: P 59 ASN cc_start: 0.9097 (t0) cc_final: 0.8672 (t0) REVERT: P 77 ASP cc_start: 0.8960 (m-30) cc_final: 0.8729 (m-30) REVERT: Q 50 GLN cc_start: 0.8684 (mt0) cc_final: 0.8457 (mt0) REVERT: Q 59 ASN cc_start: 0.9111 (t0) cc_final: 0.8701 (t160) REVERT: Q 101 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: R 101 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7663 (mm-30) REVERT: S 101 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7559 (tp30) REVERT: T 101 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7881 (mt-10) outliers start: 26 outliers final: 13 residues processed: 292 average time/residue: 1.0373 time to fit residues: 348.6120 Evaluate side-chains 284 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 262 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 25 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 I residue 50 GLN Chi-restraints excluded: chain I 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 101 GLU Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain O residue 33 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 210 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 177 optimal weight: 0.6980 chunk 241 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 J 50 GLN L 50 GLN P 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.110070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.090627 restraints weight = 22591.528| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 1.64 r_work: 0.2750 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 19280 Z= 0.108 Angle : 0.444 6.828 26420 Z= 0.245 Chirality : 0.042 0.156 3320 Planarity : 0.003 0.024 3360 Dihedral : 4.467 14.902 2700 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.19 % Allowed : 8.94 % Favored : 89.86 % 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: 1.90 (0.16), residues: 2620 helix: 3.42 (0.18), residues: 700 sheet: 2.05 (0.17), residues: 940 loop : -1.34 (0.15), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 92 HIS 0.004 0.002 HIS E 68 PHE 0.011 0.001 PHE K 55 TYR 0.009 0.001 TYR P 143 ARG 0.002 0.000 ARG P 124 Details of bonding type rmsd hydrogen bonds : bond 0.05355 ( 915) hydrogen bonds : angle 3.31393 ( 3135) covalent geometry : bond 0.00234 (19280) covalent geometry : angle 0.44436 (26420) *********************** REFINEMENT MACRO_CYCLE 6 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 298 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 272 time to evaluate : 2.019 Fit side-chains REVERT: B 50 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8480 (mt0) REVERT: D 116 SER cc_start: 0.8617 (p) cc_final: 0.8137 (m) REVERT: E 94 ASP cc_start: 0.7723 (m-30) cc_final: 0.7160 (m-30) REVERT: E 101 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7735 (tp30) REVERT: F 59 ASN cc_start: 0.9000 (t0) cc_final: 0.8719 (t0) REVERT: G 59 ASN cc_start: 0.8932 (t0) cc_final: 0.8548 (t0) REVERT: H 143 TYR cc_start: 0.8612 (t80) cc_final: 0.8231 (t80) REVERT: I 25 ILE cc_start: 0.8853 (mt) cc_final: 0.8569 (mm) REVERT: I 50 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8580 (mt0) REVERT: J 94 ASP cc_start: 0.8029 (m-30) cc_final: 0.7766 (t0) REVERT: L 88 ASP cc_start: 0.8008 (t70) cc_final: 0.7713 (t70) REVERT: M 130 ASP cc_start: 0.8205 (m-30) cc_final: 0.7985 (m-30) REVERT: O 25 ILE cc_start: 0.8937 (mt) cc_final: 0.8640 (mm) REVERT: O 69 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8245 (tp30) REVERT: P 59 ASN cc_start: 0.9019 (t0) cc_final: 0.8600 (t0) REVERT: P 77 ASP cc_start: 0.8982 (m-30) cc_final: 0.8752 (m-30) REVERT: Q 50 GLN cc_start: 0.8642 (mt0) cc_final: 0.8411 (mt0) REVERT: Q 59 ASN cc_start: 0.9108 (t0) cc_final: 0.8712 (t160) REVERT: Q 101 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: R 101 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7702 (mm-30) REVERT: S 101 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7552 (tp30) REVERT: T 101 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7839 (mt-10) outliers start: 26 outliers final: 13 residues processed: 283 average time/residue: 1.0464 time to fit residues: 341.2207 Evaluate side-chains 287 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 268 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain K 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 223 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 J 50 GLN L 50 GLN P 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.108674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.089312 restraints weight = 22535.081| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.63 r_work: 0.2733 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19280 Z= 0.120 Angle : 0.463 7.487 26420 Z= 0.255 Chirality : 0.043 0.160 3320 Planarity : 0.003 0.024 3360 Dihedral : 4.514 17.760 2700 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.28 % Allowed : 9.13 % Favored : 89.59 % 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: 1.80 (0.16), residues: 2620 helix: 3.38 (0.18), residues: 700 sheet: 1.87 (0.17), residues: 960 loop : -1.36 (0.15), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 92 HIS 0.005 0.002 HIS E 68 PHE 0.013 0.001 PHE K 55 TYR 0.009 0.001 TYR P 143 ARG 0.001 0.000 ARG P 124 Details of bonding type rmsd hydrogen bonds : bond 0.05914 ( 915) hydrogen bonds : angle 3.41018 ( 3135) covalent geometry : bond 0.00268 (19280) covalent geometry : angle 0.46251 (26420) *********************** REFINEMENT MACRO_CYCLE 7 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 299 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 271 time to evaluate : 2.202 Fit side-chains REVERT: B 50 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8453 (mt0) REVERT: D 116 SER cc_start: 0.8614 (p) cc_final: 0.8129 (m) REVERT: D 130 ASP cc_start: 0.8469 (m-30) cc_final: 0.8195 (m-30) REVERT: E 94 ASP cc_start: 0.7877 (m-30) cc_final: 0.7304 (m-30) REVERT: F 59 ASN cc_start: 0.9011 (t0) cc_final: 0.8727 (t0) REVERT: G 59 ASN cc_start: 0.8966 (t0) cc_final: 0.8586 (t0) REVERT: H 143 TYR cc_start: 0.8633 (t80) cc_final: 0.8308 (t80) REVERT: I 25 ILE cc_start: 0.8872 (mt) cc_final: 0.8593 (mm) REVERT: I 50 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8586 (mt0) REVERT: J 94 ASP cc_start: 0.8077 (m-30) cc_final: 0.7799 (t0) REVERT: L 88 ASP cc_start: 0.8043 (t70) cc_final: 0.7742 (t70) REVERT: M 130 ASP cc_start: 0.8234 (m-30) cc_final: 0.8012 (m-30) REVERT: O 25 ILE cc_start: 0.8908 (mt) cc_final: 0.8615 (mm) REVERT: P 59 ASN cc_start: 0.9045 (t0) cc_final: 0.8629 (t0) REVERT: P 77 ASP cc_start: 0.8973 (m-30) cc_final: 0.8742 (m-30) REVERT: Q 50 GLN cc_start: 0.8668 (mt0) cc_final: 0.8436 (mt0) REVERT: Q 59 ASN cc_start: 0.9116 (t0) cc_final: 0.8722 (t160) REVERT: Q 101 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: R 101 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7656 (mm-30) REVERT: S 101 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7603 (tp30) REVERT: T 101 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7862 (mt-10) outliers start: 28 outliers final: 11 residues processed: 287 average time/residue: 1.0372 time to fit residues: 343.2029 Evaluate side-chains 282 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 265 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain K 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 228 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 175 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 144 ASN F 50 GLN H 50 GLN J 50 GLN L 50 GLN P 50 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.112786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.095399 restraints weight = 21985.838| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 1.48 r_work: 0.2691 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 19280 Z= 0.172 Angle : 0.533 7.797 26420 Z= 0.294 Chirality : 0.045 0.175 3320 Planarity : 0.003 0.026 3360 Dihedral : 4.912 19.815 2700 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.06 % Allowed : 9.45 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.16), residues: 2620 helix: 2.81 (0.18), residues: 720 sheet: 1.65 (0.17), residues: 960 loop : -1.37 (0.15), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 92 HIS 0.008 0.003 HIS E 68 PHE 0.018 0.002 PHE K 55 TYR 0.011 0.001 TYR P 143 ARG 0.002 0.000 ARG P 124 Details of bonding type rmsd hydrogen bonds : bond 0.07399 ( 915) hydrogen bonds : angle 3.70972 ( 3135) covalent geometry : bond 0.00408 (19280) covalent geometry : angle 0.53340 (26420) *********************** REFINEMENT MACRO_CYCLE 8 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 290 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 267 time to evaluate : 2.030 Fit side-chains REVERT: B 50 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8502 (mt0) REVERT: D 116 SER cc_start: 0.8861 (p) cc_final: 0.8378 (m) REVERT: E 94 ASP cc_start: 0.8046 (m-30) cc_final: 0.7407 (m-30) REVERT: F 59 ASN cc_start: 0.9032 (t0) cc_final: 0.8738 (t0) REVERT: G 59 ASN cc_start: 0.9021 (t0) cc_final: 0.8650 (t0) REVERT: H 101 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.8030 (mt-10) REVERT: I 25 ILE cc_start: 0.8909 (mt) cc_final: 0.8644 (mm) REVERT: I 50 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: J 56 ASP cc_start: 0.8581 (t70) cc_final: 0.8242 (t70) REVERT: J 88 ASP cc_start: 0.8022 (t0) cc_final: 0.7802 (t0) REVERT: M 40 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8126 (tt) REVERT: M 130 ASP cc_start: 0.8253 (m-30) cc_final: 0.7982 (m-30) REVERT: N 25 ILE cc_start: 0.8958 (mt) cc_final: 0.8562 (mm) REVERT: O 25 ILE cc_start: 0.8938 (mt) cc_final: 0.8661 (mm) REVERT: P 59 ASN cc_start: 0.9108 (t0) cc_final: 0.8693 (t0) REVERT: P 77 ASP cc_start: 0.8963 (m-30) cc_final: 0.8732 (m-30) REVERT: P 143 TYR cc_start: 0.8283 (t80) cc_final: 0.8080 (t80) REVERT: Q 50 GLN cc_start: 0.8704 (mt0) cc_final: 0.8483 (mt0) REVERT: Q 59 ASN cc_start: 0.9113 (t0) cc_final: 0.8706 (t160) REVERT: R 101 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: S 101 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7548 (tp30) REVERT: T 101 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7886 (mt-10) outliers start: 23 outliers final: 13 residues processed: 273 average time/residue: 1.0708 time to fit residues: 335.4111 Evaluate side-chains 285 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 265 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 100 THR 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 101 GLU Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain R residue 40 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 12 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 125 optimal weight: 0.2980 chunk 24 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 251 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 J 50 GLN L 50 GLN P 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.105409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.085990 restraints weight = 22841.086| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 1.64 r_work: 0.2665 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19280 Z= 0.163 Angle : 0.523 7.511 26420 Z= 0.288 Chirality : 0.045 0.184 3320 Planarity : 0.003 0.028 3360 Dihedral : 4.907 19.670 2700 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.19 % Allowed : 9.68 % Favored : 89.13 % 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: 1.39 (0.16), residues: 2620 helix: 2.81 (0.18), residues: 720 sheet: 1.57 (0.17), residues: 960 loop : -1.42 (0.15), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 92 HIS 0.007 0.003 HIS E 68 PHE 0.016 0.002 PHE K 55 TYR 0.010 0.001 TYR P 143 ARG 0.002 0.000 ARG P 124 Details of bonding type rmsd hydrogen bonds : bond 0.07117 ( 915) hydrogen bonds : angle 3.65790 ( 3135) covalent geometry : bond 0.00384 (19280) covalent geometry : angle 0.52290 (26420) *********************** REFINEMENT MACRO_CYCLE 9 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 281 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 255 time to evaluate : 2.145 Fit side-chains REVERT: A 22 MET cc_start: 0.9083 (mmp) cc_final: 0.8767 (mmp) REVERT: B 50 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8507 (mt0) REVERT: C 90 LYS cc_start: 0.8825 (mtmt) cc_final: 0.8504 (mtmt) REVERT: D 116 SER cc_start: 0.8787 (p) cc_final: 0.8273 (m) REVERT: F 59 ASN cc_start: 0.9023 (t0) cc_final: 0.8723 (t0) REVERT: G 22 MET cc_start: 0.9049 (mmp) cc_final: 0.8806 (mmp) REVERT: G 59 ASN cc_start: 0.9036 (t0) cc_final: 0.8678 (t0) REVERT: H 101 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: I 25 ILE cc_start: 0.8877 (mt) cc_final: 0.8596 (mm) REVERT: I 50 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: I 101 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7540 (mm-30) REVERT: J 56 ASP cc_start: 0.8593 (t70) cc_final: 0.8229 (t70) REVERT: J 88 ASP cc_start: 0.8025 (t0) cc_final: 0.7764 (t0) REVERT: M 40 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7993 (tt) REVERT: M 130 ASP cc_start: 0.8279 (m-30) cc_final: 0.8013 (m-30) REVERT: N 25 ILE cc_start: 0.8926 (mt) cc_final: 0.8525 (mm) REVERT: O 25 ILE cc_start: 0.8921 (mt) cc_final: 0.8637 (mm) REVERT: P 59 ASN cc_start: 0.9121 (t0) cc_final: 0.8746 (t0) REVERT: P 77 ASP cc_start: 0.8893 (m-30) cc_final: 0.8657 (m-30) REVERT: Q 50 GLN cc_start: 0.8693 (mt0) cc_final: 0.8466 (mt0) REVERT: Q 59 ASN cc_start: 0.9112 (t0) cc_final: 0.8702 (t160) REVERT: R 101 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7612 (mm-30) REVERT: S 101 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7563 (tp30) REVERT: T 94 ASP cc_start: 0.7947 (m-30) cc_final: 0.7532 (m-30) REVERT: T 101 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7870 (mt-10) outliers start: 26 outliers final: 13 residues processed: 264 average time/residue: 1.0660 time to fit residues: 322.0645 Evaluate side-chains 274 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 253 time to evaluate : 2.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain R residue 40 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 226 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 221 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 247 optimal weight: 0.0770 chunk 64 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 J 50 GLN L 50 GLN P 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.112482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.093350 restraints weight = 22287.251| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.62 r_work: 0.2759 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19280 Z= 0.097 Angle : 0.439 8.000 26420 Z= 0.241 Chirality : 0.042 0.189 3320 Planarity : 0.003 0.027 3360 Dihedral : 4.294 17.234 2700 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.73 % Allowed : 10.09 % Favored : 89.17 % 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: 1.94 (0.16), residues: 2620 helix: 3.52 (0.18), residues: 700 sheet: 2.04 (0.17), residues: 940 loop : -1.33 (0.15), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 92 HIS 0.003 0.002 HIS E 68 PHE 0.007 0.001 PHE K 55 TYR 0.005 0.000 TYR P 143 ARG 0.001 0.000 ARG O 124 Details of bonding type rmsd hydrogen bonds : bond 0.04696 ( 915) hydrogen bonds : angle 3.13466 ( 3135) covalent geometry : bond 0.00206 (19280) covalent geometry : angle 0.43861 (26420) ********************** REFINEMENT MACRO_CYCLE 10 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 290 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 274 time to evaluate : 2.142 Fit side-chains REVERT: A 22 MET cc_start: 0.8936 (mmp) cc_final: 0.8688 (mmp) REVERT: B 50 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8418 (mt0) REVERT: C 90 LYS cc_start: 0.8788 (mtmt) cc_final: 0.8468 (mtmt) REVERT: E 94 ASP cc_start: 0.7913 (m-30) cc_final: 0.7323 (m-30) REVERT: E 101 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7889 (tp30) REVERT: F 59 ASN cc_start: 0.9017 (t0) cc_final: 0.8722 (t0) REVERT: F 90 LYS cc_start: 0.8753 (mtpp) cc_final: 0.8492 (mtpt) REVERT: G 22 MET cc_start: 0.8908 (mmp) cc_final: 0.8692 (mmp) REVERT: G 59 ASN cc_start: 0.8938 (t0) cc_final: 0.8558 (t0) REVERT: I 50 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8576 (mt0) REVERT: J 56 ASP cc_start: 0.8392 (t70) cc_final: 0.8015 (t0) REVERT: J 94 ASP cc_start: 0.8019 (m-30) cc_final: 0.7760 (t0) REVERT: M 130 ASP cc_start: 0.8150 (m-30) cc_final: 0.7895 (m-30) REVERT: O 69 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8256 (tp30) REVERT: P 59 ASN cc_start: 0.8997 (t0) cc_final: 0.8584 (t0) REVERT: P 77 ASP cc_start: 0.8885 (m-30) cc_final: 0.8654 (m-30) REVERT: Q 50 GLN cc_start: 0.8626 (mt0) cc_final: 0.8386 (mt0) REVERT: Q 59 ASN cc_start: 0.9074 (t0) cc_final: 0.8756 (t0) REVERT: R 101 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7663 (mm-30) REVERT: S 101 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7538 (tp30) REVERT: T 101 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7782 (mt-10) outliers start: 16 outliers final: 11 residues processed: 278 average time/residue: 1.0688 time to fit residues: 341.2596 Evaluate side-chains 276 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 260 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain K residue 33 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 204 optimal weight: 2.9990 chunk 113 optimal weight: 0.0870 chunk 171 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 141 optimal weight: 0.2980 chunk 160 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 222 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 J 50 GLN L 50 GLN P 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.111357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.092061 restraints weight = 22519.858| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.64 r_work: 0.2748 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19280 Z= 0.099 Angle : 0.443 8.196 26420 Z= 0.242 Chirality : 0.042 0.182 3320 Planarity : 0.003 0.028 3360 Dihedral : 4.247 17.065 2700 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.78 % Allowed : 10.32 % Favored : 88.90 % 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: 2.04 (0.16), residues: 2620 helix: 3.54 (0.18), residues: 700 sheet: 2.16 (0.18), residues: 940 loop : -1.29 (0.15), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 92 HIS 0.003 0.002 HIS E 68 PHE 0.009 0.001 PHE K 55 TYR 0.005 0.001 TYR P 143 ARG 0.001 0.000 ARG P 124 Details of bonding type rmsd hydrogen bonds : bond 0.04941 ( 915) hydrogen bonds : angle 3.15581 ( 3135) covalent geometry : bond 0.00210 (19280) covalent geometry : angle 0.44290 (26420) =============================================================================== Job complete usr+sys time: 10718.86 seconds wall clock time: 185 minutes 46.82 seconds (11146.82 seconds total)