Starting phenix.real_space_refine on Mon Jun 16 07:02:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fj5_29215/06_2025/8fj5_29215.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fj5_29215/06_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_29215/06_2025/8fj5_29215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fj5_29215/06_2025/8fj5_29215.map" model { file = "/net/cci-nas-00/data/ceres_data/8fj5_29215/06_2025/8fj5_29215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fj5_29215/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 4.89, per 1000 atoms: 0.26 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: 4.49 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: 3.04 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: 6.69 Time building geometry restraints manager: 5.35 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: 0.19 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 38.110 Find NCS groups from input model: 0.430 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: 0.000 Load rotamer database and sin/cos tables:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.710 ------------------------------------------------------------------------------- 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 : 2.008 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: 0.9589 time to fit residues: 430.0978 Evaluate side-chains 307 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 2.080 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.091555 restraints weight = 22516.902| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 1.55 r_work: 0.2755 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- 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 : 2.066 Fit side-chains REVERT: A 56 ASP cc_start: 0.8399 (t70) cc_final: 0.8186 (t70) REVERT: D 116 SER cc_start: 0.8714 (p) cc_final: 0.8302 (m) REVERT: E 94 ASP cc_start: 0.7748 (m-30) cc_final: 0.7473 (m-30) REVERT: E 101 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7716 (tp30) REVERT: F 56 ASP cc_start: 0.8651 (t0) cc_final: 0.8385 (t70) REVERT: F 59 ASN cc_start: 0.8975 (t0) cc_final: 0.8646 (t0) REVERT: G 59 ASN cc_start: 0.8987 (t0) cc_final: 0.8622 (t0) REVERT: H 101 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: H 143 TYR cc_start: 0.8620 (t80) cc_final: 0.8343 (t80) REVERT: I 25 ILE cc_start: 0.8849 (mt) cc_final: 0.8571 (mm) REVERT: J 56 ASP cc_start: 0.8776 (t70) cc_final: 0.8572 (t70) REVERT: K 121 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8458 (mt-10) REVERT: M 130 ASP cc_start: 0.8188 (m-30) cc_final: 0.7940 (m-30) REVERT: N 130 ASP cc_start: 0.8516 (m-30) cc_final: 0.8284 (m-30) REVERT: O 69 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8260 (tp30) REVERT: O 90 LYS cc_start: 0.8785 (mtpt) cc_final: 0.8585 (mtpt) REVERT: P 50 GLN cc_start: 0.8725 (mt0) cc_final: 0.8470 (mt0) REVERT: P 56 ASP cc_start: 0.8648 (t70) cc_final: 0.8393 (t70) REVERT: Q 50 GLN cc_start: 0.8709 (mt0) cc_final: 0.8485 (mt0) REVERT: Q 59 ASN cc_start: 0.9077 (t0) cc_final: 0.8719 (t0) REVERT: Q 101 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: S 101 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7576 (tp30) REVERT: S 130 ASP cc_start: 0.8267 (m-30) cc_final: 0.7940 (m-30) REVERT: T 121 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8446 (mt-10) outliers start: 19 outliers final: 12 residues processed: 320 average time/residue: 1.0189 time to fit residues: 378.0922 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 : 2.022 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.0060 overall best weight: 0.4494 ------------------------------------------------------------------------------- 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 = 0.3165 r_free = 0.3165 target = 0.114910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.095727 restraints weight = 22216.004| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.63 r_work: 0.2812 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1878 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= 0.094 Angle : 0.434 5.865 26420 Z= 0.239 Chirality : 0.042 0.137 3320 Planarity : 0.002 0.020 3360 Dihedral : 4.350 14.569 2700 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.73 % Allowed : 6.70 % Favored : 92.57 % 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: 2.06 (0.16), residues: 2620 helix: 3.42 (0.18), residues: 700 sheet: 2.13 (0.17), residues: 940 loop : -1.12 (0.16), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP T 92 HIS 0.003 0.001 HIS Q 68 PHE 0.007 0.001 PHE K 55 TYR 0.004 0.000 TYR P 143 ARG 0.001 0.000 ARG I 124 Details of bonding type rmsd hydrogen bonds : bond 0.04616 ( 915) hydrogen bonds : angle 3.23417 ( 3135) covalent geometry : bond 0.00193 (19280) covalent geometry : angle 0.43365 (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 300 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 284 time to evaluate : 2.152 Fit side-chains REVERT: A 56 ASP cc_start: 0.8307 (t70) cc_final: 0.8061 (t70) REVERT: B 50 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8626 (mt0) REVERT: B 101 GLU cc_start: 0.8258 (tp30) cc_final: 0.7805 (tt0) REVERT: D 116 SER cc_start: 0.8603 (p) cc_final: 0.8167 (m) REVERT: E 94 ASP cc_start: 0.7639 (m-30) cc_final: 0.7130 (m-30) REVERT: E 101 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7780 (tp30) REVERT: F 56 ASP cc_start: 0.8583 (t0) cc_final: 0.8366 (t70) REVERT: F 59 ASN cc_start: 0.8963 (t0) cc_final: 0.8653 (t0) REVERT: F 90 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8176 (mtpt) REVERT: G 59 ASN cc_start: 0.8925 (t0) cc_final: 0.8498 (t0) REVERT: J 56 ASP cc_start: 0.8655 (t70) cc_final: 0.8447 (t0) REVERT: J 94 ASP cc_start: 0.7990 (m-30) cc_final: 0.7692 (t0) REVERT: K 54 ASP cc_start: 0.8577 (t70) cc_final: 0.8377 (t0) REVERT: K 121 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8400 (mt-10) REVERT: L 88 ASP cc_start: 0.7696 (t70) cc_final: 0.7288 (t70) REVERT: M 130 ASP cc_start: 0.8198 (m-30) cc_final: 0.7966 (m-30) REVERT: N 130 ASP cc_start: 0.8444 (m-30) cc_final: 0.8205 (m-30) REVERT: O 69 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8241 (tp30) REVERT: P 50 GLN cc_start: 0.8664 (mt0) cc_final: 0.8421 (mt0) REVERT: P 77 ASP cc_start: 0.8968 (m-30) cc_final: 0.8733 (m-30) REVERT: Q 50 GLN cc_start: 0.8593 (mt0) cc_final: 0.8350 (mt0) REVERT: Q 59 ASN cc_start: 0.9081 (t0) cc_final: 0.8730 (t0) REVERT: Q 101 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7872 (tt0) REVERT: S 101 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7508 (tp30) REVERT: S 130 ASP cc_start: 0.8176 (m-30) cc_final: 0.7842 (m-30) REVERT: T 101 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: T 121 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8413 (mt-10) outliers start: 16 outliers final: 8 residues processed: 286 average time/residue: 1.0770 time to fit residues: 354.7923 Evaluate side-chains 285 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 274 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 50 GLN 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 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: 0.9980 chunk 109 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3121 r_free = 0.3121 target = 0.111603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.093375 restraints weight = 22378.418| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.50 r_work: 0.2771 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 19280 Z= 0.110 Angle : 0.450 6.419 26420 Z= 0.249 Chirality : 0.042 0.147 3320 Planarity : 0.002 0.022 3360 Dihedral : 4.440 14.972 2700 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.01 % Allowed : 7.02 % Favored : 91.97 % 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: 1.98 (0.16), residues: 2620 helix: 3.45 (0.18), residues: 700 sheet: 1.98 (0.17), residues: 960 loop : -1.20 (0.16), residues: 960 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 0.007 0.001 TYR P 143 ARG 0.002 0.000 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.05481 ( 915) hydrogen bonds : angle 3.36197 ( 3135) covalent geometry : bond 0.00240 (19280) covalent geometry : angle 0.45028 (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 304 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 282 time to evaluate : 2.822 Fit side-chains REVERT: B 50 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8551 (mt0) REVERT: E 94 ASP cc_start: 0.7765 (m-30) cc_final: 0.7225 (m-30) REVERT: E 101 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7693 (tp30) REVERT: F 56 ASP cc_start: 0.8615 (t0) cc_final: 0.8398 (t70) REVERT: F 59 ASN cc_start: 0.9023 (t0) cc_final: 0.8741 (t0) REVERT: G 59 ASN cc_start: 0.8951 (t0) cc_final: 0.8555 (t0) REVERT: I 25 ILE cc_start: 0.8885 (mt) cc_final: 0.8603 (mm) REVERT: I 50 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: J 56 ASP cc_start: 0.8673 (t70) cc_final: 0.8456 (t70) REVERT: J 94 ASP cc_start: 0.8070 (m-30) cc_final: 0.7815 (t0) REVERT: K 121 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8433 (mt-10) REVERT: M 130 ASP cc_start: 0.8180 (m-30) cc_final: 0.7943 (m-30) REVERT: N 130 ASP cc_start: 0.8509 (m-30) cc_final: 0.8290 (m-30) REVERT: O 25 ILE cc_start: 0.8936 (mt) cc_final: 0.8659 (mm) REVERT: O 69 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8269 (tp30) REVERT: P 50 GLN cc_start: 0.8688 (mt0) cc_final: 0.8434 (mt0) REVERT: P 59 ASN cc_start: 0.9066 (t0) cc_final: 0.8613 (t0) REVERT: P 77 ASP cc_start: 0.9021 (m-30) cc_final: 0.8801 (m-30) REVERT: Q 50 GLN cc_start: 0.8646 (mt0) cc_final: 0.8403 (mt0) REVERT: Q 59 ASN cc_start: 0.9089 (t0) cc_final: 0.8720 (t0) REVERT: Q 101 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: S 101 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7530 (tp30) REVERT: S 130 ASP cc_start: 0.8181 (m-30) cc_final: 0.7804 (m-30) REVERT: T 101 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: T 121 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8527 (mt-10) outliers start: 22 outliers final: 11 residues processed: 290 average time/residue: 1.1272 time to fit residues: 375.4322 Evaluate side-chains 295 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 278 time to evaluate : 2.234 ------------------------------------------------------------------------------- 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 F residue 37 VAL 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 J residue 101 GLU Chi-restraints excluded: chain K residue 33 ILE 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 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: 0.6980 chunk 11 optimal weight: 0.0970 chunk 202 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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 = 0.3132 r_free = 0.3132 target = 0.111968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.094627 restraints weight = 22007.435| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 1.47 r_work: 0.2676 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 19280 Z= 0.198 Angle : 0.560 6.848 26420 Z= 0.310 Chirality : 0.046 0.155 3320 Planarity : 0.003 0.025 3360 Dihedral : 5.104 17.704 2700 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.38 % Allowed : 8.03 % 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: 1.38 (0.16), residues: 2620 helix: 2.65 (0.18), residues: 720 sheet: 1.63 (0.17), residues: 960 loop : -1.37 (0.15), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 92 HIS 0.009 0.004 HIS E 68 PHE 0.021 0.002 PHE K 55 TYR 0.012 0.002 TYR P 143 ARG 0.003 0.000 ARG P 124 Details of bonding type rmsd hydrogen bonds : bond 0.07963 ( 915) hydrogen bonds : angle 3.84953 ( 3135) covalent geometry : bond 0.00476 (19280) covalent geometry : angle 0.55974 (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 295 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 2.829 Fit side-chains REVERT: B 50 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8446 (mt0) REVERT: C 90 LYS cc_start: 0.8873 (mtmt) cc_final: 0.8548 (mtmt) REVERT: D 116 SER cc_start: 0.8868 (p) cc_final: 0.8458 (m) REVERT: E 94 ASP cc_start: 0.8093 (m-30) cc_final: 0.7445 (m-30) REVERT: F 59 ASN cc_start: 0.9012 (t0) cc_final: 0.8754 (t0) REVERT: G 59 ASN cc_start: 0.9059 (t0) cc_final: 0.8687 (t0) REVERT: I 25 ILE cc_start: 0.8888 (mt) cc_final: 0.8648 (mm) REVERT: I 50 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: I 101 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7580 (mm-30) REVERT: J 56 ASP cc_start: 0.8843 (t70) cc_final: 0.8541 (t70) REVERT: K 121 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8491 (mt-10) REVERT: M 40 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8128 (tt) REVERT: M 130 ASP cc_start: 0.8264 (m-30) cc_final: 0.8005 (m-30) REVERT: O 25 ILE cc_start: 0.8938 (mt) cc_final: 0.8672 (mm) REVERT: P 59 ASN cc_start: 0.9104 (t0) cc_final: 0.8684 (t0) REVERT: P 77 ASP cc_start: 0.8967 (m-30) cc_final: 0.8739 (m-30) REVERT: Q 50 GLN cc_start: 0.8722 (mt0) cc_final: 0.8495 (mt0) REVERT: Q 59 ASN cc_start: 0.9110 (t0) cc_final: 0.8705 (t160) REVERT: R 101 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: S 101 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7593 (tp30) REVERT: T 94 ASP cc_start: 0.8228 (m-30) cc_final: 0.7775 (m-30) REVERT: T 101 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7883 (mt-10) outliers start: 30 outliers final: 14 residues processed: 275 average time/residue: 1.2807 time to fit residues: 403.6100 Evaluate side-chains 268 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 247 time to evaluate : 3.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE 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 F residue 37 VAL Chi-restraints excluded: chain G 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 J residue 101 GLU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain 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 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: 4.9990 chunk 13 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 157 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 177 optimal weight: 0.9980 chunk 241 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 = 0.3040 r_free = 0.3040 target = 0.105457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.087136 restraints weight = 22753.895| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 1.50 r_work: 0.2678 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19280 Z= 0.178 Angle : 0.535 7.788 26420 Z= 0.296 Chirality : 0.045 0.152 3320 Planarity : 0.003 0.026 3360 Dihedral : 5.057 17.421 2700 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.38 % Allowed : 9.08 % Favored : 89.54 % 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: 1.29 (0.16), residues: 2620 helix: 2.84 (0.18), residues: 700 sheet: 1.50 (0.17), residues: 960 loop : -1.49 (0.14), residues: 960 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 0.019 0.002 PHE K 55 TYR 0.013 0.001 TYR P 143 ARG 0.002 0.000 ARG P 124 Details of bonding type rmsd hydrogen bonds : bond 0.07473 ( 915) hydrogen bonds : angle 3.76400 ( 3135) covalent geometry : bond 0.00424 (19280) covalent geometry : angle 0.53540 (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 280 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 2.003 Fit side-chains REVERT: A 40 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8361 (tp) REVERT: B 50 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8455 (mt0) REVERT: D 116 SER cc_start: 0.8858 (p) cc_final: 0.8441 (m) REVERT: F 59 ASN cc_start: 0.9039 (t0) cc_final: 0.8789 (t0) REVERT: G 59 ASN cc_start: 0.9042 (t0) cc_final: 0.8673 (t0) REVERT: H 40 LEU cc_start: 0.8308 (tt) cc_final: 0.7920 (mt) REVERT: I 25 ILE cc_start: 0.8872 (mt) cc_final: 0.8623 (mm) REVERT: I 50 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: I 101 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7588 (mm-30) REVERT: J 56 ASP cc_start: 0.8824 (t70) cc_final: 0.8538 (t70) REVERT: K 121 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8474 (mt-10) REVERT: L 25 ILE cc_start: 0.8572 (mt) cc_final: 0.8259 (tp) REVERT: M 40 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8114 (tt) REVERT: M 130 ASP cc_start: 0.8279 (m-30) cc_final: 0.8034 (m-30) REVERT: N 25 ILE cc_start: 0.8969 (mt) cc_final: 0.8570 (mm) REVERT: O 25 ILE cc_start: 0.8959 (mt) cc_final: 0.8679 (mm) REVERT: P 59 ASN cc_start: 0.9108 (t0) cc_final: 0.8679 (t0) REVERT: P 77 ASP cc_start: 0.8886 (m-30) cc_final: 0.8661 (m-30) REVERT: Q 50 GLN cc_start: 0.8734 (mt0) cc_final: 0.8515 (mt0) REVERT: Q 59 ASN cc_start: 0.9111 (t0) cc_final: 0.8701 (t160) REVERT: R 101 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7747 (mm-30) REVERT: S 101 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7599 (tp30) REVERT: T 94 ASP cc_start: 0.8155 (m-30) cc_final: 0.7736 (m-30) REVERT: T 101 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7886 (mt-10) outliers start: 30 outliers final: 15 residues processed: 261 average time/residue: 1.1578 time to fit residues: 344.2967 Evaluate side-chains 269 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 40 LEU 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 F residue 37 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 223 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3073 r_free = 0.3073 target = 0.108038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.088632 restraints weight = 22601.532| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.64 r_work: 0.2729 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19280 Z= 0.120 Angle : 0.463 7.622 26420 Z= 0.256 Chirality : 0.043 0.161 3320 Planarity : 0.003 0.025 3360 Dihedral : 4.627 18.401 2700 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.10 % Allowed : 9.59 % Favored : 89.31 % 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: 1.58 (0.16), residues: 2620 helix: 3.25 (0.18), residues: 700 sheet: 1.66 (0.17), residues: 960 loop : -1.45 (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 0.011 0.001 PHE K 55 TYR 0.009 0.001 TYR P 143 ARG 0.001 0.000 ARG A 124 Details of bonding type rmsd hydrogen bonds : bond 0.05888 ( 915) hydrogen bonds : angle 3.43029 ( 3135) covalent geometry : bond 0.00269 (19280) covalent geometry : angle 0.46316 (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 285 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 261 time to evaluate : 2.021 Fit side-chains REVERT: A 56 ASP cc_start: 0.8411 (t70) cc_final: 0.8181 (t70) REVERT: B 50 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8524 (mt0) REVERT: C 90 LYS cc_start: 0.8811 (mtmt) cc_final: 0.8464 (mtmt) REVERT: D 116 SER cc_start: 0.8722 (p) cc_final: 0.8266 (m) REVERT: E 94 ASP cc_start: 0.7996 (m-30) cc_final: 0.7386 (m-30) REVERT: F 59 ASN cc_start: 0.9014 (t0) cc_final: 0.8750 (t0) REVERT: G 59 ASN cc_start: 0.9000 (t0) cc_final: 0.8633 (t0) REVERT: I 25 ILE cc_start: 0.8842 (mt) cc_final: 0.8580 (mm) REVERT: I 50 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8599 (mt0) REVERT: J 56 ASP cc_start: 0.8760 (t70) cc_final: 0.8468 (t70) REVERT: J 94 ASP cc_start: 0.8043 (m-30) cc_final: 0.7763 (t0) REVERT: L 25 ILE cc_start: 0.8501 (mt) cc_final: 0.8176 (tp) REVERT: M 130 ASP cc_start: 0.8211 (m-30) cc_final: 0.7949 (m-30) REVERT: N 25 ILE cc_start: 0.8894 (mt) cc_final: 0.8469 (mm) REVERT: O 25 ILE cc_start: 0.8905 (mt) cc_final: 0.8623 (mm) REVERT: P 59 ASN cc_start: 0.9041 (t0) cc_final: 0.8629 (t0) REVERT: P 77 ASP cc_start: 0.8956 (m-30) cc_final: 0.8724 (m-30) REVERT: Q 50 GLN cc_start: 0.8694 (mt0) cc_final: 0.8470 (mt0) REVERT: Q 59 ASN cc_start: 0.9095 (t0) cc_final: 0.8691 (t160) REVERT: R 101 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7660 (mm-30) REVERT: S 101 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7552 (tp30) REVERT: T 101 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7851 (mt-10) outliers start: 24 outliers final: 13 residues processed: 269 average time/residue: 1.1123 time to fit residues: 341.9814 Evaluate side-chains 274 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 256 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE 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 F residue 37 VAL 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 J residue 101 GLU 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 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: 3.9990 chunk 198 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 175 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 227 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 P 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.112205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.094876 restraints weight = 22059.260| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 1.47 r_work: 0.2683 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 19280 Z= 0.179 Angle : 0.539 8.357 26420 Z= 0.297 Chirality : 0.046 0.172 3320 Planarity : 0.003 0.027 3360 Dihedral : 4.984 19.899 2700 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.28 % Allowed : 9.82 % 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: 1.25 (0.16), residues: 2620 helix: 2.70 (0.18), residues: 720 sheet: 1.48 (0.17), residues: 960 loop : -1.51 (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 0.014 0.001 TYR P 143 ARG 0.002 0.000 ARG P 124 Details of bonding type rmsd hydrogen bonds : bond 0.07544 ( 915) hydrogen bonds : angle 3.75864 ( 3135) covalent geometry : bond 0.00427 (19280) covalent geometry : angle 0.53891 (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 286 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 2.050 Fit side-chains REVERT: B 50 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8451 (mt0) REVERT: D 116 SER cc_start: 0.8854 (p) cc_final: 0.8445 (m) REVERT: F 59 ASN cc_start: 0.9050 (t0) cc_final: 0.8809 (t0) REVERT: G 59 ASN cc_start: 0.9039 (t0) cc_final: 0.8677 (t0) REVERT: H 40 LEU cc_start: 0.8320 (tt) cc_final: 0.7946 (mt) REVERT: H 101 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7922 (mt-10) REVERT: I 25 ILE cc_start: 0.8904 (mt) cc_final: 0.8655 (mm) REVERT: I 50 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: J 56 ASP cc_start: 0.8831 (t70) cc_final: 0.8535 (t70) REVERT: L 25 ILE cc_start: 0.8564 (mt) cc_final: 0.8241 (tp) REVERT: M 130 ASP cc_start: 0.8268 (m-30) cc_final: 0.8001 (m-30) REVERT: N 25 ILE cc_start: 0.8969 (mt) cc_final: 0.8568 (mm) REVERT: O 25 ILE cc_start: 0.8934 (mt) cc_final: 0.8675 (mm) REVERT: P 59 ASN cc_start: 0.9117 (t0) cc_final: 0.8703 (t0) REVERT: P 77 ASP cc_start: 0.8892 (m-30) cc_final: 0.8665 (m-30) REVERT: Q 50 GLN cc_start: 0.8731 (mt0) cc_final: 0.8519 (mt0) REVERT: Q 59 ASN cc_start: 0.9109 (t0) cc_final: 0.8696 (t160) REVERT: R 101 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7648 (mm-30) REVERT: S 101 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7553 (tp30) REVERT: T 94 ASP cc_start: 0.8093 (m-30) cc_final: 0.7697 (m-30) REVERT: T 101 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7880 (mt-10) outliers start: 28 outliers final: 14 residues processed: 271 average time/residue: 1.1959 time to fit residues: 370.7867 Evaluate side-chains 272 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 252 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE 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 F residue 37 VAL 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 J residue 101 GLU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 16 VAL 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 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: 0.7980 chunk 125 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 251 optimal weight: 3.9990 chunk 120 optimal weight: 20.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 P 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.106135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.086706 restraints weight = 22813.065| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 1.64 r_work: 0.2699 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19280 Z= 0.143 Angle : 0.504 8.004 26420 Z= 0.277 Chirality : 0.044 0.188 3320 Planarity : 0.003 0.027 3360 Dihedral : 4.809 19.425 2700 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.06 % Allowed : 10.00 % Favored : 88.94 % 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: 2.87 (0.18), residues: 720 sheet: 1.55 (0.17), residues: 960 loop : -1.46 (0.15), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 92 HIS 0.006 0.003 HIS E 68 PHE 0.014 0.002 PHE K 55 TYR 0.013 0.001 TYR P 143 ARG 0.002 0.000 ARG P 124 Details of bonding type rmsd hydrogen bonds : bond 0.06641 ( 915) hydrogen bonds : angle 3.58404 ( 3135) covalent geometry : bond 0.00328 (19280) covalent geometry : angle 0.50370 (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 277 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 254 time to evaluate : 2.131 Fit side-chains REVERT: B 50 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8466 (mt0) REVERT: D 116 SER cc_start: 0.8778 (p) cc_final: 0.8326 (m) REVERT: F 59 ASN cc_start: 0.9032 (t0) cc_final: 0.8741 (t0) REVERT: G 59 ASN cc_start: 0.9027 (t0) cc_final: 0.8666 (t0) REVERT: I 25 ILE cc_start: 0.8840 (mt) cc_final: 0.8573 (mm) REVERT: I 50 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8517 (mt0) REVERT: J 56 ASP cc_start: 0.8803 (t70) cc_final: 0.8501 (t70) REVERT: J 94 ASP cc_start: 0.8077 (m-30) cc_final: 0.7785 (t0) REVERT: K 121 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8443 (mt-10) REVERT: L 25 ILE cc_start: 0.8526 (mt) cc_final: 0.8178 (tp) REVERT: M 40 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7993 (tt) REVERT: M 130 ASP cc_start: 0.8255 (m-30) cc_final: 0.7993 (m-30) REVERT: N 25 ILE cc_start: 0.8896 (mt) cc_final: 0.8496 (mm) REVERT: O 25 ILE cc_start: 0.8915 (mt) cc_final: 0.8629 (mm) REVERT: P 59 ASN cc_start: 0.9052 (t0) cc_final: 0.8659 (t0) REVERT: P 77 ASP cc_start: 0.8898 (m-30) cc_final: 0.8669 (m-30) REVERT: Q 50 GLN cc_start: 0.8718 (mt0) cc_final: 0.8493 (mt0) REVERT: Q 59 ASN cc_start: 0.9107 (t0) cc_final: 0.8698 (t160) REVERT: R 101 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7549 (mm-30) REVERT: S 101 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7587 (tp30) REVERT: T 101 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7884 (mt-10) outliers start: 23 outliers final: 15 residues processed: 263 average time/residue: 1.0985 time to fit residues: 331.1830 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 : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE 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 F residue 37 VAL 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 I residue 50 GLN 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 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: 10.0000 chunk 60 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 247 optimal weight: 0.3980 chunk 64 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 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 P 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.108901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.089552 restraints weight = 22519.569| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.64 r_work: 0.2737 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19280 Z= 0.109 Angle : 0.461 8.496 26420 Z= 0.252 Chirality : 0.042 0.161 3320 Planarity : 0.003 0.026 3360 Dihedral : 4.497 18.180 2700 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.87 % Allowed : 10.09 % Favored : 89.04 % 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: 1.77 (0.16), residues: 2620 helix: 3.38 (0.18), residues: 700 sheet: 1.88 (0.17), residues: 940 loop : -1.36 (0.15), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 141 HIS 0.004 0.002 HIS E 68 PHE 0.010 0.001 PHE K 55 TYR 0.010 0.001 TYR P 143 ARG 0.001 0.000 ARG P 124 Details of bonding type rmsd hydrogen bonds : bond 0.05450 ( 915) hydrogen bonds : angle 3.33033 ( 3135) covalent geometry : bond 0.00233 (19280) covalent geometry : angle 0.46113 (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 282 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 263 time to evaluate : 2.250 Fit side-chains REVERT: A 56 ASP cc_start: 0.8375 (t70) cc_final: 0.8168 (t70) REVERT: B 50 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8442 (mt0) REVERT: C 90 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8465 (mtmt) REVERT: D 116 SER cc_start: 0.8722 (p) cc_final: 0.8264 (m) REVERT: E 94 ASP cc_start: 0.7983 (m-30) cc_final: 0.7337 (m-30) REVERT: F 59 ASN cc_start: 0.9007 (t0) cc_final: 0.8742 (t0) REVERT: G 59 ASN cc_start: 0.8986 (t0) cc_final: 0.8622 (t0) REVERT: I 50 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8594 (mt0) REVERT: J 56 ASP cc_start: 0.8502 (t70) cc_final: 0.8220 (t70) REVERT: J 94 ASP cc_start: 0.8046 (m-30) cc_final: 0.7789 (t0) REVERT: L 25 ILE cc_start: 0.8493 (mt) cc_final: 0.8161 (tp) REVERT: M 130 ASP cc_start: 0.8227 (m-30) cc_final: 0.7968 (m-30) REVERT: N 25 ILE cc_start: 0.8822 (mt) cc_final: 0.8423 (mm) REVERT: O 25 ILE cc_start: 0.8898 (mt) cc_final: 0.8598 (mm) REVERT: P 59 ASN cc_start: 0.9040 (t0) cc_final: 0.8623 (t0) REVERT: P 77 ASP cc_start: 0.8876 (m-30) cc_final: 0.8644 (m-30) REVERT: Q 50 GLN cc_start: 0.8680 (mt0) cc_final: 0.8455 (mt0) REVERT: Q 59 ASN cc_start: 0.9081 (t0) cc_final: 0.8777 (t0) REVERT: R 101 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7649 (mm-30) REVERT: S 101 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7602 (tp30) REVERT: T 101 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7855 (mt-10) outliers start: 19 outliers final: 15 residues processed: 267 average time/residue: 1.1882 time to fit residues: 362.2532 Evaluate side-chains 284 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 264 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 33 ILE 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 F residue 37 VAL 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 I residue 50 GLN 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 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: 3.9990 chunk 113 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 141 optimal weight: 0.0980 chunk 160 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 34 optimal weight: 6.9990 chunk 222 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 185 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 P 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.107475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.088075 restraints weight = 22742.065| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.64 r_work: 0.2720 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2038 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= 0.126 Angle : 0.485 8.461 26420 Z= 0.265 Chirality : 0.043 0.168 3320 Planarity : 0.003 0.027 3360 Dihedral : 4.594 18.391 2700 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.92 % Allowed : 10.14 % Favored : 88.94 % 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: 1.73 (0.16), residues: 2620 helix: 3.10 (0.18), residues: 720 sheet: 1.88 (0.17), residues: 940 loop : -1.32 (0.15), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 92 HIS 0.005 0.002 HIS E 68 PHE 0.014 0.001 PHE K 55 TYR 0.011 0.001 TYR P 143 ARG 0.001 0.000 ARG P 124 Details of bonding type rmsd hydrogen bonds : bond 0.06067 ( 915) hydrogen bonds : angle 3.43463 ( 3135) covalent geometry : bond 0.00283 (19280) covalent geometry : angle 0.48550 (26420) =============================================================================== Job complete usr+sys time: 13091.99 seconds wall clock time: 228 minutes 49.50 seconds (13729.50 seconds total)