Starting phenix.real_space_refine on Fri Sep 19 09:02:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5z1l_6876/09_2025/5z1l_6876.cif Found real_map, /net/cci-nas-00/data/ceres_data/5z1l_6876/09_2025/5z1l_6876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5z1l_6876/09_2025/5z1l_6876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5z1l_6876/09_2025/5z1l_6876.map" model { file = "/net/cci-nas-00/data/ceres_data/5z1l_6876/09_2025/5z1l_6876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5z1l_6876/09_2025/5z1l_6876.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= -0.000 sd= 1.000 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 54 5.16 5 C 16038 2.51 5 N 4122 2.21 5 O 5346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25560 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1420 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R Time building chain proxies: 2.25, per 1000 atoms: 0.09 Number of scatterers: 25560 At special positions: 0 Unit cell: (117.03, 114.21, 221.37, 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 54 16.00 O 5346 8.00 N 4122 7.00 C 16038 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: 2.05 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6444 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 54 sheets defined 28.6% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 4 through 27 removed outlier: 3.748A pdb=" N ILE A 8 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA A 12 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 48 removed outlier: 4.393A pdb=" N LEU A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.171A pdb=" N ASN A 116 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'B' and resid 4 through 27 removed outlier: 3.749A pdb=" N ILE B 8 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL B 9 " --> pdb=" O GLY B 5 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA B 12 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 48 removed outlier: 4.393A pdb=" N LEU B 31 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR B 37 " --> pdb=" O GLN B 33 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B 38 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B 40 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN B 45 " --> pdb=" O GLU B 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 4.171A pdb=" N ASN B 116 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'C' and resid 4 through 27 removed outlier: 3.748A pdb=" N ILE C 8 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL C 9 " --> pdb=" O GLY C 5 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA C 12 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 48 removed outlier: 4.393A pdb=" N LEU C 31 " --> pdb=" O THR C 27 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR C 37 " --> pdb=" O GLN C 33 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR C 38 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS C 40 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN C 45 " --> pdb=" O GLU C 41 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.171A pdb=" N ASN C 116 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'D' and resid 4 through 27 removed outlier: 3.748A pdb=" N ILE D 8 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL D 9 " --> pdb=" O GLY D 5 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA D 12 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 48 removed outlier: 4.393A pdb=" N LEU D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR D 37 " --> pdb=" O GLN D 33 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR D 38 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS D 40 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN D 45 " --> pdb=" O GLU D 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 46 " --> pdb=" O SER D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 4.171A pdb=" N ASN D 116 " --> pdb=" O VAL D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.748A pdb=" N ILE E 8 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL E 9 " --> pdb=" O GLY E 5 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA E 12 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 48 removed outlier: 4.393A pdb=" N LEU E 31 " --> pdb=" O THR E 27 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR E 37 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR E 38 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY E 39 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS E 40 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU E 44 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN E 45 " --> pdb=" O GLU E 41 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 46 " --> pdb=" O SER E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 116 removed outlier: 4.171A pdb=" N ASN E 116 " --> pdb=" O VAL E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 160 Processing helix chain 'F' and resid 4 through 27 removed outlier: 3.747A pdb=" N ILE F 8 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL F 9 " --> pdb=" O GLY F 5 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE F 11 " --> pdb=" O LEU F 7 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA F 12 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 48 removed outlier: 4.393A pdb=" N LEU F 31 " --> pdb=" O THR F 27 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR F 37 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS F 40 " --> pdb=" O SER F 36 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 116 removed outlier: 4.171A pdb=" N ASN F 116 " --> pdb=" O VAL F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 160 Processing helix chain 'G' and resid 4 through 27 removed outlier: 3.748A pdb=" N ILE G 8 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL G 9 " --> pdb=" O GLY G 5 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE G 11 " --> pdb=" O LEU G 7 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA G 12 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 48 removed outlier: 4.393A pdb=" N LEU G 31 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR G 37 " --> pdb=" O GLN G 33 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY G 39 " --> pdb=" O ALA G 35 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS G 40 " --> pdb=" O SER G 36 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU G 44 " --> pdb=" O LYS G 40 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN G 45 " --> pdb=" O GLU G 41 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL G 46 " --> pdb=" O SER G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 removed outlier: 4.171A pdb=" N ASN G 116 " --> pdb=" O VAL G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 160 Processing helix chain 'H' and resid 4 through 27 removed outlier: 3.748A pdb=" N ILE H 8 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL H 9 " --> pdb=" O GLY H 5 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE H 11 " --> pdb=" O LEU H 7 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA H 12 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 48 removed outlier: 4.393A pdb=" N LEU H 31 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR H 37 " --> pdb=" O GLN H 33 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR H 38 " --> pdb=" O LYS H 34 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS H 40 " --> pdb=" O SER H 36 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN H 45 " --> pdb=" O GLU H 41 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL H 46 " --> pdb=" O SER H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 116 removed outlier: 4.171A pdb=" N ASN H 116 " --> pdb=" O VAL H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 160 Processing helix chain 'I' and resid 4 through 27 removed outlier: 3.748A pdb=" N ILE I 8 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL I 9 " --> pdb=" O GLY I 5 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE I 11 " --> pdb=" O LEU I 7 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA I 12 " --> pdb=" O ILE I 8 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 48 removed outlier: 4.392A pdb=" N LEU I 31 " --> pdb=" O THR I 27 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR I 37 " --> pdb=" O GLN I 33 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR I 38 " --> pdb=" O LYS I 34 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY I 39 " --> pdb=" O ALA I 35 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS I 40 " --> pdb=" O SER I 36 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU I 44 " --> pdb=" O LYS I 40 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN I 45 " --> pdb=" O GLU I 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL I 46 " --> pdb=" O SER I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 116 removed outlier: 4.171A pdb=" N ASN I 116 " --> pdb=" O VAL I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 160 Processing helix chain 'J' and resid 4 through 27 removed outlier: 3.748A pdb=" N ILE J 8 " --> pdb=" O ILE J 4 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL J 9 " --> pdb=" O GLY J 5 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE J 11 " --> pdb=" O LEU J 7 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA J 12 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 48 removed outlier: 4.394A pdb=" N LEU J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR J 37 " --> pdb=" O GLN J 33 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR J 38 " --> pdb=" O LYS J 34 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS J 40 " --> pdb=" O SER J 36 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU J 44 " --> pdb=" O LYS J 40 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN J 45 " --> pdb=" O GLU J 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL J 46 " --> pdb=" O SER J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 116 removed outlier: 4.171A pdb=" N ASN J 116 " --> pdb=" O VAL J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 160 Processing helix chain 'K' and resid 4 through 27 removed outlier: 3.748A pdb=" N ILE K 8 " --> pdb=" O ILE K 4 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL K 9 " --> pdb=" O GLY K 5 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE K 11 " --> pdb=" O LEU K 7 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA K 12 " --> pdb=" O ILE K 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 48 removed outlier: 4.393A pdb=" N LEU K 31 " --> pdb=" O THR K 27 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR K 37 " --> pdb=" O GLN K 33 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR K 38 " --> pdb=" O LYS K 34 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY K 39 " --> pdb=" O ALA K 35 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS K 40 " --> pdb=" O SER K 36 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU K 44 " --> pdb=" O LYS K 40 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN K 45 " --> pdb=" O GLU K 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL K 46 " --> pdb=" O SER K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 116 removed outlier: 4.171A pdb=" N ASN K 116 " --> pdb=" O VAL K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 160 Processing helix chain 'L' and resid 4 through 27 removed outlier: 3.748A pdb=" N ILE L 8 " --> pdb=" O ILE L 4 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL L 9 " --> pdb=" O GLY L 5 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 48 removed outlier: 4.393A pdb=" N LEU L 31 " --> pdb=" O THR L 27 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR L 37 " --> pdb=" O GLN L 33 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR L 38 " --> pdb=" O LYS L 34 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY L 39 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS L 40 " --> pdb=" O SER L 36 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU L 44 " --> pdb=" O LYS L 40 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN L 45 " --> pdb=" O GLU L 41 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL L 46 " --> pdb=" O SER L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 116 removed outlier: 4.171A pdb=" N ASN L 116 " --> pdb=" O VAL L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 155 through 160 Processing helix chain 'M' and resid 4 through 27 removed outlier: 3.748A pdb=" N ILE M 8 " --> pdb=" O ILE M 4 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL M 9 " --> pdb=" O GLY M 5 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE M 11 " --> pdb=" O LEU M 7 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA M 12 " --> pdb=" O ILE M 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU M 24 " --> pdb=" O ALA M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 48 removed outlier: 4.392A pdb=" N LEU M 31 " --> pdb=" O THR M 27 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR M 37 " --> pdb=" O GLN M 33 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR M 38 " --> pdb=" O LYS M 34 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY M 39 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS M 40 " --> pdb=" O SER M 36 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU M 44 " --> pdb=" O LYS M 40 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN M 45 " --> pdb=" O GLU M 41 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL M 46 " --> pdb=" O SER M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 116 removed outlier: 4.170A pdb=" N ASN M 116 " --> pdb=" O VAL M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 155 through 160 Processing helix chain 'N' and resid 4 through 27 removed outlier: 3.748A pdb=" N ILE N 8 " --> pdb=" O ILE N 4 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL N 9 " --> pdb=" O GLY N 5 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE N 11 " --> pdb=" O LEU N 7 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA N 12 " --> pdb=" O ILE N 8 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU N 24 " --> pdb=" O ALA N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 48 removed outlier: 4.393A pdb=" N LEU N 31 " --> pdb=" O THR N 27 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR N 37 " --> pdb=" O GLN N 33 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR N 38 " --> pdb=" O LYS N 34 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY N 39 " --> pdb=" O ALA N 35 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS N 40 " --> pdb=" O SER N 36 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN N 45 " --> pdb=" O GLU N 41 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL N 46 " --> pdb=" O SER N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 116 removed outlier: 4.171A pdb=" N ASN N 116 " --> pdb=" O VAL N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 155 through 160 Processing helix chain 'O' and resid 4 through 27 removed outlier: 3.748A pdb=" N ILE O 8 " --> pdb=" O ILE O 4 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL O 9 " --> pdb=" O GLY O 5 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE O 11 " --> pdb=" O LEU O 7 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA O 12 " --> pdb=" O ILE O 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU O 24 " --> pdb=" O ALA O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 27 through 48 removed outlier: 4.393A pdb=" N LEU O 31 " --> pdb=" O THR O 27 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR O 37 " --> pdb=" O GLN O 33 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR O 38 " --> pdb=" O LYS O 34 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY O 39 " --> pdb=" O ALA O 35 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS O 40 " --> pdb=" O SER O 36 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU O 44 " --> pdb=" O LYS O 40 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN O 45 " --> pdb=" O GLU O 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL O 46 " --> pdb=" O SER O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 116 removed outlier: 4.170A pdb=" N ASN O 116 " --> pdb=" O VAL O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 155 through 160 Processing helix chain 'P' and resid 4 through 27 removed outlier: 3.748A pdb=" N ILE P 8 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL P 9 " --> pdb=" O GLY P 5 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA P 12 " --> pdb=" O ILE P 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU P 24 " --> pdb=" O ALA P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 27 through 48 removed outlier: 4.392A pdb=" N LEU P 31 " --> pdb=" O THR P 27 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR P 37 " --> pdb=" O GLN P 33 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR P 38 " --> pdb=" O LYS P 34 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY P 39 " --> pdb=" O ALA P 35 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS P 40 " --> pdb=" O SER P 36 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU P 44 " --> pdb=" O LYS P 40 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN P 45 " --> pdb=" O GLU P 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL P 46 " --> pdb=" O SER P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 116 removed outlier: 4.171A pdb=" N ASN P 116 " --> pdb=" O VAL P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 155 through 160 Processing helix chain 'Q' and resid 4 through 27 removed outlier: 3.748A pdb=" N ILE Q 8 " --> pdb=" O ILE Q 4 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL Q 9 " --> pdb=" O GLY Q 5 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE Q 11 " --> pdb=" O LEU Q 7 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU Q 24 " --> pdb=" O ALA Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 48 removed outlier: 4.393A pdb=" N LEU Q 31 " --> pdb=" O THR Q 27 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR Q 37 " --> pdb=" O GLN Q 33 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR Q 38 " --> pdb=" O LYS Q 34 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY Q 39 " --> pdb=" O ALA Q 35 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS Q 40 " --> pdb=" O SER Q 36 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU Q 44 " --> pdb=" O LYS Q 40 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN Q 45 " --> pdb=" O GLU Q 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL Q 46 " --> pdb=" O SER Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 116 removed outlier: 4.171A pdb=" N ASN Q 116 " --> pdb=" O VAL Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 155 through 160 Processing helix chain 'R' and resid 4 through 27 removed outlier: 3.748A pdb=" N ILE R 8 " --> pdb=" O ILE R 4 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL R 9 " --> pdb=" O GLY R 5 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ILE R 11 " --> pdb=" O LEU R 7 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA R 12 " --> pdb=" O ILE R 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU R 24 " --> pdb=" O ALA R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 48 removed outlier: 4.392A pdb=" N LEU R 31 " --> pdb=" O THR R 27 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR R 37 " --> pdb=" O GLN R 33 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR R 38 " --> pdb=" O LYS R 34 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS R 40 " --> pdb=" O SER R 36 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU R 44 " --> pdb=" O LYS R 40 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN R 45 " --> pdb=" O GLU R 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL R 46 " --> pdb=" O SER R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 116 removed outlier: 4.171A pdb=" N ASN R 116 " --> pdb=" O VAL R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 160 Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 105 removed outlier: 7.047A pdb=" N GLY A 99 " --> pdb=" O PHE A 125 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N VAL A 127 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N GLY A 101 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE A 129 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 13.989A pdb=" N ASN A 103 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 14.861A pdb=" N GLN A 131 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 12.202A pdb=" N ASP A 105 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR A 124 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP A 154 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA A 148 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 66 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY A 54 " --> pdb=" O TYR A 70 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA A 72 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE A 52 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY A 57 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU A 197 " --> pdb=" O GLY A 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 97 removed outlier: 3.584A pdb=" N ASP A 90 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER A 170 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 171 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 99 through 105 removed outlier: 7.046A pdb=" N GLY B 99 " --> pdb=" O PHE B 125 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N VAL B 127 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY B 101 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE B 129 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 13.990A pdb=" N ASN B 103 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 14.861A pdb=" N GLN B 131 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 12.201A pdb=" N ASP B 105 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR B 124 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP B 154 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA B 148 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 66 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLY B 54 " --> pdb=" O TYR B 70 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA B 72 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE B 52 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY B 57 " --> pdb=" O GLU B 197 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU B 197 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'B' and resid 94 through 97 removed outlier: 3.584A pdb=" N ASP B 90 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER B 170 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 171 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 99 through 105 removed outlier: 7.047A pdb=" N GLY C 99 " --> pdb=" O PHE C 125 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N VAL C 127 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY C 101 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE C 129 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 13.990A pdb=" N ASN C 103 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 14.860A pdb=" N GLN C 131 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 12.201A pdb=" N ASP C 105 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR C 124 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP C 154 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA C 148 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU C 66 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY C 54 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA C 72 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE C 52 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY C 57 " --> pdb=" O GLU C 197 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU C 197 " --> pdb=" O GLY C 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AA9, first strand: chain 'C' and resid 94 through 97 removed outlier: 3.584A pdb=" N ASP C 90 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER C 170 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY C 171 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 99 through 105 removed outlier: 7.046A pdb=" N GLY D 99 " --> pdb=" O PHE D 125 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N VAL D 127 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY D 101 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE D 129 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 13.989A pdb=" N ASN D 103 " --> pdb=" O ILE D 129 " (cutoff:3.500A) removed outlier: 14.860A pdb=" N GLN D 131 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 12.202A pdb=" N ASP D 105 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR D 124 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP D 154 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA D 148 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU D 66 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLY D 54 " --> pdb=" O TYR D 70 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA D 72 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE D 52 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY D 57 " --> pdb=" O GLU D 197 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLU D 197 " --> pdb=" O GLY D 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AB3, first strand: chain 'D' and resid 94 through 97 removed outlier: 3.585A pdb=" N ASP D 90 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER D 170 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY D 171 " --> pdb=" O ILE D 183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 99 through 105 removed outlier: 7.046A pdb=" N GLY E 99 " --> pdb=" O PHE E 125 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N VAL E 127 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N GLY E 101 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE E 129 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 13.990A pdb=" N ASN E 103 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 14.861A pdb=" N GLN E 131 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 12.201A pdb=" N ASP E 105 " --> pdb=" O GLN E 131 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR E 124 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP E 154 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA E 148 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU E 66 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLY E 54 " --> pdb=" O TYR E 70 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA E 72 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE E 52 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY E 57 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU E 197 " --> pdb=" O GLY E 57 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 80 through 81 Processing sheet with id=AB6, first strand: chain 'E' and resid 94 through 97 removed outlier: 3.585A pdb=" N ASP E 90 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER E 170 " --> pdb=" O ASP E 90 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY E 171 " --> pdb=" O ILE E 183 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 99 through 105 removed outlier: 7.046A pdb=" N GLY F 99 " --> pdb=" O PHE F 125 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N VAL F 127 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY F 101 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 11.757A pdb=" N ILE F 129 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 13.989A pdb=" N ASN F 103 " --> pdb=" O ILE F 129 " (cutoff:3.500A) removed outlier: 14.861A pdb=" N GLN F 131 " --> pdb=" O ASN F 103 " (cutoff:3.500A) removed outlier: 12.202A pdb=" N ASP F 105 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR F 124 " --> pdb=" O ASP F 154 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP F 154 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA F 148 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU F 66 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY F 54 " --> pdb=" O TYR F 70 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA F 72 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE F 52 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY F 57 " --> pdb=" O GLU F 197 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLU F 197 " --> pdb=" O GLY F 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 80 through 81 Processing sheet with id=AB9, first strand: chain 'F' and resid 94 through 97 removed outlier: 3.584A pdb=" N ASP F 90 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER F 170 " --> pdb=" O ASP F 90 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY F 171 " --> pdb=" O ILE F 183 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 99 through 105 removed outlier: 7.047A pdb=" N GLY G 99 " --> pdb=" O PHE G 125 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N VAL G 127 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N GLY G 101 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE G 129 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 13.989A pdb=" N ASN G 103 " --> pdb=" O ILE G 129 " (cutoff:3.500A) removed outlier: 14.860A pdb=" N GLN G 131 " --> pdb=" O ASN G 103 " (cutoff:3.500A) removed outlier: 12.202A pdb=" N ASP G 105 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR G 124 " --> pdb=" O ASP G 154 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP G 154 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA G 148 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU G 66 " --> pdb=" O SER G 58 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY G 54 " --> pdb=" O TYR G 70 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA G 72 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE G 52 " --> pdb=" O ALA G 72 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY G 57 " --> pdb=" O GLU G 197 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU G 197 " --> pdb=" O GLY G 57 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 80 through 81 Processing sheet with id=AC3, first strand: chain 'G' and resid 94 through 97 removed outlier: 3.584A pdb=" N ASP G 90 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER G 170 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY G 171 " --> pdb=" O ILE G 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 99 through 105 removed outlier: 7.046A pdb=" N GLY H 99 " --> pdb=" O PHE H 125 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N VAL H 127 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY H 101 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE H 129 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 13.988A pdb=" N ASN H 103 " --> pdb=" O ILE H 129 " (cutoff:3.500A) removed outlier: 14.860A pdb=" N GLN H 131 " --> pdb=" O ASN H 103 " (cutoff:3.500A) removed outlier: 12.202A pdb=" N ASP H 105 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR H 124 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP H 154 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA H 148 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU H 66 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLY H 54 " --> pdb=" O TYR H 70 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA H 72 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE H 52 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY H 57 " --> pdb=" O GLU H 197 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU H 197 " --> pdb=" O GLY H 57 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 80 through 81 Processing sheet with id=AC6, first strand: chain 'H' and resid 94 through 97 removed outlier: 3.584A pdb=" N ASP H 90 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER H 170 " --> pdb=" O ASP H 90 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY H 171 " --> pdb=" O ILE H 183 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 99 through 105 removed outlier: 7.046A pdb=" N GLY I 99 " --> pdb=" O PHE I 125 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N VAL I 127 " --> pdb=" O GLY I 99 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY I 101 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE I 129 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 13.990A pdb=" N ASN I 103 " --> pdb=" O ILE I 129 " (cutoff:3.500A) removed outlier: 14.861A pdb=" N GLN I 131 " --> pdb=" O ASN I 103 " (cutoff:3.500A) removed outlier: 12.201A pdb=" N ASP I 105 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR I 124 " --> pdb=" O ASP I 154 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP I 154 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA I 148 " --> pdb=" O LEU I 130 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU I 66 " --> pdb=" O SER I 58 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLY I 54 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA I 72 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE I 52 " --> pdb=" O ALA I 72 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY I 57 " --> pdb=" O GLU I 197 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU I 197 " --> pdb=" O GLY I 57 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AC9, first strand: chain 'I' and resid 94 through 97 removed outlier: 3.585A pdb=" N ASP I 90 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER I 170 " --> pdb=" O ASP I 90 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY I 171 " --> pdb=" O ILE I 183 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 99 through 105 removed outlier: 7.047A pdb=" N GLY J 99 " --> pdb=" O PHE J 125 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N VAL J 127 " --> pdb=" O GLY J 99 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY J 101 " --> pdb=" O VAL J 127 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE J 129 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 13.989A pdb=" N ASN J 103 " --> pdb=" O ILE J 129 " (cutoff:3.500A) removed outlier: 14.860A pdb=" N GLN J 131 " --> pdb=" O ASN J 103 " (cutoff:3.500A) removed outlier: 12.201A pdb=" N ASP J 105 " --> pdb=" O GLN J 131 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR J 124 " --> pdb=" O ASP J 154 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP J 154 " --> pdb=" O THR J 124 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA J 148 " --> pdb=" O LEU J 130 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU J 66 " --> pdb=" O SER J 58 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY J 54 " --> pdb=" O TYR J 70 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA J 72 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE J 52 " --> pdb=" O ALA J 72 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY J 57 " --> pdb=" O GLU J 197 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLU J 197 " --> pdb=" O GLY J 57 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 80 through 81 Processing sheet with id=AD3, first strand: chain 'J' and resid 94 through 97 removed outlier: 3.584A pdb=" N ASP J 90 " --> pdb=" O SER J 170 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER J 170 " --> pdb=" O ASP J 90 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY J 171 " --> pdb=" O ILE J 183 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 99 through 105 removed outlier: 7.047A pdb=" N GLY K 99 " --> pdb=" O PHE K 125 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N VAL K 127 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N GLY K 101 " --> pdb=" O VAL K 127 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE K 129 " --> pdb=" O GLY K 101 " (cutoff:3.500A) removed outlier: 13.989A pdb=" N ASN K 103 " --> pdb=" O ILE K 129 " (cutoff:3.500A) removed outlier: 14.862A pdb=" N GLN K 131 " --> pdb=" O ASN K 103 " (cutoff:3.500A) removed outlier: 12.202A pdb=" N ASP K 105 " --> pdb=" O GLN K 131 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR K 124 " --> pdb=" O ASP K 154 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP K 154 " --> pdb=" O THR K 124 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA K 148 " --> pdb=" O LEU K 130 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU K 66 " --> pdb=" O SER K 58 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY K 54 " --> pdb=" O TYR K 70 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA K 72 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE K 52 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY K 57 " --> pdb=" O GLU K 197 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLU K 197 " --> pdb=" O GLY K 57 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 80 through 81 Processing sheet with id=AD6, first strand: chain 'K' and resid 94 through 97 removed outlier: 3.585A pdb=" N ASP K 90 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER K 170 " --> pdb=" O ASP K 90 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY K 171 " --> pdb=" O ILE K 183 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 99 through 105 removed outlier: 7.046A pdb=" N GLY L 99 " --> pdb=" O PHE L 125 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N VAL L 127 " --> pdb=" O GLY L 99 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N GLY L 101 " --> pdb=" O VAL L 127 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE L 129 " --> pdb=" O GLY L 101 " (cutoff:3.500A) removed outlier: 13.990A pdb=" N ASN L 103 " --> pdb=" O ILE L 129 " (cutoff:3.500A) removed outlier: 14.860A pdb=" N GLN L 131 " --> pdb=" O ASN L 103 " (cutoff:3.500A) removed outlier: 12.202A pdb=" N ASP L 105 " --> pdb=" O GLN L 131 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR L 124 " --> pdb=" O ASP L 154 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP L 154 " --> pdb=" O THR L 124 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA L 148 " --> pdb=" O LEU L 130 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU L 66 " --> pdb=" O SER L 58 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLY L 54 " --> pdb=" O TYR L 70 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA L 72 " --> pdb=" O ILE L 52 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE L 52 " --> pdb=" O ALA L 72 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY L 57 " --> pdb=" O GLU L 197 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLU L 197 " --> pdb=" O GLY L 57 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 80 through 81 Processing sheet with id=AD9, first strand: chain 'L' and resid 94 through 97 removed outlier: 3.585A pdb=" N ASP L 90 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER L 170 " --> pdb=" O ASP L 90 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY L 171 " --> pdb=" O ILE L 183 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 99 through 105 removed outlier: 7.047A pdb=" N GLY M 99 " --> pdb=" O PHE M 125 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N VAL M 127 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY M 101 " --> pdb=" O VAL M 127 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE M 129 " --> pdb=" O GLY M 101 " (cutoff:3.500A) removed outlier: 13.989A pdb=" N ASN M 103 " --> pdb=" O ILE M 129 " (cutoff:3.500A) removed outlier: 14.860A pdb=" N GLN M 131 " --> pdb=" O ASN M 103 " (cutoff:3.500A) removed outlier: 12.201A pdb=" N ASP M 105 " --> pdb=" O GLN M 131 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR M 124 " --> pdb=" O ASP M 154 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP M 154 " --> pdb=" O THR M 124 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA M 148 " --> pdb=" O LEU M 130 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU M 66 " --> pdb=" O SER M 58 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLY M 54 " --> pdb=" O TYR M 70 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA M 72 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE M 52 " --> pdb=" O ALA M 72 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY M 57 " --> pdb=" O GLU M 197 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLU M 197 " --> pdb=" O GLY M 57 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 80 through 81 Processing sheet with id=AE3, first strand: chain 'M' and resid 94 through 97 removed outlier: 3.585A pdb=" N ASP M 90 " --> pdb=" O SER M 170 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER M 170 " --> pdb=" O ASP M 90 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY M 171 " --> pdb=" O ILE M 183 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 99 through 105 removed outlier: 7.046A pdb=" N GLY N 99 " --> pdb=" O PHE N 125 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N VAL N 127 " --> pdb=" O GLY N 99 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY N 101 " --> pdb=" O VAL N 127 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE N 129 " --> pdb=" O GLY N 101 " (cutoff:3.500A) removed outlier: 13.989A pdb=" N ASN N 103 " --> pdb=" O ILE N 129 " (cutoff:3.500A) removed outlier: 14.861A pdb=" N GLN N 131 " --> pdb=" O ASN N 103 " (cutoff:3.500A) removed outlier: 12.201A pdb=" N ASP N 105 " --> pdb=" O GLN N 131 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR N 124 " --> pdb=" O ASP N 154 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP N 154 " --> pdb=" O THR N 124 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA N 148 " --> pdb=" O LEU N 130 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU N 66 " --> pdb=" O SER N 58 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLY N 54 " --> pdb=" O TYR N 70 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA N 72 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE N 52 " --> pdb=" O ALA N 72 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY N 57 " --> pdb=" O GLU N 197 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU N 197 " --> pdb=" O GLY N 57 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 80 through 81 Processing sheet with id=AE6, first strand: chain 'N' and resid 94 through 97 removed outlier: 3.584A pdb=" N ASP N 90 " --> pdb=" O SER N 170 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER N 170 " --> pdb=" O ASP N 90 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY N 171 " --> pdb=" O ILE N 183 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 99 through 105 removed outlier: 7.047A pdb=" N GLY O 99 " --> pdb=" O PHE O 125 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N VAL O 127 " --> pdb=" O GLY O 99 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N GLY O 101 " --> pdb=" O VAL O 127 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE O 129 " --> pdb=" O GLY O 101 " (cutoff:3.500A) removed outlier: 13.989A pdb=" N ASN O 103 " --> pdb=" O ILE O 129 " (cutoff:3.500A) removed outlier: 14.861A pdb=" N GLN O 131 " --> pdb=" O ASN O 103 " (cutoff:3.500A) removed outlier: 12.201A pdb=" N ASP O 105 " --> pdb=" O GLN O 131 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR O 124 " --> pdb=" O ASP O 154 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP O 154 " --> pdb=" O THR O 124 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA O 148 " --> pdb=" O LEU O 130 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU O 66 " --> pdb=" O SER O 58 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY O 54 " --> pdb=" O TYR O 70 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA O 72 " --> pdb=" O ILE O 52 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE O 52 " --> pdb=" O ALA O 72 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY O 57 " --> pdb=" O GLU O 197 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLU O 197 " --> pdb=" O GLY O 57 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 80 through 81 Processing sheet with id=AE9, first strand: chain 'O' and resid 94 through 97 removed outlier: 3.584A pdb=" N ASP O 90 " --> pdb=" O SER O 170 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER O 170 " --> pdb=" O ASP O 90 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY O 171 " --> pdb=" O ILE O 183 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 99 through 105 removed outlier: 7.046A pdb=" N GLY P 99 " --> pdb=" O PHE P 125 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N VAL P 127 " --> pdb=" O GLY P 99 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY P 101 " --> pdb=" O VAL P 127 " (cutoff:3.500A) removed outlier: 11.755A pdb=" N ILE P 129 " --> pdb=" O GLY P 101 " (cutoff:3.500A) removed outlier: 13.989A pdb=" N ASN P 103 " --> pdb=" O ILE P 129 " (cutoff:3.500A) removed outlier: 14.860A pdb=" N GLN P 131 " --> pdb=" O ASN P 103 " (cutoff:3.500A) removed outlier: 12.201A pdb=" N ASP P 105 " --> pdb=" O GLN P 131 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR P 124 " --> pdb=" O ASP P 154 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP P 154 " --> pdb=" O THR P 124 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA P 148 " --> pdb=" O LEU P 130 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU P 66 " --> pdb=" O SER P 58 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLY P 54 " --> pdb=" O TYR P 70 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA P 72 " --> pdb=" O ILE P 52 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE P 52 " --> pdb=" O ALA P 72 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY P 57 " --> pdb=" O GLU P 197 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLU P 197 " --> pdb=" O GLY P 57 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 80 through 81 Processing sheet with id=AF3, first strand: chain 'P' and resid 94 through 97 removed outlier: 3.583A pdb=" N ASP P 90 " --> pdb=" O SER P 170 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER P 170 " --> pdb=" O ASP P 90 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY P 171 " --> pdb=" O ILE P 183 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 99 through 105 removed outlier: 7.047A pdb=" N GLY Q 99 " --> pdb=" O PHE Q 125 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N VAL Q 127 " --> pdb=" O GLY Q 99 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N GLY Q 101 " --> pdb=" O VAL Q 127 " (cutoff:3.500A) removed outlier: 11.755A pdb=" N ILE Q 129 " --> pdb=" O GLY Q 101 " (cutoff:3.500A) removed outlier: 13.989A pdb=" N ASN Q 103 " --> pdb=" O ILE Q 129 " (cutoff:3.500A) removed outlier: 14.861A pdb=" N GLN Q 131 " --> pdb=" O ASN Q 103 " (cutoff:3.500A) removed outlier: 12.201A pdb=" N ASP Q 105 " --> pdb=" O GLN Q 131 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR Q 124 " --> pdb=" O ASP Q 154 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP Q 154 " --> pdb=" O THR Q 124 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA Q 148 " --> pdb=" O LEU Q 130 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU Q 66 " --> pdb=" O SER Q 58 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY Q 54 " --> pdb=" O TYR Q 70 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA Q 72 " --> pdb=" O ILE Q 52 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILE Q 52 " --> pdb=" O ALA Q 72 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY Q 57 " --> pdb=" O GLU Q 197 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU Q 197 " --> pdb=" O GLY Q 57 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 80 through 81 Processing sheet with id=AF6, first strand: chain 'Q' and resid 94 through 97 removed outlier: 3.584A pdb=" N ASP Q 90 " --> pdb=" O SER Q 170 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER Q 170 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY Q 171 " --> pdb=" O ILE Q 183 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'R' and resid 99 through 105 removed outlier: 7.047A pdb=" N GLY R 99 " --> pdb=" O PHE R 125 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N VAL R 127 " --> pdb=" O GLY R 99 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY R 101 " --> pdb=" O VAL R 127 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N ILE R 129 " --> pdb=" O GLY R 101 " (cutoff:3.500A) removed outlier: 13.989A pdb=" N ASN R 103 " --> pdb=" O ILE R 129 " (cutoff:3.500A) removed outlier: 14.860A pdb=" N GLN R 131 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 12.201A pdb=" N ASP R 105 " --> pdb=" O GLN R 131 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR R 124 " --> pdb=" O ASP R 154 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP R 154 " --> pdb=" O THR R 124 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA R 148 " --> pdb=" O LEU R 130 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU R 66 " --> pdb=" O SER R 58 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLY R 54 " --> pdb=" O TYR R 70 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA R 72 " --> pdb=" O ILE R 52 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE R 52 " --> pdb=" O ALA R 72 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY R 57 " --> pdb=" O GLU R 197 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLU R 197 " --> pdb=" O GLY R 57 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 80 through 81 Processing sheet with id=AF9, first strand: chain 'R' and resid 94 through 97 removed outlier: 3.585A pdb=" N ASP R 90 " --> pdb=" O SER R 170 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER R 170 " --> pdb=" O ASP R 90 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY R 171 " --> pdb=" O ILE R 183 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2700 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: 4.43 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8383 1.34 - 1.46: 3989 1.46 - 1.57: 13368 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 25848 Sorted by residual: bond pdb=" CA ASN O 140 " pdb=" CB ASN O 140 " ideal model delta sigma weight residual 1.532 1.551 -0.019 1.51e-02 4.39e+03 1.59e+00 bond pdb=" CB ASN F 140 " pdb=" CG ASN F 140 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.55e+00 bond pdb=" CA ASN P 140 " pdb=" CB ASN P 140 " ideal model delta sigma weight residual 1.532 1.551 -0.019 1.51e-02 4.39e+03 1.54e+00 bond pdb=" CB ASN G 140 " pdb=" CG ASN G 140 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.53e+00 bond pdb=" CB ASN Q 140 " pdb=" CG ASN Q 140 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.52e+00 ... (remaining 25843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 33449 1.97 - 3.94: 1486 3.94 - 5.92: 183 5.92 - 7.89: 108 7.89 - 9.86: 18 Bond angle restraints: 35244 Sorted by residual: angle pdb=" C ASP Q 134 " pdb=" N ASP Q 135 " pdb=" CA ASP Q 135 " ideal model delta sigma weight residual 121.54 131.40 -9.86 1.91e+00 2.74e-01 2.66e+01 angle pdb=" C ASP K 134 " pdb=" N ASP K 135 " pdb=" CA ASP K 135 " ideal model delta sigma weight residual 121.54 131.40 -9.86 1.91e+00 2.74e-01 2.66e+01 angle pdb=" C ASP N 134 " pdb=" N ASP N 135 " pdb=" CA ASP N 135 " ideal model delta sigma weight residual 121.54 131.38 -9.84 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C ASP D 134 " pdb=" N ASP D 135 " pdb=" CA ASP D 135 " ideal model delta sigma weight residual 121.54 131.37 -9.83 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C ASP F 134 " pdb=" N ASP F 135 " pdb=" CA ASP F 135 " ideal model delta sigma weight residual 121.54 131.37 -9.83 1.91e+00 2.74e-01 2.65e+01 ... (remaining 35239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.60: 11890 6.60 - 13.21: 2294 13.21 - 19.81: 719 19.81 - 26.42: 235 26.42 - 33.02: 180 Dihedral angle restraints: 15318 sinusoidal: 5220 harmonic: 10098 Sorted by residual: dihedral pdb=" CA ASN F 140 " pdb=" C ASN F 140 " pdb=" N ALA F 141 " pdb=" CA ALA F 141 " ideal model delta harmonic sigma weight residual 180.00 157.75 22.25 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ASN I 140 " pdb=" C ASN I 140 " pdb=" N ALA I 141 " pdb=" CA ALA I 141 " ideal model delta harmonic sigma weight residual 180.00 157.76 22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ASN K 140 " pdb=" C ASN K 140 " pdb=" N ALA K 141 " pdb=" CA ALA K 141 " ideal model delta harmonic sigma weight residual 180.00 157.76 22.24 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 15315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 3488 0.075 - 0.150: 838 0.150 - 0.225: 108 0.225 - 0.300: 12 0.300 - 0.374: 18 Chirality restraints: 4464 Sorted by residual: chirality pdb=" CB ILE M 163 " pdb=" CA ILE M 163 " pdb=" CG1 ILE M 163 " pdb=" CG2 ILE M 163 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE F 163 " pdb=" CA ILE F 163 " pdb=" CG1 ILE F 163 " pdb=" CG2 ILE F 163 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" CB ILE P 163 " pdb=" CA ILE P 163 " pdb=" CG1 ILE P 163 " pdb=" CG2 ILE P 163 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 4461 not shown) Planarity restraints: 4554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 173 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.20e+00 pdb=" C VAL H 173 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL H 173 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN H 174 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 173 " 0.012 2.00e-02 2.50e+03 2.49e-02 6.19e+00 pdb=" C VAL A 173 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL A 173 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN A 174 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 173 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C VAL N 173 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL N 173 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN N 174 " 0.014 2.00e-02 2.50e+03 ... (remaining 4551 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 9679 2.88 - 3.39: 21447 3.39 - 3.89: 36890 3.89 - 4.40: 37486 4.40 - 4.90: 70857 Nonbonded interactions: 176359 Sorted by model distance: nonbonded pdb=" OE1 GLU K 44 " pdb=" OG SER K 78 " model vdw 2.380 3.040 nonbonded pdb=" OE1 GLU J 44 " pdb=" OG SER J 78 " model vdw 2.381 3.040 nonbonded pdb=" OE1 GLU O 44 " pdb=" OG SER O 78 " model vdw 2.381 3.040 nonbonded pdb=" OE1 GLU D 44 " pdb=" OG SER D 78 " model vdw 2.381 3.040 nonbonded pdb=" OE1 GLU G 44 " pdb=" OG SER G 78 " model vdw 2.381 3.040 ... (remaining 176354 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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 group one per residue 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: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.320 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 0.031 25848 Z= 0.221 Angle : 0.988 9.859 35244 Z= 0.544 Chirality : 0.069 0.374 4464 Planarity : 0.006 0.048 4554 Dihedral : 9.074 33.022 8874 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.52 % Favored : 87.48 % Rotamer: Outliers : 0.65 % Allowed : 1.94 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.25 (0.12), residues: 3546 helix: -2.79 (0.14), residues: 792 sheet: -0.20 (0.19), residues: 756 loop : -4.14 (0.10), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 166 TYR 0.005 0.001 TYR K 91 PHE 0.036 0.004 PHE G 185 Details of bonding type rmsd covalent geometry : bond 0.00433 (25848) covalent geometry : angle 0.98764 (35244) hydrogen bonds : bond 0.17599 ( 972) hydrogen bonds : angle 8.12455 ( 2700) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 945 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.7719 (mtp) cc_final: 0.7394 (mtp) REVERT: A 45 GLN cc_start: 0.7879 (tt0) cc_final: 0.7564 (mt0) REVERT: A 53 ASN cc_start: 0.8525 (p0) cc_final: 0.8267 (p0) REVERT: A 129 ILE cc_start: 0.8857 (mt) cc_final: 0.8656 (mt) REVERT: A 130 LEU cc_start: 0.9111 (mt) cc_final: 0.8906 (mt) REVERT: A 132 ASP cc_start: 0.8275 (t0) cc_final: 0.7923 (t0) REVERT: A 135 ASP cc_start: 0.8375 (p0) cc_final: 0.8079 (p0) REVERT: A 140 ASN cc_start: 0.7559 (p0) cc_final: 0.6511 (m-40) REVERT: B 27 THR cc_start: 0.8971 (t) cc_final: 0.8759 (m) REVERT: B 37 THR cc_start: 0.8062 (p) cc_final: 0.6934 (p) REVERT: B 134 ASP cc_start: 0.7950 (p0) cc_final: 0.7727 (p0) REVERT: C 53 ASN cc_start: 0.8894 (p0) cc_final: 0.8509 (p0) REVERT: C 55 ILE cc_start: 0.9211 (mt) cc_final: 0.8928 (mp) REVERT: C 105 ASP cc_start: 0.8929 (t0) cc_final: 0.8355 (t0) REVERT: D 48 SER cc_start: 0.9595 (m) cc_final: 0.9372 (m) REVERT: D 53 ASN cc_start: 0.8859 (p0) cc_final: 0.7937 (p0) REVERT: D 103 ASN cc_start: 0.7279 (t0) cc_final: 0.6763 (p0) REVERT: D 105 ASP cc_start: 0.8948 (t0) cc_final: 0.8537 (t0) REVERT: D 131 GLN cc_start: 0.8313 (tt0) cc_final: 0.7995 (tt0) REVERT: D 139 ASP cc_start: 0.6324 (t70) cc_final: 0.6045 (t0) REVERT: D 195 LEU cc_start: 0.8991 (tm) cc_final: 0.8701 (tt) REVERT: E 44 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6706 (mm-30) REVERT: E 84 GLN cc_start: 0.8116 (mt0) cc_final: 0.7846 (mt0) REVERT: F 32 GLN cc_start: 0.8408 (pt0) cc_final: 0.8042 (pt0) REVERT: F 132 ASP cc_start: 0.7975 (t0) cc_final: 0.7492 (t0) REVERT: F 134 ASP cc_start: 0.8374 (p0) cc_final: 0.7900 (p0) REVERT: F 147 ASP cc_start: 0.9170 (m-30) cc_final: 0.8947 (m-30) REVERT: G 26 ASN cc_start: 0.8525 (m110) cc_final: 0.7930 (t0) REVERT: G 38 THR cc_start: 0.8547 (m) cc_final: 0.8323 (m) REVERT: G 88 MET cc_start: 0.7904 (mpp) cc_final: 0.7673 (mpp) REVERT: G 132 ASP cc_start: 0.7746 (t0) cc_final: 0.7419 (t0) REVERT: G 139 ASP cc_start: 0.7069 (t70) cc_final: 0.6817 (t0) REVERT: H 53 ASN cc_start: 0.8836 (p0) cc_final: 0.8509 (p0) REVERT: H 94 LYS cc_start: 0.7647 (mttt) cc_final: 0.7287 (mttt) REVERT: I 167 THR cc_start: 0.8755 (p) cc_final: 0.8470 (p) REVERT: I 177 PHE cc_start: 0.8295 (p90) cc_final: 0.8089 (p90) REVERT: I 184 SER cc_start: 0.7625 (t) cc_final: 0.6747 (m) REVERT: J 25 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8098 (mp) REVERT: J 53 ASN cc_start: 0.8192 (p0) cc_final: 0.7970 (p0) REVERT: J 103 ASN cc_start: 0.7556 (t0) cc_final: 0.7275 (t0) REVERT: J 182 VAL cc_start: 0.8784 (t) cc_final: 0.8539 (p) REVERT: K 11 ILE cc_start: 0.7409 (mt) cc_final: 0.7169 (mt) REVERT: L 26 ASN cc_start: 0.7937 (m110) cc_final: 0.7708 (m110) REVERT: L 51 LEU cc_start: 0.9293 (tp) cc_final: 0.9082 (tp) REVERT: L 53 ASN cc_start: 0.8089 (p0) cc_final: 0.7795 (p0) REVERT: L 84 GLN cc_start: 0.8290 (mt0) cc_final: 0.7467 (mt0) REVERT: L 132 ASP cc_start: 0.7890 (t0) cc_final: 0.7256 (t0) REVERT: L 147 ASP cc_start: 0.9164 (m-30) cc_final: 0.8936 (m-30) REVERT: M 132 ASP cc_start: 0.7811 (t0) cc_final: 0.7387 (t0) REVERT: M 134 ASP cc_start: 0.9049 (p0) cc_final: 0.8323 (p0) REVERT: M 135 ASP cc_start: 0.8803 (p0) cc_final: 0.8268 (p0) REVERT: M 147 ASP cc_start: 0.9218 (m-30) cc_final: 0.8931 (m-30) REVERT: M 182 VAL cc_start: 0.8359 (t) cc_final: 0.8153 (m) REVERT: N 26 ASN cc_start: 0.8207 (m110) cc_final: 0.7875 (t0) REVERT: N 104 GLN cc_start: 0.8213 (pp30) cc_final: 0.7653 (pp30) REVERT: N 132 ASP cc_start: 0.7826 (t0) cc_final: 0.7582 (t0) REVERT: N 139 ASP cc_start: 0.7087 (t70) cc_final: 0.6849 (t0) REVERT: O 25 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6584 (mp) REVERT: O 53 ASN cc_start: 0.8769 (p0) cc_final: 0.8544 (p0) REVERT: O 118 THR cc_start: 0.4392 (t) cc_final: 0.4124 (m) REVERT: O 132 ASP cc_start: 0.7847 (t0) cc_final: 0.7435 (t0) REVERT: O 135 ASP cc_start: 0.8682 (p0) cc_final: 0.8402 (p0) REVERT: O 147 ASP cc_start: 0.8715 (m-30) cc_final: 0.8170 (m-30) REVERT: P 55 ILE cc_start: 0.9100 (mt) cc_final: 0.8869 (mp) REVERT: P 106 MET cc_start: 0.7110 (ptm) cc_final: 0.6884 (tmm) REVERT: P 154 ASP cc_start: 0.8534 (t70) cc_final: 0.8250 (t0) REVERT: P 184 SER cc_start: 0.8267 (t) cc_final: 0.7660 (m) REVERT: Q 94 LYS cc_start: 0.8326 (mttt) cc_final: 0.8113 (mttt) REVERT: Q 132 ASP cc_start: 0.7129 (t0) cc_final: 0.6705 (t0) REVERT: Q 135 ASP cc_start: 0.8585 (p0) cc_final: 0.8304 (m-30) REVERT: Q 147 ASP cc_start: 0.8911 (m-30) cc_final: 0.8484 (m-30) REVERT: R 53 ASN cc_start: 0.8423 (p0) cc_final: 0.8147 (p0) REVERT: R 74 ASN cc_start: 0.8761 (t0) cc_final: 0.8557 (t0) REVERT: R 103 ASN cc_start: 0.7583 (t0) cc_final: 0.7295 (t0) REVERT: R 132 ASP cc_start: 0.8235 (t0) cc_final: 0.7666 (t0) REVERT: R 140 ASN cc_start: 0.8179 (p0) cc_final: 0.7483 (t0) REVERT: R 147 ASP cc_start: 0.8954 (m-30) cc_final: 0.8556 (m-30) REVERT: R 177 PHE cc_start: 0.8048 (p90) cc_final: 0.7813 (p90) outliers start: 18 outliers final: 6 residues processed: 951 average time/residue: 0.1273 time to fit residues: 208.3493 Evaluate side-chains 742 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 734 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain P residue 25 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.0870 chunk 155 optimal weight: 50.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 8.9990 overall best weight: 4.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN B 26 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN E 174 GLN F 26 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN G 84 GLN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 174 GLN J 26 ASN J 84 GLN K 26 ASN M 26 ASN M 174 GLN ** N 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 26 ASN P 131 GLN ** Q 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 26 ASN ** R 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 174 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.170658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.131093 restraints weight = 33202.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.132005 restraints weight = 24208.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.134542 restraints weight = 19489.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.136367 restraints weight = 15526.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.136609 restraints weight = 13335.689| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25848 Z= 0.166 Angle : 0.712 9.825 35244 Z= 0.385 Chirality : 0.052 0.295 4464 Planarity : 0.004 0.044 4554 Dihedral : 6.062 38.249 3688 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.25 % Favored : 86.75 % Rotamer: Outliers : 4.52 % Allowed : 12.51 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.62 (0.12), residues: 3546 helix: -1.09 (0.17), residues: 810 sheet: -0.13 (0.19), residues: 738 loop : -4.16 (0.10), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 166 TYR 0.008 0.001 TYR O 70 PHE 0.018 0.002 PHE Q 30 Details of bonding type rmsd covalent geometry : bond 0.00362 (25848) covalent geometry : angle 0.71182 (35244) hydrogen bonds : bond 0.03758 ( 972) hydrogen bonds : angle 5.36262 ( 2700) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 767 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8636 (tt) REVERT: A 45 GLN cc_start: 0.7608 (tt0) cc_final: 0.7401 (mt0) REVERT: A 84 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8506 (mp10) REVERT: A 129 ILE cc_start: 0.8924 (mt) cc_final: 0.8686 (mt) REVERT: A 132 ASP cc_start: 0.8422 (t0) cc_final: 0.7872 (t0) REVERT: A 147 ASP cc_start: 0.8889 (m-30) cc_final: 0.8536 (m-30) REVERT: B 65 LYS cc_start: 0.8583 (pttp) cc_final: 0.8169 (pttm) REVERT: B 66 LEU cc_start: 0.8712 (mp) cc_final: 0.8373 (mt) REVERT: B 147 ASP cc_start: 0.8650 (m-30) cc_final: 0.8431 (m-30) REVERT: C 53 ASN cc_start: 0.8784 (p0) cc_final: 0.8562 (p0) REVERT: C 55 ILE cc_start: 0.9082 (mt) cc_final: 0.8811 (mp) REVERT: C 105 ASP cc_start: 0.9126 (t0) cc_final: 0.8720 (t0) REVERT: C 173 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8682 (m) REVERT: D 53 ASN cc_start: 0.8780 (p0) cc_final: 0.8116 (p0) REVERT: D 84 GLN cc_start: 0.8807 (mt0) cc_final: 0.8598 (mt0) REVERT: D 103 ASN cc_start: 0.7255 (t0) cc_final: 0.6851 (p0) REVERT: D 105 ASP cc_start: 0.8976 (t0) cc_final: 0.8699 (t0) REVERT: D 195 LEU cc_start: 0.9075 (tm) cc_final: 0.8831 (tt) REVERT: F 32 GLN cc_start: 0.8147 (pt0) cc_final: 0.7663 (pt0) REVERT: F 53 ASN cc_start: 0.8415 (p0) cc_final: 0.8101 (p0) REVERT: F 132 ASP cc_start: 0.8080 (t0) cc_final: 0.7611 (t0) REVERT: F 134 ASP cc_start: 0.8241 (p0) cc_final: 0.7592 (p0) REVERT: F 147 ASP cc_start: 0.9259 (m-30) cc_final: 0.8964 (m-30) REVERT: G 26 ASN cc_start: 0.8330 (m110) cc_final: 0.8122 (t0) REVERT: G 132 ASP cc_start: 0.7876 (t0) cc_final: 0.7425 (t0) REVERT: H 53 ASN cc_start: 0.8768 (p0) cc_final: 0.8555 (p0) REVERT: H 88 MET cc_start: 0.8010 (mpp) cc_final: 0.7638 (mtt) REVERT: H 198 LEU cc_start: 0.8989 (mp) cc_final: 0.8738 (mt) REVERT: I 53 ASN cc_start: 0.8883 (p0) cc_final: 0.8498 (p0) REVERT: I 70 TYR cc_start: 0.8552 (m-80) cc_final: 0.8341 (m-80) REVERT: I 177 PHE cc_start: 0.8505 (p90) cc_final: 0.8290 (p90) REVERT: J 53 ASN cc_start: 0.8049 (p0) cc_final: 0.7843 (p0) REVERT: J 104 GLN cc_start: 0.8241 (pp30) cc_final: 0.7161 (pp30) REVERT: J 134 ASP cc_start: 0.8856 (p0) cc_final: 0.8368 (p0) REVERT: L 53 ASN cc_start: 0.8029 (p0) cc_final: 0.7743 (p0) REVERT: L 132 ASP cc_start: 0.7916 (t0) cc_final: 0.7244 (t0) REVERT: L 135 ASP cc_start: 0.8605 (p0) cc_final: 0.8373 (p0) REVERT: L 147 ASP cc_start: 0.9141 (m-30) cc_final: 0.8874 (m-30) REVERT: M 132 ASP cc_start: 0.8055 (t0) cc_final: 0.7445 (t0) REVERT: M 134 ASP cc_start: 0.8906 (p0) cc_final: 0.8321 (p0) REVERT: M 147 ASP cc_start: 0.9334 (m-30) cc_final: 0.8984 (m-30) REVERT: N 26 ASN cc_start: 0.8077 (m110) cc_final: 0.7854 (m-40) REVERT: N 65 LYS cc_start: 0.9131 (pttt) cc_final: 0.8745 (pttt) REVERT: N 132 ASP cc_start: 0.8000 (t0) cc_final: 0.7584 (t0) REVERT: N 154 ASP cc_start: 0.8472 (t0) cc_final: 0.8253 (t0) REVERT: O 132 ASP cc_start: 0.7946 (t0) cc_final: 0.7573 (t0) REVERT: O 147 ASP cc_start: 0.8818 (m-30) cc_final: 0.8204 (m-30) REVERT: P 55 ILE cc_start: 0.9048 (mt) cc_final: 0.8816 (mp) REVERT: P 84 GLN cc_start: 0.8604 (mp10) cc_final: 0.8190 (mp10) REVERT: P 154 ASP cc_start: 0.8564 (t70) cc_final: 0.8209 (t0) REVERT: P 173 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8394 (t) REVERT: Q 94 LYS cc_start: 0.8125 (mttt) cc_final: 0.7924 (mttt) REVERT: Q 132 ASP cc_start: 0.7115 (t0) cc_final: 0.6793 (t0) REVERT: Q 147 ASP cc_start: 0.9087 (m-30) cc_final: 0.8725 (m-30) REVERT: R 10 PHE cc_start: 0.7092 (t80) cc_final: 0.6827 (t80) REVERT: R 53 ASN cc_start: 0.8416 (p0) cc_final: 0.8204 (p0) REVERT: R 103 ASN cc_start: 0.7357 (t0) cc_final: 0.7123 (t0) REVERT: R 132 ASP cc_start: 0.8558 (t0) cc_final: 0.8097 (t0) REVERT: R 147 ASP cc_start: 0.9091 (m-30) cc_final: 0.8709 (m-30) outliers start: 126 outliers final: 77 residues processed: 841 average time/residue: 0.1329 time to fit residues: 191.1342 Evaluate side-chains 808 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 727 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 GLN Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 155 VAL Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain M residue 45 GLN Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 169 ILE Chi-restraints excluded: chain N residue 186 THR Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 50 LEU Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 50 LEU Chi-restraints excluded: chain P residue 129 ILE Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 192 THR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 155 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 123 optimal weight: 9.9990 chunk 198 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 chunk 125 optimal weight: 0.0980 chunk 247 optimal weight: 50.0000 chunk 165 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 154 optimal weight: 20.0000 chunk 297 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN C 131 GLN E 131 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN J 174 GLN L 26 ASN M 174 GLN ** N 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 26 ASN O 84 GLN O 92 ASN Q 140 ASN ** R 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 131 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.165426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.123897 restraints weight = 33574.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.127396 restraints weight = 22839.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.129772 restraints weight = 17667.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.131182 restraints weight = 14868.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.132266 restraints weight = 13336.395| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25848 Z= 0.187 Angle : 0.719 8.903 35244 Z= 0.392 Chirality : 0.053 0.285 4464 Planarity : 0.004 0.055 4554 Dihedral : 5.918 37.563 3680 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.75 % Favored : 85.25 % Rotamer: Outliers : 4.34 % Allowed : 14.80 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.38 (0.13), residues: 3546 helix: 0.24 (0.20), residues: 702 sheet: -0.42 (0.19), residues: 774 loop : -4.18 (0.10), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 166 TYR 0.010 0.001 TYR I 70 PHE 0.027 0.002 PHE J 185 Details of bonding type rmsd covalent geometry : bond 0.00420 (25848) covalent geometry : angle 0.71851 (35244) hydrogen bonds : bond 0.03885 ( 972) hydrogen bonds : angle 5.18857 ( 2700) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 762 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8621 (tt) REVERT: A 45 GLN cc_start: 0.7826 (tt0) cc_final: 0.7544 (mt0) REVERT: A 132 ASP cc_start: 0.8479 (t0) cc_final: 0.7948 (t0) REVERT: A 134 ASP cc_start: 0.8412 (p0) cc_final: 0.8206 (p0) REVERT: A 147 ASP cc_start: 0.8881 (m-30) cc_final: 0.8523 (m-30) REVERT: C 105 ASP cc_start: 0.9300 (t0) cc_final: 0.9077 (t0) REVERT: C 173 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8534 (m) REVERT: D 53 ASN cc_start: 0.8624 (p0) cc_final: 0.8002 (p0) REVERT: D 103 ASN cc_start: 0.7384 (t0) cc_final: 0.6881 (p0) REVERT: D 105 ASP cc_start: 0.9156 (t0) cc_final: 0.8873 (t0) REVERT: D 195 LEU cc_start: 0.9124 (tm) cc_final: 0.8895 (tt) REVERT: F 32 GLN cc_start: 0.7865 (pt0) cc_final: 0.7561 (pt0) REVERT: F 44 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7968 (mm-30) REVERT: F 53 ASN cc_start: 0.8436 (p0) cc_final: 0.8183 (p0) REVERT: F 104 GLN cc_start: 0.8406 (pp30) cc_final: 0.7191 (pp30) REVERT: F 132 ASP cc_start: 0.7957 (t0) cc_final: 0.7687 (t0) REVERT: F 134 ASP cc_start: 0.8429 (p0) cc_final: 0.7787 (p0) REVERT: G 30 PHE cc_start: 0.7679 (t80) cc_final: 0.6840 (t80) REVERT: G 132 ASP cc_start: 0.7964 (t0) cc_final: 0.7535 (t0) REVERT: H 53 ASN cc_start: 0.8681 (p0) cc_final: 0.8412 (p0) REVERT: H 84 GLN cc_start: 0.8091 (mp10) cc_final: 0.7672 (mp10) REVERT: H 105 ASP cc_start: 0.9156 (t0) cc_final: 0.8841 (t0) REVERT: H 154 ASP cc_start: 0.8289 (t0) cc_final: 0.8083 (t0) REVERT: I 53 ASN cc_start: 0.8817 (p0) cc_final: 0.8430 (p0) REVERT: J 11 ILE cc_start: 0.8082 (mt) cc_final: 0.7878 (mt) REVERT: J 30 PHE cc_start: 0.7641 (t80) cc_final: 0.6905 (t80) REVERT: J 34 LYS cc_start: 0.8481 (tttp) cc_final: 0.8235 (ttmm) REVERT: J 104 GLN cc_start: 0.8193 (pp30) cc_final: 0.7044 (pp30) REVERT: J 134 ASP cc_start: 0.8446 (p0) cc_final: 0.8099 (p0) REVERT: K 132 ASP cc_start: 0.8175 (t0) cc_final: 0.7879 (t0) REVERT: L 53 ASN cc_start: 0.7891 (p0) cc_final: 0.7632 (p0) REVERT: L 132 ASP cc_start: 0.7878 (t0) cc_final: 0.7202 (t0) REVERT: L 147 ASP cc_start: 0.9143 (m-30) cc_final: 0.8894 (m-30) REVERT: M 30 PHE cc_start: 0.7704 (t80) cc_final: 0.7338 (t80) REVERT: M 132 ASP cc_start: 0.7915 (t0) cc_final: 0.7333 (t0) REVERT: M 134 ASP cc_start: 0.8919 (p0) cc_final: 0.8364 (p0) REVERT: M 147 ASP cc_start: 0.9398 (m-30) cc_final: 0.9085 (m-30) REVERT: N 65 LYS cc_start: 0.9099 (pttt) cc_final: 0.8638 (pttt) REVERT: N 132 ASP cc_start: 0.8057 (t0) cc_final: 0.7650 (t0) REVERT: N 154 ASP cc_start: 0.8634 (t0) cc_final: 0.8333 (t0) REVERT: O 132 ASP cc_start: 0.7825 (t0) cc_final: 0.7540 (t0) REVERT: O 135 ASP cc_start: 0.8735 (p0) cc_final: 0.8225 (p0) REVERT: O 147 ASP cc_start: 0.8783 (m-30) cc_final: 0.8206 (m-30) REVERT: O 177 PHE cc_start: 0.8133 (p90) cc_final: 0.7691 (p90) REVERT: P 55 ILE cc_start: 0.8951 (mt) cc_final: 0.8669 (mp) REVERT: P 154 ASP cc_start: 0.8688 (t70) cc_final: 0.8406 (t0) REVERT: Q 132 ASP cc_start: 0.7100 (t0) cc_final: 0.6859 (t0) REVERT: Q 135 ASP cc_start: 0.8675 (p0) cc_final: 0.8294 (p0) REVERT: Q 147 ASP cc_start: 0.9130 (m-30) cc_final: 0.8828 (m-30) REVERT: R 103 ASN cc_start: 0.7507 (t0) cc_final: 0.7248 (t0) REVERT: R 104 GLN cc_start: 0.8367 (pp30) cc_final: 0.7233 (pp30) REVERT: R 106 MET cc_start: 0.7599 (ptp) cc_final: 0.7265 (ttp) REVERT: R 132 ASP cc_start: 0.8310 (t0) cc_final: 0.7945 (t0) REVERT: R 134 ASP cc_start: 0.8267 (p0) cc_final: 0.7620 (p0) REVERT: R 147 ASP cc_start: 0.9114 (m-30) cc_final: 0.8711 (m-30) REVERT: R 177 PHE cc_start: 0.8168 (p90) cc_final: 0.7683 (p90) outliers start: 121 outliers final: 81 residues processed: 831 average time/residue: 0.1338 time to fit residues: 189.5350 Evaluate side-chains 801 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 718 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 174 GLN Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 177 PHE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 62 SER Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain M residue 45 GLN Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 169 ILE Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain P residue 129 ILE Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 45 GLN Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 88 MET Chi-restraints excluded: chain R residue 152 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 296 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 58 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 chunk 281 optimal weight: 5.9990 chunk 152 optimal weight: 50.0000 chunk 153 optimal weight: 50.0000 chunk 19 optimal weight: 120.0000 chunk 299 optimal weight: 4.9990 chunk 203 optimal weight: 20.0000 chunk 286 optimal weight: 9.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN B 26 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN E 131 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 26 ASN O 92 ASN ** P 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 174 GLN R 26 ASN R 33 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.163314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.122046 restraints weight = 33629.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.125276 restraints weight = 22785.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.127823 restraints weight = 17654.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.129274 restraints weight = 14878.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.130230 restraints weight = 13280.469| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25848 Z= 0.204 Angle : 0.724 8.869 35244 Z= 0.399 Chirality : 0.054 0.274 4464 Planarity : 0.004 0.047 4554 Dihedral : 5.881 37.042 3674 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.88 % Favored : 84.12 % Rotamer: Outliers : 5.27 % Allowed : 16.59 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.27 (0.13), residues: 3546 helix: -0.15 (0.19), residues: 792 sheet: -0.17 (0.19), residues: 738 loop : -4.09 (0.11), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 166 TYR 0.010 0.001 TYR I 70 PHE 0.031 0.002 PHE J 185 Details of bonding type rmsd covalent geometry : bond 0.00464 (25848) covalent geometry : angle 0.72411 (35244) hydrogen bonds : bond 0.04073 ( 972) hydrogen bonds : angle 5.18925 ( 2700) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 724 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8643 (tt) REVERT: A 45 GLN cc_start: 0.7885 (tt0) cc_final: 0.7577 (mt0) REVERT: A 84 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8602 (mp10) REVERT: A 132 ASP cc_start: 0.8500 (t0) cc_final: 0.8104 (t0) REVERT: A 147 ASP cc_start: 0.8903 (m-30) cc_final: 0.8528 (m-30) REVERT: C 174 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8046 (mp10) REVERT: D 53 ASN cc_start: 0.8585 (p0) cc_final: 0.7858 (p0) REVERT: D 103 ASN cc_start: 0.7503 (t0) cc_final: 0.6927 (p0) REVERT: D 105 ASP cc_start: 0.9233 (t0) cc_final: 0.8888 (t0) REVERT: D 195 LEU cc_start: 0.9120 (tm) cc_final: 0.8873 (tt) REVERT: F 32 GLN cc_start: 0.7942 (pt0) cc_final: 0.7654 (pt0) REVERT: F 44 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7978 (mm-30) REVERT: F 53 ASN cc_start: 0.8512 (p0) cc_final: 0.8196 (p0) REVERT: F 104 GLN cc_start: 0.8417 (pp30) cc_final: 0.7577 (pp30) REVERT: F 132 ASP cc_start: 0.7973 (t0) cc_final: 0.7514 (t0) REVERT: F 134 ASP cc_start: 0.8418 (p0) cc_final: 0.7903 (p0) REVERT: F 147 ASP cc_start: 0.9038 (m-30) cc_final: 0.8745 (m-30) REVERT: G 66 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8545 (mp) REVERT: G 132 ASP cc_start: 0.7945 (t0) cc_final: 0.7509 (t0) REVERT: H 53 ASN cc_start: 0.8698 (p0) cc_final: 0.8343 (p0) REVERT: H 82 LEU cc_start: 0.9444 (mt) cc_final: 0.9143 (mt) REVERT: H 84 GLN cc_start: 0.8391 (mp10) cc_final: 0.7826 (mp10) REVERT: H 105 ASP cc_start: 0.9215 (t0) cc_final: 0.8908 (t0) REVERT: H 132 ASP cc_start: 0.8037 (t0) cc_final: 0.7674 (t0) REVERT: H 154 ASP cc_start: 0.8185 (t0) cc_final: 0.7903 (t0) REVERT: I 53 ASN cc_start: 0.8792 (p0) cc_final: 0.8578 (p0) REVERT: J 30 PHE cc_start: 0.7770 (t80) cc_final: 0.7155 (t80) REVERT: J 34 LYS cc_start: 0.8585 (tttp) cc_final: 0.8240 (ttmm) REVERT: J 104 GLN cc_start: 0.8140 (pp30) cc_final: 0.7096 (pp30) REVERT: J 134 ASP cc_start: 0.8554 (p0) cc_final: 0.8154 (p0) REVERT: K 53 ASN cc_start: 0.8665 (p0) cc_final: 0.8403 (p0) REVERT: K 132 ASP cc_start: 0.8243 (t0) cc_final: 0.8014 (t0) REVERT: L 53 ASN cc_start: 0.7799 (p0) cc_final: 0.7512 (p0) REVERT: L 132 ASP cc_start: 0.7962 (t0) cc_final: 0.7437 (t0) REVERT: L 135 ASP cc_start: 0.8728 (p0) cc_final: 0.8417 (p0) REVERT: L 147 ASP cc_start: 0.9087 (m-30) cc_final: 0.8840 (m-30) REVERT: M 132 ASP cc_start: 0.7879 (t0) cc_final: 0.7389 (t0) REVERT: M 134 ASP cc_start: 0.8887 (p0) cc_final: 0.8290 (p0) REVERT: N 65 LYS cc_start: 0.9056 (pttt) cc_final: 0.8681 (pttt) REVERT: N 66 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8300 (mp) REVERT: N 132 ASP cc_start: 0.8075 (t0) cc_final: 0.7648 (t0) REVERT: N 154 ASP cc_start: 0.8720 (t0) cc_final: 0.8411 (t0) REVERT: O 132 ASP cc_start: 0.7919 (t0) cc_final: 0.7712 (t0) REVERT: O 135 ASP cc_start: 0.8812 (p0) cc_final: 0.8256 (p0) REVERT: O 147 ASP cc_start: 0.8773 (m-30) cc_final: 0.8229 (m-30) REVERT: P 55 ILE cc_start: 0.8962 (mt) cc_final: 0.8659 (mp) REVERT: P 84 GLN cc_start: 0.8741 (mp10) cc_final: 0.8348 (mp10) REVERT: P 154 ASP cc_start: 0.8745 (t70) cc_final: 0.8505 (t0) REVERT: Q 135 ASP cc_start: 0.8553 (p0) cc_final: 0.8233 (p0) REVERT: Q 147 ASP cc_start: 0.8966 (m-30) cc_final: 0.8564 (m-30) REVERT: R 104 GLN cc_start: 0.8284 (pp30) cc_final: 0.6878 (pp30) REVERT: R 132 ASP cc_start: 0.8427 (t0) cc_final: 0.8048 (t0) REVERT: R 134 ASP cc_start: 0.8252 (p0) cc_final: 0.7621 (p0) REVERT: R 177 PHE cc_start: 0.8123 (p90) cc_final: 0.7643 (p90) outliers start: 147 outliers final: 109 residues processed: 808 average time/residue: 0.1325 time to fit residues: 181.4648 Evaluate side-chains 816 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 702 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 174 GLN Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 177 PHE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 177 PHE Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 62 SER Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 33 GLN Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 45 GLN Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 124 THR Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 169 ILE Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain P residue 88 MET Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 140 ASN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 192 THR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 32 GLN Chi-restraints excluded: chain Q residue 45 GLN Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain Q residue 142 VAL Chi-restraints excluded: chain R residue 33 GLN Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 74 ASN Chi-restraints excluded: chain R residue 88 MET Chi-restraints excluded: chain R residue 152 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 136 optimal weight: 30.0000 chunk 147 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 329 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 319 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 229 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN ** P 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 33 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.163698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.124948 restraints weight = 33711.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.127794 restraints weight = 22917.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.128749 restraints weight = 17895.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.129723 restraints weight = 15773.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.129855 restraints weight = 14457.149| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25848 Z= 0.159 Angle : 0.689 8.109 35244 Z= 0.378 Chirality : 0.053 0.374 4464 Planarity : 0.004 0.056 4554 Dihedral : 5.662 37.264 3674 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.44 % Favored : 85.56 % Rotamer: Outliers : 4.91 % Allowed : 18.78 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.16 (0.13), residues: 3546 helix: -0.11 (0.19), residues: 828 sheet: -0.10 (0.19), residues: 738 loop : -4.07 (0.11), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 166 TYR 0.008 0.001 TYR I 70 PHE 0.032 0.002 PHE J 185 Details of bonding type rmsd covalent geometry : bond 0.00353 (25848) covalent geometry : angle 0.68896 (35244) hydrogen bonds : bond 0.03610 ( 972) hydrogen bonds : angle 5.03702 ( 2700) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 722 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8665 (tt) REVERT: A 84 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8572 (mp10) REVERT: A 132 ASP cc_start: 0.8472 (t0) cc_final: 0.8086 (t0) REVERT: A 147 ASP cc_start: 0.8892 (m-30) cc_final: 0.8531 (m-30) REVERT: D 53 ASN cc_start: 0.8608 (p0) cc_final: 0.7949 (p0) REVERT: D 88 MET cc_start: 0.8272 (mpp) cc_final: 0.8064 (mtm) REVERT: D 103 ASN cc_start: 0.7456 (t0) cc_final: 0.7009 (p0) REVERT: D 195 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8845 (tt) REVERT: E 41 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7385 (mt-10) REVERT: F 32 GLN cc_start: 0.7916 (pt0) cc_final: 0.7556 (pt0) REVERT: F 44 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7887 (mm-30) REVERT: F 53 ASN cc_start: 0.8420 (p0) cc_final: 0.8099 (p0) REVERT: F 104 GLN cc_start: 0.8471 (pp30) cc_final: 0.7714 (pp30) REVERT: F 132 ASP cc_start: 0.7968 (t0) cc_final: 0.7619 (t0) REVERT: F 134 ASP cc_start: 0.8336 (p0) cc_final: 0.7803 (p0) REVERT: F 147 ASP cc_start: 0.9045 (m-30) cc_final: 0.8753 (m-30) REVERT: G 66 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8643 (mp) REVERT: G 82 LEU cc_start: 0.9575 (mt) cc_final: 0.9353 (mt) REVERT: G 132 ASP cc_start: 0.7917 (t0) cc_final: 0.7458 (t0) REVERT: G 154 ASP cc_start: 0.8880 (t0) cc_final: 0.8569 (t0) REVERT: H 53 ASN cc_start: 0.8676 (p0) cc_final: 0.8312 (p0) REVERT: H 82 LEU cc_start: 0.9438 (mt) cc_final: 0.9118 (mt) REVERT: H 105 ASP cc_start: 0.9141 (t0) cc_final: 0.8885 (t0) REVERT: H 132 ASP cc_start: 0.7999 (t0) cc_final: 0.7640 (t0) REVERT: H 154 ASP cc_start: 0.8161 (t0) cc_final: 0.7845 (t0) REVERT: I 53 ASN cc_start: 0.8756 (p0) cc_final: 0.8516 (p0) REVERT: I 65 LYS cc_start: 0.8661 (pttm) cc_final: 0.8353 (ptpt) REVERT: J 30 PHE cc_start: 0.7825 (t80) cc_final: 0.7275 (t80) REVERT: J 34 LYS cc_start: 0.8458 (tttp) cc_final: 0.8183 (ttmm) REVERT: J 104 GLN cc_start: 0.8096 (pp30) cc_final: 0.7104 (pp30) REVERT: J 134 ASP cc_start: 0.8520 (p0) cc_final: 0.8097 (p0) REVERT: K 132 ASP cc_start: 0.8206 (t0) cc_final: 0.7980 (t0) REVERT: L 33 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6838 (pp30) REVERT: L 53 ASN cc_start: 0.7803 (p0) cc_final: 0.7476 (p0) REVERT: L 132 ASP cc_start: 0.7967 (t0) cc_final: 0.7416 (t0) REVERT: L 135 ASP cc_start: 0.8786 (p0) cc_final: 0.8502 (p0) REVERT: L 147 ASP cc_start: 0.9165 (m-30) cc_final: 0.8935 (m-30) REVERT: M 53 ASN cc_start: 0.8954 (p0) cc_final: 0.8651 (p0) REVERT: M 132 ASP cc_start: 0.7945 (t0) cc_final: 0.7465 (t0) REVERT: M 134 ASP cc_start: 0.8884 (p0) cc_final: 0.8289 (p0) REVERT: N 65 LYS cc_start: 0.8996 (pttt) cc_final: 0.8633 (pttt) REVERT: N 66 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8437 (mp) REVERT: N 132 ASP cc_start: 0.8044 (t0) cc_final: 0.7583 (t0) REVERT: N 154 ASP cc_start: 0.8681 (t0) cc_final: 0.8419 (t0) REVERT: O 132 ASP cc_start: 0.7939 (t0) cc_final: 0.7723 (t0) REVERT: O 135 ASP cc_start: 0.8763 (p0) cc_final: 0.8242 (p0) REVERT: O 147 ASP cc_start: 0.8790 (m-30) cc_final: 0.8260 (m-30) REVERT: P 84 GLN cc_start: 0.8734 (mp10) cc_final: 0.8139 (mp10) REVERT: R 104 GLN cc_start: 0.8247 (pp30) cc_final: 0.7145 (pp30) REVERT: R 106 MET cc_start: 0.7394 (ptp) cc_final: 0.7167 (ttp) REVERT: R 132 ASP cc_start: 0.8375 (t0) cc_final: 0.8091 (t0) REVERT: R 134 ASP cc_start: 0.8289 (p0) cc_final: 0.7650 (p0) REVERT: R 174 GLN cc_start: 0.8570 (mt0) cc_final: 0.8320 (mt0) REVERT: R 177 PHE cc_start: 0.8158 (p90) cc_final: 0.7712 (p90) outliers start: 137 outliers final: 116 residues processed: 803 average time/residue: 0.1338 time to fit residues: 181.9935 Evaluate side-chains 827 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 705 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 174 GLN Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 174 GLN Chi-restraints excluded: chain D residue 177 PHE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 177 PHE Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 62 SER Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 33 GLN Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 139 ASP Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 45 GLN Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 169 ILE Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 112 SER Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain P residue 88 MET Chi-restraints excluded: chain P residue 140 ASN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 186 THR Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 192 THR Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 32 GLN Chi-restraints excluded: chain Q residue 45 GLN Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 88 MET Chi-restraints excluded: chain R residue 140 ASN Chi-restraints excluded: chain R residue 152 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 106 optimal weight: 10.0000 chunk 335 optimal weight: 0.6980 chunk 14 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 78 optimal weight: 50.0000 chunk 197 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 278 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN B 26 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** C 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 140 ASN R 33 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.171392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.130496 restraints weight = 33483.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.134011 restraints weight = 22764.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.136234 restraints weight = 17613.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.138118 restraints weight = 14867.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.139095 restraints weight = 13180.584| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25848 Z= 0.116 Angle : 0.637 8.781 35244 Z= 0.348 Chirality : 0.051 0.319 4464 Planarity : 0.003 0.055 4554 Dihedral : 5.112 21.998 3672 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.72 % Favored : 87.28 % Rotamer: Outliers : 4.16 % Allowed : 20.18 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.86 (0.13), residues: 3546 helix: 0.18 (0.19), residues: 828 sheet: 0.14 (0.19), residues: 738 loop : -3.92 (0.11), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 166 TYR 0.005 0.001 TYR I 91 PHE 0.029 0.002 PHE J 185 Details of bonding type rmsd covalent geometry : bond 0.00235 (25848) covalent geometry : angle 0.63650 (35244) hydrogen bonds : bond 0.02873 ( 972) hydrogen bonds : angle 4.67061 ( 2700) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 760 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8550 (mp10) REVERT: A 132 ASP cc_start: 0.8358 (t0) cc_final: 0.7902 (t0) REVERT: A 147 ASP cc_start: 0.8919 (m-30) cc_final: 0.8589 (m-30) REVERT: D 53 ASN cc_start: 0.8501 (p0) cc_final: 0.7877 (p0) REVERT: D 103 ASN cc_start: 0.7403 (t0) cc_final: 0.7080 (p0) REVERT: F 32 GLN cc_start: 0.8024 (pt0) cc_final: 0.7695 (pt0) REVERT: F 44 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7805 (mm-30) REVERT: F 53 ASN cc_start: 0.8295 (p0) cc_final: 0.7947 (p0) REVERT: F 104 GLN cc_start: 0.8427 (pp30) cc_final: 0.7688 (pp30) REVERT: F 132 ASP cc_start: 0.8088 (t0) cc_final: 0.7640 (t0) REVERT: F 134 ASP cc_start: 0.8129 (p0) cc_final: 0.7645 (p0) REVERT: F 147 ASP cc_start: 0.9025 (m-30) cc_final: 0.8681 (m-30) REVERT: G 100 TYR cc_start: 0.8924 (t80) cc_final: 0.8329 (t80) REVERT: G 132 ASP cc_start: 0.7819 (t0) cc_final: 0.7459 (t0) REVERT: H 53 ASN cc_start: 0.8580 (p0) cc_final: 0.8301 (p0) REVERT: H 105 ASP cc_start: 0.9143 (t0) cc_final: 0.8865 (t0) REVERT: H 152 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.9023 (tt) REVERT: H 154 ASP cc_start: 0.8038 (t0) cc_final: 0.7805 (t0) REVERT: I 53 ASN cc_start: 0.8772 (p0) cc_final: 0.8343 (p0) REVERT: I 65 LYS cc_start: 0.8592 (pttm) cc_final: 0.8237 (ptpt) REVERT: J 30 PHE cc_start: 0.7506 (t80) cc_final: 0.6772 (t80) REVERT: J 34 LYS cc_start: 0.8320 (tttp) cc_final: 0.8006 (ttmm) REVERT: J 104 GLN cc_start: 0.8166 (pp30) cc_final: 0.7186 (pp30) REVERT: J 134 ASP cc_start: 0.8385 (p0) cc_final: 0.8100 (p0) REVERT: L 30 PHE cc_start: 0.7589 (t80) cc_final: 0.7149 (t80) REVERT: L 33 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.6730 (pp30) REVERT: L 53 ASN cc_start: 0.7742 (p0) cc_final: 0.7430 (p0) REVERT: L 132 ASP cc_start: 0.7878 (t0) cc_final: 0.7328 (t0) REVERT: L 135 ASP cc_start: 0.8736 (p0) cc_final: 0.8500 (p0) REVERT: L 147 ASP cc_start: 0.9184 (m-30) cc_final: 0.8960 (m-30) REVERT: M 53 ASN cc_start: 0.8769 (p0) cc_final: 0.8500 (p0) REVERT: M 132 ASP cc_start: 0.7869 (t0) cc_final: 0.7255 (t0) REVERT: M 134 ASP cc_start: 0.8937 (p0) cc_final: 0.8460 (p0) REVERT: M 147 ASP cc_start: 0.9371 (m-30) cc_final: 0.9129 (m-30) REVERT: N 33 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7537 (tm-30) REVERT: N 65 LYS cc_start: 0.8954 (pttt) cc_final: 0.8625 (pttt) REVERT: N 66 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8347 (mp) REVERT: N 104 GLN cc_start: 0.8396 (pp30) cc_final: 0.7615 (pp30) REVERT: N 132 ASP cc_start: 0.8020 (t0) cc_final: 0.7593 (t0) REVERT: O 131 GLN cc_start: 0.8271 (tt0) cc_final: 0.7909 (tt0) REVERT: O 132 ASP cc_start: 0.7846 (t0) cc_final: 0.7579 (t0) REVERT: O 135 ASP cc_start: 0.8730 (p0) cc_final: 0.8246 (p0) REVERT: O 147 ASP cc_start: 0.8756 (m-30) cc_final: 0.8155 (m-30) REVERT: P 84 GLN cc_start: 0.8690 (mp10) cc_final: 0.7994 (mp10) REVERT: Q 10 PHE cc_start: 0.6937 (t80) cc_final: 0.6605 (t80) REVERT: R 104 GLN cc_start: 0.8282 (pp30) cc_final: 0.7449 (pp30) REVERT: R 132 ASP cc_start: 0.8466 (t0) cc_final: 0.7956 (t0) REVERT: R 134 ASP cc_start: 0.8187 (p0) cc_final: 0.7607 (p0) REVERT: R 177 PHE cc_start: 0.8223 (p90) cc_final: 0.7795 (p90) outliers start: 116 outliers final: 92 residues processed: 823 average time/residue: 0.1369 time to fit residues: 191.7771 Evaluate side-chains 814 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 718 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 62 SER Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 33 GLN Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain K residue 139 ASP Chi-restraints excluded: chain K residue 140 ASN Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 195 LEU Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 112 SER Chi-restraints excluded: chain O residue 195 LEU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain P residue 140 ASN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 192 THR Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 45 GLN Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain R residue 33 GLN Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 88 MET Chi-restraints excluded: chain R residue 140 ASN Chi-restraints excluded: chain R residue 165 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 333 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 321 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN B 26 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN J 26 ASN L 26 ASN ** N 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.163948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.125796 restraints weight = 33685.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.127853 restraints weight = 23652.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.130148 restraints weight = 19156.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.131142 restraints weight = 14889.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.131375 restraints weight = 13626.904| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25848 Z= 0.169 Angle : 0.698 10.655 35244 Z= 0.381 Chirality : 0.053 0.299 4464 Planarity : 0.004 0.060 4554 Dihedral : 5.339 24.548 3672 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.93 % Favored : 84.07 % Rotamer: Outliers : 4.95 % Allowed : 21.25 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.79 (0.14), residues: 3546 helix: 0.55 (0.20), residues: 792 sheet: 0.03 (0.19), residues: 738 loop : -3.88 (0.11), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.008 0.001 TYR I 70 PHE 0.035 0.002 PHE J 185 Details of bonding type rmsd covalent geometry : bond 0.00377 (25848) covalent geometry : angle 0.69827 (35244) hydrogen bonds : bond 0.03674 ( 972) hydrogen bonds : angle 4.91831 ( 2700) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 708 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8597 (mp10) REVERT: A 132 ASP cc_start: 0.8449 (t0) cc_final: 0.7827 (t0) REVERT: A 147 ASP cc_start: 0.8877 (m-30) cc_final: 0.8563 (m-30) REVERT: C 55 ILE cc_start: 0.9168 (mt) cc_final: 0.8920 (mp) REVERT: C 66 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8483 (mt) REVERT: D 53 ASN cc_start: 0.8551 (p0) cc_final: 0.7819 (p0) REVERT: D 103 ASN cc_start: 0.7460 (t0) cc_final: 0.7201 (p0) REVERT: F 32 GLN cc_start: 0.7996 (pt0) cc_final: 0.7657 (pt0) REVERT: F 44 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7961 (mm-30) REVERT: F 53 ASN cc_start: 0.8397 (p0) cc_final: 0.7993 (p0) REVERT: F 104 GLN cc_start: 0.8452 (pp30) cc_final: 0.7678 (pp30) REVERT: F 132 ASP cc_start: 0.8042 (t0) cc_final: 0.7580 (t0) REVERT: F 134 ASP cc_start: 0.8330 (p0) cc_final: 0.7884 (p0) REVERT: F 147 ASP cc_start: 0.9059 (m-30) cc_final: 0.8723 (m-30) REVERT: G 132 ASP cc_start: 0.7900 (t0) cc_final: 0.7452 (t0) REVERT: G 198 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8751 (mp) REVERT: H 53 ASN cc_start: 0.8675 (p0) cc_final: 0.8338 (p0) REVERT: H 154 ASP cc_start: 0.8111 (t0) cc_final: 0.7838 (t0) REVERT: I 53 ASN cc_start: 0.8772 (p0) cc_final: 0.8495 (p0) REVERT: I 92 ASN cc_start: 0.7808 (t0) cc_final: 0.7588 (t0) REVERT: J 30 PHE cc_start: 0.7807 (t80) cc_final: 0.7309 (t80) REVERT: J 34 LYS cc_start: 0.8462 (tttp) cc_final: 0.8012 (ttmm) REVERT: J 104 GLN cc_start: 0.8113 (pp30) cc_final: 0.7099 (pp30) REVERT: J 134 ASP cc_start: 0.8520 (p0) cc_final: 0.8141 (p0) REVERT: K 132 ASP cc_start: 0.8280 (t0) cc_final: 0.8071 (t0) REVERT: L 33 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6990 (pp30) REVERT: L 53 ASN cc_start: 0.7860 (p0) cc_final: 0.7501 (p0) REVERT: L 132 ASP cc_start: 0.7948 (t0) cc_final: 0.7415 (t0) REVERT: L 135 ASP cc_start: 0.8680 (p0) cc_final: 0.8426 (p0) REVERT: L 147 ASP cc_start: 0.9188 (m-30) cc_final: 0.8981 (m-30) REVERT: M 132 ASP cc_start: 0.7878 (t0) cc_final: 0.7328 (t0) REVERT: M 134 ASP cc_start: 0.8717 (p0) cc_final: 0.8151 (p0) REVERT: M 147 ASP cc_start: 0.9372 (m-30) cc_final: 0.9119 (m-30) REVERT: N 33 GLN cc_start: 0.7777 (tm-30) cc_final: 0.7553 (tm-30) REVERT: N 65 LYS cc_start: 0.9101 (pttt) cc_final: 0.8688 (pttt) REVERT: N 66 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8417 (mp) REVERT: N 132 ASP cc_start: 0.8124 (t0) cc_final: 0.7729 (t0) REVERT: O 132 ASP cc_start: 0.7949 (t0) cc_final: 0.7703 (t0) REVERT: O 135 ASP cc_start: 0.8777 (p0) cc_final: 0.8259 (p0) REVERT: O 147 ASP cc_start: 0.8726 (m-30) cc_final: 0.8159 (m-30) REVERT: O 177 PHE cc_start: 0.7902 (p90) cc_final: 0.7501 (p90) REVERT: P 55 ILE cc_start: 0.8972 (mt) cc_final: 0.8760 (mp) REVERT: P 184 SER cc_start: 0.8852 (t) cc_final: 0.8171 (p) REVERT: Q 10 PHE cc_start: 0.7069 (t80) cc_final: 0.6649 (t80) REVERT: R 33 GLN cc_start: 0.6010 (pp30) cc_final: 0.5614 (pp30) REVERT: R 66 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8308 (mp) REVERT: R 104 GLN cc_start: 0.8238 (pp30) cc_final: 0.7190 (pp30) REVERT: R 132 ASP cc_start: 0.8562 (t0) cc_final: 0.8196 (t0) REVERT: R 134 ASP cc_start: 0.8207 (p0) cc_final: 0.7608 (p0) REVERT: R 177 PHE cc_start: 0.8270 (p90) cc_final: 0.7801 (p90) outliers start: 138 outliers final: 117 residues processed: 791 average time/residue: 0.1326 time to fit residues: 177.8614 Evaluate side-chains 820 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 697 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 177 PHE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 62 SER Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 33 GLN Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 112 SER Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 140 ASN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 186 THR Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 192 THR Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 32 GLN Chi-restraints excluded: chain Q residue 45 GLN Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 67 LEU Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 88 MET Chi-restraints excluded: chain R residue 140 ASN Chi-restraints excluded: chain R residue 165 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 316 optimal weight: 5.9990 chunk 302 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 chunk 230 optimal weight: 6.9990 chunk 293 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 312 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN B 26 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN ** N 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 33 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.165068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.127128 restraints weight = 33532.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.128975 restraints weight = 24136.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.131381 restraints weight = 19515.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.133033 restraints weight = 15216.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.133399 restraints weight = 13171.242| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25848 Z= 0.145 Angle : 0.676 10.329 35244 Z= 0.369 Chirality : 0.053 0.272 4464 Planarity : 0.004 0.055 4554 Dihedral : 5.260 23.662 3672 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.02 % Favored : 85.98 % Rotamer: Outliers : 4.59 % Allowed : 22.15 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.14), residues: 3546 helix: 0.49 (0.19), residues: 810 sheet: 0.10 (0.19), residues: 738 loop : -3.80 (0.11), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.007 0.001 TYR I 70 PHE 0.030 0.002 PHE J 185 Details of bonding type rmsd covalent geometry : bond 0.00317 (25848) covalent geometry : angle 0.67559 (35244) hydrogen bonds : bond 0.03334 ( 972) hydrogen bonds : angle 4.81721 ( 2700) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 713 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8577 (mp10) REVERT: A 132 ASP cc_start: 0.8416 (t0) cc_final: 0.7797 (t0) REVERT: A 147 ASP cc_start: 0.8855 (m-30) cc_final: 0.8550 (m-30) REVERT: C 55 ILE cc_start: 0.9134 (mt) cc_final: 0.8875 (mp) REVERT: D 53 ASN cc_start: 0.8525 (p0) cc_final: 0.7850 (p0) REVERT: D 103 ASN cc_start: 0.7433 (t0) cc_final: 0.7215 (p0) REVERT: F 32 GLN cc_start: 0.8112 (pt0) cc_final: 0.7802 (pt0) REVERT: F 44 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7966 (mm-30) REVERT: F 53 ASN cc_start: 0.8367 (p0) cc_final: 0.7974 (p0) REVERT: F 104 GLN cc_start: 0.8458 (pp30) cc_final: 0.7675 (pp30) REVERT: F 132 ASP cc_start: 0.7934 (t0) cc_final: 0.7534 (t0) REVERT: F 134 ASP cc_start: 0.8274 (p0) cc_final: 0.7820 (p0) REVERT: F 147 ASP cc_start: 0.9056 (m-30) cc_final: 0.8720 (m-30) REVERT: G 100 TYR cc_start: 0.8941 (t80) cc_final: 0.8263 (t80) REVERT: G 132 ASP cc_start: 0.7914 (t0) cc_final: 0.7503 (t0) REVERT: G 198 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8632 (mp) REVERT: H 53 ASN cc_start: 0.8615 (p0) cc_final: 0.8259 (p0) REVERT: H 154 ASP cc_start: 0.8040 (t0) cc_final: 0.7798 (t0) REVERT: I 53 ASN cc_start: 0.8740 (p0) cc_final: 0.8471 (p0) REVERT: J 30 PHE cc_start: 0.7898 (t80) cc_final: 0.7525 (t80) REVERT: J 34 LYS cc_start: 0.8366 (tttp) cc_final: 0.8043 (ttmm) REVERT: J 104 GLN cc_start: 0.8136 (pp30) cc_final: 0.7120 (pp30) REVERT: J 134 ASP cc_start: 0.8529 (p0) cc_final: 0.8126 (p0) REVERT: K 53 ASN cc_start: 0.8595 (p0) cc_final: 0.8332 (p0) REVERT: L 33 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.6656 (pp30) REVERT: L 53 ASN cc_start: 0.7841 (p0) cc_final: 0.7473 (p0) REVERT: L 132 ASP cc_start: 0.7943 (t0) cc_final: 0.7410 (t0) REVERT: L 135 ASP cc_start: 0.8714 (p0) cc_final: 0.8424 (p0) REVERT: L 147 ASP cc_start: 0.9205 (m-30) cc_final: 0.8980 (m-30) REVERT: M 53 ASN cc_start: 0.8739 (p0) cc_final: 0.8364 (p0) REVERT: M 132 ASP cc_start: 0.7904 (t0) cc_final: 0.7345 (t0) REVERT: M 134 ASP cc_start: 0.8756 (p0) cc_final: 0.8223 (p0) REVERT: M 147 ASP cc_start: 0.9389 (m-30) cc_final: 0.9123 (m-30) REVERT: N 65 LYS cc_start: 0.8991 (pttt) cc_final: 0.8568 (pttt) REVERT: N 66 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8328 (mp) REVERT: N 132 ASP cc_start: 0.8093 (t0) cc_final: 0.7699 (t0) REVERT: O 132 ASP cc_start: 0.7888 (t0) cc_final: 0.7579 (t0) REVERT: O 135 ASP cc_start: 0.8696 (p0) cc_final: 0.8440 (p0) REVERT: O 147 ASP cc_start: 0.8670 (m-30) cc_final: 0.8191 (m-30) REVERT: P 55 ILE cc_start: 0.8909 (mt) cc_final: 0.8705 (mp) REVERT: P 84 GLN cc_start: 0.8855 (mp10) cc_final: 0.8609 (mp10) REVERT: P 184 SER cc_start: 0.8935 (t) cc_final: 0.8243 (p) REVERT: Q 10 PHE cc_start: 0.7105 (t80) cc_final: 0.6696 (t80) REVERT: R 66 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8281 (mp) REVERT: R 104 GLN cc_start: 0.8320 (pp30) cc_final: 0.7266 (pp30) REVERT: R 132 ASP cc_start: 0.8596 (t0) cc_final: 0.8181 (t0) REVERT: R 134 ASP cc_start: 0.8213 (p0) cc_final: 0.7592 (p0) outliers start: 128 outliers final: 113 residues processed: 795 average time/residue: 0.1279 time to fit residues: 172.3811 Evaluate side-chains 824 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 706 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 62 SER Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 33 GLN Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 112 SER Chi-restraints excluded: chain O residue 195 LEU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 140 ASN Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 192 THR Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 32 GLN Chi-restraints excluded: chain Q residue 45 GLN Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 33 GLN Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 88 MET Chi-restraints excluded: chain R residue 140 ASN Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 165 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 61 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 39 optimal weight: 30.0000 chunk 273 optimal weight: 7.9990 chunk 282 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 179 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 59 optimal weight: 40.0000 chunk 323 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 ASN J 53 ASN J 126 GLN ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN ** P 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 174 GLN R 33 GLN R 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.161710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.123694 restraints weight = 33893.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.125777 restraints weight = 23538.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.128079 restraints weight = 18667.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.129263 restraints weight = 14927.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.129448 restraints weight = 13182.328| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25848 Z= 0.205 Angle : 0.748 11.191 35244 Z= 0.410 Chirality : 0.055 0.275 4464 Planarity : 0.004 0.058 4554 Dihedral : 5.600 24.359 3672 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 17.77 % Favored : 82.21 % Rotamer: Outliers : 5.48 % Allowed : 21.65 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.82 (0.13), residues: 3546 helix: 0.64 (0.20), residues: 792 sheet: -0.07 (0.18), residues: 738 loop : -3.92 (0.11), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.010 0.001 TYR I 70 PHE 0.040 0.002 PHE J 185 Details of bonding type rmsd covalent geometry : bond 0.00470 (25848) covalent geometry : angle 0.74789 (35244) hydrogen bonds : bond 0.04103 ( 972) hydrogen bonds : angle 5.12908 ( 2700) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 703 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8570 (tt) REVERT: A 84 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8631 (mp10) REVERT: A 132 ASP cc_start: 0.8538 (t0) cc_final: 0.7933 (t0) REVERT: A 147 ASP cc_start: 0.8799 (m-30) cc_final: 0.8514 (m-30) REVERT: D 53 ASN cc_start: 0.8596 (p0) cc_final: 0.8125 (p0) REVERT: D 103 ASN cc_start: 0.7602 (t0) cc_final: 0.7215 (p0) REVERT: F 32 GLN cc_start: 0.8102 (pt0) cc_final: 0.7784 (pt0) REVERT: F 44 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8028 (mm-30) REVERT: F 53 ASN cc_start: 0.8531 (p0) cc_final: 0.8158 (p0) REVERT: F 104 GLN cc_start: 0.8605 (pp30) cc_final: 0.7798 (pp30) REVERT: F 132 ASP cc_start: 0.7920 (t0) cc_final: 0.7507 (t0) REVERT: F 134 ASP cc_start: 0.8455 (p0) cc_final: 0.7922 (p0) REVERT: F 147 ASP cc_start: 0.9073 (m-30) cc_final: 0.8738 (m-30) REVERT: F 162 GLU cc_start: 0.5561 (pm20) cc_final: 0.5019 (pm20) REVERT: G 132 ASP cc_start: 0.7906 (t0) cc_final: 0.7515 (t0) REVERT: G 198 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8798 (mp) REVERT: H 53 ASN cc_start: 0.8689 (p0) cc_final: 0.8366 (p0) REVERT: H 154 ASP cc_start: 0.8116 (t0) cc_final: 0.7791 (t0) REVERT: I 53 ASN cc_start: 0.8811 (p0) cc_final: 0.8521 (p0) REVERT: I 65 LYS cc_start: 0.8594 (pttm) cc_final: 0.8286 (pttm) REVERT: J 8 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7819 (mt) REVERT: J 30 PHE cc_start: 0.7942 (t80) cc_final: 0.7556 (t80) REVERT: J 34 LYS cc_start: 0.8423 (tttp) cc_final: 0.8078 (ttmm) REVERT: J 134 ASP cc_start: 0.8588 (p0) cc_final: 0.8174 (p0) REVERT: K 53 ASN cc_start: 0.8650 (p0) cc_final: 0.8371 (p0) REVERT: L 33 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6889 (pp30) REVERT: L 53 ASN cc_start: 0.7878 (p0) cc_final: 0.7489 (p0) REVERT: L 132 ASP cc_start: 0.8018 (t0) cc_final: 0.7493 (t0) REVERT: L 135 ASP cc_start: 0.8714 (p0) cc_final: 0.8409 (p0) REVERT: L 147 ASP cc_start: 0.9102 (m-30) cc_final: 0.8896 (m-30) REVERT: L 154 ASP cc_start: 0.8490 (t0) cc_final: 0.8223 (t0) REVERT: M 132 ASP cc_start: 0.7954 (t0) cc_final: 0.7480 (t0) REVERT: M 134 ASP cc_start: 0.8778 (p0) cc_final: 0.8236 (p0) REVERT: M 147 ASP cc_start: 0.9373 (m-30) cc_final: 0.9149 (m-30) REVERT: N 65 LYS cc_start: 0.9099 (pttt) cc_final: 0.8768 (pttt) REVERT: N 66 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8273 (mp) REVERT: N 132 ASP cc_start: 0.8045 (t0) cc_final: 0.7656 (t0) REVERT: N 184 SER cc_start: 0.9064 (t) cc_final: 0.8632 (p) REVERT: O 10 PHE cc_start: 0.7068 (t80) cc_final: 0.6712 (t80) REVERT: O 132 ASP cc_start: 0.8000 (t0) cc_final: 0.7688 (t0) REVERT: O 135 ASP cc_start: 0.8742 (p0) cc_final: 0.8429 (p0) REVERT: O 147 ASP cc_start: 0.8568 (m-30) cc_final: 0.8154 (m-30) REVERT: O 177 PHE cc_start: 0.7904 (p90) cc_final: 0.7483 (p90) REVERT: P 84 GLN cc_start: 0.8798 (mp10) cc_final: 0.8502 (mp10) REVERT: P 184 SER cc_start: 0.9028 (t) cc_final: 0.8305 (p) REVERT: R 66 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8324 (mp) REVERT: R 104 GLN cc_start: 0.8273 (pp30) cc_final: 0.7206 (pp30) REVERT: R 132 ASP cc_start: 0.8529 (t0) cc_final: 0.8203 (t0) REVERT: R 134 ASP cc_start: 0.8287 (p0) cc_final: 0.7724 (p0) outliers start: 153 outliers final: 129 residues processed: 793 average time/residue: 0.1318 time to fit residues: 176.7589 Evaluate side-chains 834 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 698 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 13 MET Chi-restraints excluded: chain H residue 25 ILE Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 62 SER Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 53 ASN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 92 ASN Chi-restraints excluded: chain O residue 112 SER Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 195 LEU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 186 THR Chi-restraints excluded: chain P residue 190 SER Chi-restraints excluded: chain P residue 192 THR Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 32 GLN Chi-restraints excluded: chain Q residue 45 GLN Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 33 GLN Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 88 MET Chi-restraints excluded: chain R residue 140 ASN Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 165 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 304 optimal weight: 9.9990 chunk 321 optimal weight: 20.0000 chunk 188 optimal weight: 6.9990 chunk 246 optimal weight: 0.0670 chunk 253 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 316 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 214 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN H 131 GLN J 53 ASN K 33 GLN L 26 ASN M 140 ASN N 84 GLN ** N 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN P 174 GLN R 33 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.164074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.126236 restraints weight = 33660.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.128353 restraints weight = 24050.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.130849 restraints weight = 18467.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.132226 restraints weight = 14756.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.132321 restraints weight = 13043.761| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25848 Z= 0.150 Angle : 0.707 10.116 35244 Z= 0.387 Chirality : 0.054 0.263 4464 Planarity : 0.004 0.057 4554 Dihedral : 5.403 23.564 3672 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.21 % Favored : 85.79 % Rotamer: Outliers : 4.37 % Allowed : 22.72 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.14), residues: 3546 helix: 0.56 (0.20), residues: 810 sheet: 0.04 (0.19), residues: 738 loop : -3.81 (0.11), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.007 0.001 TYR I 70 PHE 0.037 0.002 PHE J 185 Details of bonding type rmsd covalent geometry : bond 0.00328 (25848) covalent geometry : angle 0.70675 (35244) hydrogen bonds : bond 0.03531 ( 972) hydrogen bonds : angle 4.90857 ( 2700) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7092 Ramachandran restraints generated. 3546 Oldfield, 0 Emsley, 3546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 719 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8604 (mp10) REVERT: A 132 ASP cc_start: 0.8471 (t0) cc_final: 0.8055 (t0) REVERT: A 147 ASP cc_start: 0.8854 (m-30) cc_final: 0.8479 (m-30) REVERT: B 104 GLN cc_start: 0.8442 (pp30) cc_final: 0.8169 (pp30) REVERT: C 55 ILE cc_start: 0.9121 (mt) cc_final: 0.8858 (mp) REVERT: D 53 ASN cc_start: 0.8585 (p0) cc_final: 0.7816 (p0) REVERT: D 103 ASN cc_start: 0.7569 (t0) cc_final: 0.7250 (p0) REVERT: F 32 GLN cc_start: 0.8110 (pt0) cc_final: 0.7788 (pt0) REVERT: F 44 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7971 (mm-30) REVERT: F 53 ASN cc_start: 0.8401 (p0) cc_final: 0.8073 (p0) REVERT: F 104 GLN cc_start: 0.8576 (pp30) cc_final: 0.7813 (pp30) REVERT: F 132 ASP cc_start: 0.7943 (t0) cc_final: 0.7561 (t0) REVERT: F 134 ASP cc_start: 0.8311 (p0) cc_final: 0.7756 (p0) REVERT: F 147 ASP cc_start: 0.9039 (m-30) cc_final: 0.8702 (m-30) REVERT: G 132 ASP cc_start: 0.7830 (t0) cc_final: 0.7451 (t0) REVERT: G 198 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8727 (mp) REVERT: H 53 ASN cc_start: 0.8634 (p0) cc_final: 0.8302 (p0) REVERT: H 154 ASP cc_start: 0.8005 (t0) cc_final: 0.7750 (t0) REVERT: I 53 ASN cc_start: 0.8763 (p0) cc_final: 0.8486 (p0) REVERT: I 65 LYS cc_start: 0.8561 (pttm) cc_final: 0.8269 (ptpt) REVERT: I 92 ASN cc_start: 0.7783 (t0) cc_final: 0.7569 (t0) REVERT: J 8 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7798 (mt) REVERT: J 30 PHE cc_start: 0.7944 (t80) cc_final: 0.7575 (t80) REVERT: J 34 LYS cc_start: 0.8177 (tttp) cc_final: 0.7922 (ttmm) REVERT: J 104 GLN cc_start: 0.8114 (pp30) cc_final: 0.7116 (pp30) REVERT: J 134 ASP cc_start: 0.8521 (p0) cc_final: 0.8092 (p0) REVERT: K 53 ASN cc_start: 0.8599 (p0) cc_final: 0.8332 (p0) REVERT: L 30 PHE cc_start: 0.7739 (t80) cc_final: 0.7488 (t80) REVERT: L 33 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6836 (pp30) REVERT: L 53 ASN cc_start: 0.7850 (p0) cc_final: 0.7465 (p0) REVERT: L 132 ASP cc_start: 0.7970 (t0) cc_final: 0.7447 (t0) REVERT: L 135 ASP cc_start: 0.8692 (p0) cc_final: 0.8358 (p0) REVERT: L 147 ASP cc_start: 0.9173 (m-30) cc_final: 0.8970 (m-30) REVERT: L 154 ASP cc_start: 0.8309 (t0) cc_final: 0.8044 (t0) REVERT: M 132 ASP cc_start: 0.7711 (t0) cc_final: 0.7210 (t0) REVERT: M 134 ASP cc_start: 0.8717 (p0) cc_final: 0.8162 (p0) REVERT: M 147 ASP cc_start: 0.9327 (m-30) cc_final: 0.9127 (m-30) REVERT: M 154 ASP cc_start: 0.8261 (t70) cc_final: 0.7748 (t0) REVERT: N 65 LYS cc_start: 0.8997 (pttt) cc_final: 0.8616 (pttt) REVERT: N 66 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8319 (mp) REVERT: N 104 GLN cc_start: 0.8501 (pp30) cc_final: 0.8163 (pp30) REVERT: N 132 ASP cc_start: 0.8073 (t0) cc_final: 0.7660 (t0) REVERT: N 184 SER cc_start: 0.8918 (t) cc_final: 0.8698 (m) REVERT: O 13 MET cc_start: 0.7305 (mtp) cc_final: 0.7065 (mtp) REVERT: O 132 ASP cc_start: 0.7977 (t0) cc_final: 0.7653 (t0) REVERT: O 135 ASP cc_start: 0.8694 (p0) cc_final: 0.8406 (p0) REVERT: O 145 LYS cc_start: 0.9078 (ttpp) cc_final: 0.8599 (tmtt) REVERT: O 147 ASP cc_start: 0.8551 (m-30) cc_final: 0.8104 (m-30) REVERT: P 55 ILE cc_start: 0.8909 (mt) cc_final: 0.8673 (mp) REVERT: P 84 GLN cc_start: 0.8892 (mp10) cc_final: 0.8608 (mp10) REVERT: P 184 SER cc_start: 0.8973 (t) cc_final: 0.8311 (p) REVERT: Q 10 PHE cc_start: 0.7228 (t80) cc_final: 0.6819 (t80) REVERT: Q 135 ASP cc_start: 0.8394 (m-30) cc_final: 0.7859 (m-30) REVERT: R 66 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8302 (mp) REVERT: R 104 GLN cc_start: 0.8288 (pp30) cc_final: 0.7224 (pp30) REVERT: R 132 ASP cc_start: 0.8494 (t0) cc_final: 0.8086 (t0) REVERT: R 134 ASP cc_start: 0.8252 (p0) cc_final: 0.7627 (p0) outliers start: 122 outliers final: 108 residues processed: 796 average time/residue: 0.1304 time to fit residues: 175.9871 Evaluate side-chains 827 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 713 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 13 MET Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 62 SER Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 53 ASN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain K residue 31 LEU Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 33 GLN Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain M residue 33 GLN Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 192 THR Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 25 ILE Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 66 LEU Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 92 ASN Chi-restraints excluded: chain O residue 112 SER Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 195 LEU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 192 THR Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 32 GLN Chi-restraints excluded: chain Q residue 45 GLN Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 33 GLN Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 88 MET Chi-restraints excluded: chain R residue 140 ASN Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 165 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 256 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 165 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 206 optimal weight: 0.5980 chunk 292 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 211 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 ASN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 ASN J 53 ASN K 33 GLN ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 ASN ** P 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 174 GLN R 33 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.163120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.123693 restraints weight = 33588.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.127131 restraints weight = 23211.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.128475 restraints weight = 18662.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.130165 restraints weight = 15400.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.130719 restraints weight = 13087.134| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25848 Z= 0.194 Angle : 0.742 10.939 35244 Z= 0.407 Chirality : 0.055 0.277 4464 Planarity : 0.004 0.059 4554 Dihedral : 5.552 23.947 3672 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 17.32 % Favored : 82.66 % Rotamer: Outliers : 4.87 % Allowed : 22.33 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.76 (0.14), residues: 3546 helix: 0.57 (0.20), residues: 810 sheet: -0.06 (0.18), residues: 738 loop : -3.86 (0.11), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.009 0.001 TYR I 70 PHE 0.046 0.002 PHE J 185 Details of bonding type rmsd covalent geometry : bond 0.00441 (25848) covalent geometry : angle 0.74173 (35244) hydrogen bonds : bond 0.03985 ( 972) hydrogen bonds : angle 5.07263 ( 2700) =============================================================================== Job complete usr+sys time: 4540.67 seconds wall clock time: 78 minutes 55.21 seconds (4735.21 seconds total)