Starting phenix.real_space_refine on Mon Sep 30 07:15:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1l_6876/09_2024/5z1l_6876.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1l_6876/09_2024/5z1l_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1l_6876/09_2024/5z1l_6876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1l_6876/09_2024/5z1l_6876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1l_6876/09_2024/5z1l_6876.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z1l_6876/09_2024/5z1l_6876.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, R Time building chain proxies: 5.90, per 1000 atoms: 0.23 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: 5.87 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 3.75 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: 8.10 Time building geometry restraints manager: 6.85 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 0.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.920 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 45.150 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.080 ------------------------------------------------------------------------------- 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= 0.286 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 PHE 0.036 0.004 PHE G 185 TYR 0.005 0.001 TYR K 91 ARG 0.001 0.000 ARG C 166 *********************** 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 fitting. rotamer outliers: 18 poor density : 945 time to evaluate : 2.563 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: 0.6510 (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: 0.8700 (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: 0.7420 (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: 0.6585 (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: 0.7661 (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: 0.2857 time to fit residues: 460.6760 Evaluate side-chains 742 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 734 time to evaluate : 2.606 ------------------------------------------------------------------------------- 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 288 optimal weight: 7.9990 chunk 259 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 199 optimal weight: 8.9990 chunk 310 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** 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 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 131 GLN R 174 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25848 Z= 0.288 Angle : 0.743 10.058 35244 Z= 0.403 Chirality : 0.053 0.294 4464 Planarity : 0.004 0.045 4554 Dihedral : 6.229 38.284 3688 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.16 % Favored : 85.84 % Rotamer: Outliers : 4.77 % Allowed : 12.54 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.12), residues: 3546 helix: -1.06 (0.17), residues: 810 sheet: -0.17 (0.19), residues: 738 loop : -4.21 (0.10), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHE N 185 TYR 0.008 0.001 TYR O 70 ARG 0.004 0.001 ARG L 166 *********************** 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 908 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 775 time to evaluate : 2.787 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 24 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8633 (tt) REVERT: A 45 GLN cc_start: 0.7635 (tt0) cc_final: 0.7423 (mt0) REVERT: A 84 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8485 (mp10) REVERT: A 129 ILE cc_start: 0.8820 (mt) cc_final: 0.8592 (mt) REVERT: A 132 ASP cc_start: 0.8506 (t0) cc_final: 0.7976 (t0) REVERT: A 134 ASP cc_start: 0.8479 (p0) cc_final: 0.8254 (p0) REVERT: A 147 ASP cc_start: 0.8893 (m-30) cc_final: 0.8549 (m-30) REVERT: B 66 LEU cc_start: 0.8494 (mp) cc_final: 0.8205 (mt) REVERT: B 147 ASP cc_start: 0.8746 (m-30) cc_final: 0.8482 (m-30) REVERT: C 55 ILE cc_start: 0.9116 (mt) cc_final: 0.8849 (mp) REVERT: C 105 ASP cc_start: 0.9175 (t0) cc_final: 0.8793 (t0) REVERT: D 48 SER cc_start: 0.9484 (m) cc_final: 0.9239 (m) REVERT: D 53 ASN cc_start: 0.8796 (p0) cc_final: 0.8162 (p0) REVERT: D 103 ASN cc_start: 0.7457 (t0) cc_final: 0.6862 (p0) REVERT: D 105 ASP cc_start: 0.9047 (t0) cc_final: 0.8772 (t0) REVERT: D 195 LEU cc_start: 0.9160 (tm) cc_final: 0.8898 (tt) REVERT: F 32 GLN cc_start: 0.8281 (pt0) cc_final: 0.7771 (pt0) REVERT: F 53 ASN cc_start: 0.8462 (p0) cc_final: 0.8205 (p0) REVERT: F 132 ASP cc_start: 0.8130 (t0) cc_final: 0.7617 (t0) REVERT: F 134 ASP cc_start: 0.8533 (p0) cc_final: 0.7848 (p0) REVERT: F 135 ASP cc_start: 0.8873 (p0) cc_final: 0.8584 (p0) REVERT: F 147 ASP cc_start: 0.9299 (m-30) cc_final: 0.8965 (m-30) REVERT: G 26 ASN cc_start: 0.8367 (m110) cc_final: 0.8151 (t0) REVERT: G 132 ASP cc_start: 0.7951 (t0) cc_final: 0.7470 (t0) REVERT: H 53 ASN cc_start: 0.8739 (p0) cc_final: 0.8531 (p0) REVERT: H 88 MET cc_start: 0.8028 (mpp) cc_final: 0.7681 (mtt) REVERT: H 198 LEU cc_start: 0.9000 (mp) cc_final: 0.8745 (mt) REVERT: I 53 ASN cc_start: 0.8897 (p0) cc_final: 0.8518 (p0) REVERT: I 70 TYR cc_start: 0.8600 (m-80) cc_final: 0.8393 (m-80) REVERT: J 104 GLN cc_start: 0.8264 (pp30) cc_final: 0.7037 (pp30) REVERT: J 134 ASP cc_start: 0.8488 (p0) cc_final: 0.8029 (p0) REVERT: K 132 ASP cc_start: 0.8248 (t0) cc_final: 0.7955 (t0) REVERT: K 135 ASP cc_start: 0.8569 (p0) cc_final: 0.8185 (p0) REVERT: L 53 ASN cc_start: 0.7992 (p0) cc_final: 0.7748 (p0) REVERT: L 132 ASP cc_start: 0.7978 (t0) cc_final: 0.7290 (t0) REVERT: L 135 ASP cc_start: 0.8647 (p0) cc_final: 0.8405 (p0) REVERT: L 147 ASP cc_start: 0.9146 (m-30) cc_final: 0.8890 (m-30) REVERT: M 132 ASP cc_start: 0.7986 (t0) cc_final: 0.7386 (t0) REVERT: M 134 ASP cc_start: 0.9069 (p0) cc_final: 0.8516 (p0) REVERT: M 147 ASP cc_start: 0.9384 (m-30) cc_final: 0.9066 (m-30) REVERT: N 26 ASN cc_start: 0.8115 (m110) cc_final: 0.7882 (m-40) REVERT: N 65 LYS cc_start: 0.9145 (pttt) cc_final: 0.8770 (pttt) REVERT: N 132 ASP cc_start: 0.8025 (t0) cc_final: 0.7618 (t0) REVERT: N 154 ASP cc_start: 0.8544 (t0) cc_final: 0.8265 (t0) REVERT: N 174 GLN cc_start: 0.8785 (mm110) cc_final: 0.8521 (mm-40) REVERT: O 132 ASP cc_start: 0.7988 (t0) cc_final: 0.7658 (t0) REVERT: O 147 ASP cc_start: 0.8812 (m-30) cc_final: 0.8240 (m-30) REVERT: O 177 PHE cc_start: 0.7936 (p90) cc_final: 0.7549 (p90) REVERT: P 34 LYS cc_start: 0.8049 (tppt) cc_final: 0.7848 (tppt) REVERT: P 55 ILE cc_start: 0.9071 (mt) cc_final: 0.8847 (mp) REVERT: P 84 GLN cc_start: 0.8674 (mp10) cc_final: 0.8219 (mp10) REVERT: P 154 ASP cc_start: 0.8670 (t70) cc_final: 0.8236 (t0) REVERT: P 173 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8365 (t) REVERT: Q 10 PHE cc_start: 0.7011 (t80) cc_final: 0.6769 (t80) REVERT: Q 13 MET cc_start: 0.7888 (mtp) cc_final: 0.7672 (mtp) REVERT: Q 132 ASP cc_start: 0.7127 (t0) cc_final: 0.6835 (t0) REVERT: Q 147 ASP cc_start: 0.9030 (m-30) cc_final: 0.8667 (m-30) REVERT: R 53 ASN cc_start: 0.8395 (p0) cc_final: 0.8187 (p0) REVERT: R 74 ASN cc_start: 0.8742 (t0) cc_final: 0.8477 (t0) REVERT: R 103 ASN cc_start: 0.7481 (t0) cc_final: 0.7228 (t0) REVERT: R 132 ASP cc_start: 0.8527 (t0) cc_final: 0.8074 (t0) REVERT: R 147 ASP cc_start: 0.9132 (m-30) cc_final: 0.8749 (m-30) outliers start: 133 outliers final: 75 residues processed: 854 average time/residue: 0.2895 time to fit residues: 417.2865 Evaluate side-chains 811 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 733 time to evaluate : 2.449 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 62 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 67 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain L residue 6 THR 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 85 THR Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 25 ILE Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain P residue 129 ILE Chi-restraints excluded: chain P residue 173 VAL Chi-restraints excluded: chain P residue 174 GLN 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 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 172 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 258 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 311 optimal weight: 3.9990 chunk 336 optimal weight: 20.0000 chunk 277 optimal weight: 3.9990 chunk 308 optimal weight: 30.0000 chunk 106 optimal weight: 4.9990 chunk 249 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 C 45 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN J 174 GLN L 26 ASN M 174 GLN O 84 GLN O 92 ASN ** Q 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 140 ASN R 33 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25848 Z= 0.212 Angle : 0.673 8.721 35244 Z= 0.367 Chirality : 0.052 0.269 4464 Planarity : 0.004 0.045 4554 Dihedral : 5.695 37.427 3678 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.55 % Favored : 87.45 % Rotamer: Outliers : 3.76 % Allowed : 15.41 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.13), residues: 3546 helix: 0.29 (0.20), residues: 702 sheet: -0.32 (0.19), residues: 774 loop : -4.15 (0.10), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.002 PHE J 185 TYR 0.017 0.001 TYR N 100 ARG 0.003 0.000 ARG L 166 *********************** 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 849 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 744 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8646 (tt) REVERT: A 45 GLN cc_start: 0.7684 (tt0) cc_final: 0.7439 (mt0) REVERT: A 84 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8445 (mp10) REVERT: A 132 ASP cc_start: 0.8476 (t0) cc_final: 0.7906 (t0) REVERT: A 147 ASP cc_start: 0.8866 (m-30) cc_final: 0.8506 (m-30) REVERT: C 105 ASP cc_start: 0.9303 (t0) cc_final: 0.9016 (t0) REVERT: C 174 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.8000 (mp10) REVERT: D 53 ASN cc_start: 0.8574 (p0) cc_final: 0.7916 (p0) REVERT: D 103 ASN cc_start: 0.7457 (t0) cc_final: 0.6845 (p0) REVERT: D 105 ASP cc_start: 0.9103 (t0) cc_final: 0.8719 (t0) REVERT: D 195 LEU cc_start: 0.9109 (tm) cc_final: 0.8896 (tt) REVERT: E 154 ASP cc_start: 0.8347 (t70) cc_final: 0.8091 (t0) REVERT: F 32 GLN cc_start: 0.7903 (pt0) cc_final: 0.7589 (pt0) REVERT: F 53 ASN cc_start: 0.8398 (p0) cc_final: 0.8142 (p0) REVERT: F 104 GLN cc_start: 0.8247 (pp30) cc_final: 0.7213 (pp30) REVERT: F 132 ASP cc_start: 0.7958 (t0) cc_final: 0.7667 (t0) REVERT: F 134 ASP cc_start: 0.8503 (p0) cc_final: 0.7876 (p0) REVERT: F 135 ASP cc_start: 0.8937 (p0) cc_final: 0.8607 (p0) REVERT: G 30 PHE cc_start: 0.7535 (t80) cc_final: 0.6827 (t80) REVERT: G 132 ASP cc_start: 0.8051 (t0) cc_final: 0.7630 (t0) REVERT: H 53 ASN cc_start: 0.8716 (p0) cc_final: 0.8483 (p0) REVERT: H 105 ASP cc_start: 0.9149 (t0) cc_final: 0.8822 (t0) REVERT: H 154 ASP cc_start: 0.8144 (t0) cc_final: 0.7936 (t0) REVERT: I 53 ASN cc_start: 0.8813 (p0) cc_final: 0.8440 (p0) REVERT: I 139 ASP cc_start: 0.6112 (t0) cc_final: 0.5792 (t0) REVERT: I 140 ASN cc_start: 0.8102 (p0) cc_final: 0.7845 (p0) REVERT: I 177 PHE cc_start: 0.8385 (p90) cc_final: 0.8153 (p90) REVERT: J 30 PHE cc_start: 0.7468 (t80) cc_final: 0.6883 (t80) REVERT: J 34 LYS cc_start: 0.8447 (tttp) cc_final: 0.8242 (ttmm) REVERT: J 104 GLN cc_start: 0.8248 (pp30) cc_final: 0.7005 (pp30) REVERT: J 134 ASP cc_start: 0.8453 (p0) cc_final: 0.8104 (p0) REVERT: L 53 ASN cc_start: 0.7944 (p0) cc_final: 0.7682 (p0) REVERT: L 132 ASP cc_start: 0.7887 (t0) cc_final: 0.7200 (t0) REVERT: L 147 ASP cc_start: 0.9157 (m-30) cc_final: 0.8913 (m-30) REVERT: M 53 ASN cc_start: 0.8944 (p0) cc_final: 0.8688 (p0) REVERT: M 132 ASP cc_start: 0.7890 (t0) cc_final: 0.7280 (t0) REVERT: M 134 ASP cc_start: 0.9101 (p0) cc_final: 0.8577 (p0) REVERT: M 147 ASP cc_start: 0.9412 (m-30) cc_final: 0.9082 (m-30) REVERT: N 65 LYS cc_start: 0.9077 (pttt) cc_final: 0.8683 (pttt) REVERT: N 132 ASP cc_start: 0.8018 (t0) cc_final: 0.7632 (t0) REVERT: N 154 ASP cc_start: 0.8621 (t0) cc_final: 0.8316 (t0) REVERT: O 132 ASP cc_start: 0.8065 (t0) cc_final: 0.7732 (t0) REVERT: O 135 ASP cc_start: 0.8737 (p0) cc_final: 0.8234 (p0) REVERT: O 147 ASP cc_start: 0.8793 (m-30) cc_final: 0.8201 (m-30) REVERT: O 177 PHE cc_start: 0.8135 (p90) cc_final: 0.7629 (p90) REVERT: P 55 ILE cc_start: 0.9002 (mt) cc_final: 0.8769 (mp) REVERT: P 84 GLN cc_start: 0.8740 (mp10) cc_final: 0.8034 (mp10) REVERT: P 154 ASP cc_start: 0.8657 (t70) cc_final: 0.8368 (t0) REVERT: Q 13 MET cc_start: 0.7915 (mtp) cc_final: 0.7625 (mtp) REVERT: Q 132 ASP cc_start: 0.7112 (t0) cc_final: 0.6847 (t0) REVERT: Q 135 ASP cc_start: 0.8685 (p0) cc_final: 0.8376 (p0) REVERT: Q 147 ASP cc_start: 0.8995 (m-30) cc_final: 0.8697 (m-30) REVERT: R 74 ASN cc_start: 0.8744 (t0) cc_final: 0.8449 (t0) REVERT: R 103 ASN cc_start: 0.7505 (t0) cc_final: 0.7228 (t0) REVERT: R 104 GLN cc_start: 0.8418 (pp30) cc_final: 0.7258 (pp30) REVERT: R 106 MET cc_start: 0.7604 (ptp) cc_final: 0.7354 (ttp) REVERT: R 132 ASP cc_start: 0.8273 (t0) cc_final: 0.7860 (t0) REVERT: R 134 ASP cc_start: 0.8374 (p0) cc_final: 0.7800 (p0) REVERT: R 147 ASP cc_start: 0.9102 (m-30) cc_final: 0.8702 (m-30) REVERT: R 177 PHE cc_start: 0.8193 (p90) cc_final: 0.7747 (p90) outliers start: 105 outliers final: 78 residues processed: 804 average time/residue: 0.2967 time to fit residues: 399.4890 Evaluate side-chains 793 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 712 time to evaluate : 2.567 ------------------------------------------------------------------------------- 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 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 155 VAL Chi-restraints excluded: chain D residue 165 GLU 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 51 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 113 VAL Chi-restraints excluded: chain G residue 155 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 152 ILE Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 67 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 182 VAL 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 L residue 198 LEU 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 46 VAL Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 149 VAL Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 173 VAL 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 Q residue 155 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 88 MET Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 155 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 312 optimal weight: 9.9990 chunk 330 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 295 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN F 26 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN ** N 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 174 GLN O 26 ASN O 92 ASN P 174 GLN Q 174 GLN R 26 ASN R 33 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25848 Z= 0.241 Angle : 0.677 8.270 35244 Z= 0.372 Chirality : 0.052 0.261 4464 Planarity : 0.004 0.056 4554 Dihedral : 5.538 23.964 3672 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.23 % Favored : 84.77 % Rotamer: Outliers : 4.62 % Allowed : 17.03 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.13), residues: 3546 helix: 0.60 (0.20), residues: 702 sheet: -0.33 (0.19), residues: 774 loop : -4.13 (0.10), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.002 PHE F 185 TYR 0.014 0.001 TYR N 100 ARG 0.002 0.000 ARG L 166 *********************** 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 855 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 726 time to evaluate : 2.739 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: 0.9003 (OUTLIER) cc_final: 0.8684 (tt) REVERT: A 45 GLN cc_start: 0.7804 (tt0) cc_final: 0.7520 (mt0) REVERT: A 84 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8584 (mp10) REVERT: A 132 ASP cc_start: 0.8484 (t0) cc_final: 0.8043 (t0) REVERT: A 147 ASP cc_start: 0.8886 (m-30) cc_final: 0.8529 (m-30) REVERT: C 105 ASP cc_start: 0.9320 (t0) cc_final: 0.9088 (t0) REVERT: D 53 ASN cc_start: 0.8571 (p0) cc_final: 0.7876 (p0) REVERT: D 103 ASN cc_start: 0.7465 (t0) cc_final: 0.6956 (p0) REVERT: D 105 ASP cc_start: 0.9236 (t0) cc_final: 0.8909 (t0) REVERT: E 154 ASP cc_start: 0.8452 (t70) cc_final: 0.8176 (t0) REVERT: F 32 GLN cc_start: 0.7886 (pt0) cc_final: 0.7600 (pt0) REVERT: F 53 ASN cc_start: 0.8385 (p0) cc_final: 0.8032 (p0) REVERT: F 104 GLN cc_start: 0.8373 (pp30) cc_final: 0.7367 (pp30) REVERT: F 132 ASP cc_start: 0.7961 (t0) cc_final: 0.7554 (t0) REVERT: F 134 ASP cc_start: 0.8469 (p0) cc_final: 0.7880 (p0) REVERT: F 147 ASP cc_start: 0.9021 (m-30) cc_final: 0.8687 (m-30) REVERT: G 66 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8331 (mp) REVERT: G 132 ASP cc_start: 0.7975 (t0) cc_final: 0.7523 (t0) REVERT: G 154 ASP cc_start: 0.8959 (t0) cc_final: 0.8587 (t0) REVERT: G 198 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8716 (mp) REVERT: H 53 ASN cc_start: 0.8643 (p0) cc_final: 0.8391 (p0) REVERT: H 82 LEU cc_start: 0.9386 (mt) cc_final: 0.9059 (mt) REVERT: H 84 GLN cc_start: 0.8203 (mp10) cc_final: 0.7678 (mp10) REVERT: H 105 ASP cc_start: 0.9138 (t0) cc_final: 0.8805 (t0) REVERT: H 154 ASP cc_start: 0.8195 (t0) cc_final: 0.7895 (t0) REVERT: I 53 ASN cc_start: 0.8813 (p0) cc_final: 0.8446 (p0) REVERT: I 139 ASP cc_start: 0.6590 (t0) cc_final: 0.6301 (t0) REVERT: J 104 GLN cc_start: 0.8125 (pp30) cc_final: 0.6981 (pp30) REVERT: J 134 ASP cc_start: 0.8533 (p0) cc_final: 0.8129 (p0) REVERT: K 132 ASP cc_start: 0.8255 (t0) cc_final: 0.7973 (t0) REVERT: L 53 ASN cc_start: 0.7771 (p0) cc_final: 0.7478 (p0) REVERT: L 132 ASP cc_start: 0.7969 (t0) cc_final: 0.7410 (t0) REVERT: L 135 ASP cc_start: 0.8756 (p0) cc_final: 0.8434 (p0) REVERT: L 147 ASP cc_start: 0.9146 (m-30) cc_final: 0.8907 (m-30) REVERT: M 53 ASN cc_start: 0.8941 (p0) cc_final: 0.8662 (p0) REVERT: M 132 ASP cc_start: 0.7962 (t0) cc_final: 0.7341 (t0) REVERT: M 134 ASP cc_start: 0.8968 (p0) cc_final: 0.8423 (p0) REVERT: M 147 ASP cc_start: 0.9431 (m-30) cc_final: 0.9120 (m-30) REVERT: N 65 LYS cc_start: 0.9012 (pttt) cc_final: 0.8538 (pttt) REVERT: N 66 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8249 (mp) REVERT: N 132 ASP cc_start: 0.8094 (t0) cc_final: 0.7673 (t0) REVERT: N 154 ASP cc_start: 0.8610 (t0) cc_final: 0.8309 (t0) REVERT: O 13 MET cc_start: 0.7828 (mtp) cc_final: 0.7614 (mtt) REVERT: O 132 ASP cc_start: 0.8007 (t0) cc_final: 0.7726 (t0) REVERT: O 135 ASP cc_start: 0.8797 (p0) cc_final: 0.8296 (p0) REVERT: O 147 ASP cc_start: 0.8774 (m-30) cc_final: 0.8205 (m-30) REVERT: P 45 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8326 (tm-30) REVERT: P 55 ILE cc_start: 0.8982 (mt) cc_final: 0.8706 (mp) REVERT: P 84 GLN cc_start: 0.8786 (mp10) cc_final: 0.7997 (mp10) REVERT: P 154 ASP cc_start: 0.8708 (t70) cc_final: 0.8444 (t0) REVERT: Q 13 MET cc_start: 0.8016 (mtp) cc_final: 0.7656 (mtp) REVERT: Q 132 ASP cc_start: 0.7294 (t0) cc_final: 0.7037 (t0) REVERT: Q 135 ASP cc_start: 0.8603 (p0) cc_final: 0.8221 (p0) REVERT: Q 147 ASP cc_start: 0.9127 (m-30) cc_final: 0.8843 (m-30) REVERT: R 32 GLN cc_start: 0.8216 (pt0) cc_final: 0.7979 (pt0) REVERT: R 74 ASN cc_start: 0.8739 (t0) cc_final: 0.8426 (t0) REVERT: R 103 ASN cc_start: 0.7573 (t0) cc_final: 0.7321 (t0) REVERT: R 104 GLN cc_start: 0.8418 (pp30) cc_final: 0.7354 (pp30) REVERT: R 106 MET cc_start: 0.7419 (ptp) cc_final: 0.7176 (ttp) REVERT: R 132 ASP cc_start: 0.8442 (t0) cc_final: 0.8098 (t0) REVERT: R 134 ASP cc_start: 0.8401 (p0) cc_final: 0.7786 (p0) REVERT: R 140 ASN cc_start: 0.8255 (p0) cc_final: 0.7888 (t0) REVERT: R 147 ASP cc_start: 0.9138 (m-30) cc_final: 0.8848 (m-30) REVERT: R 177 PHE cc_start: 0.8175 (p90) cc_final: 0.7703 (p90) outliers start: 129 outliers final: 89 residues processed: 802 average time/residue: 0.2891 time to fit residues: 390.3701 Evaluate side-chains 800 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 706 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 97 VAL Chi-restraints excluded: chain A residue 195 LEU 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 85 THR 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 165 GLU 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 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 51 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 G residue 198 LEU 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 124 THR Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 165 GLU 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 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 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 182 VAL Chi-restraints excluded: chain L residue 198 LEU 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 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 O residue 24 LEU Chi-restraints excluded: chain O residue 33 GLN Chi-restraints excluded: chain O residue 46 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 140 ASN Chi-restraints excluded: chain P residue 155 VAL 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 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 33 GLN Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 67 LEU 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 275 optimal weight: 6.9990 chunk 187 optimal weight: 0.5980 chunk 4 optimal weight: 20.0000 chunk 246 optimal weight: 0.8980 chunk 136 optimal weight: 9.9990 chunk 282 optimal weight: 8.9990 chunk 228 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 296 optimal weight: 5.9990 chunk 83 optimal weight: 0.0670 overall best weight: 2.5122 ------------------------------------------------------------------------------- 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** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN N 84 GLN N 174 GLN O 26 ASN O 92 ASN P 174 GLN R 33 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25848 Z= 0.170 Angle : 0.639 7.765 35244 Z= 0.349 Chirality : 0.051 0.352 4464 Planarity : 0.003 0.054 4554 Dihedral : 5.225 23.232 3672 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.10 % Favored : 87.90 % Rotamer: Outliers : 4.34 % Allowed : 18.49 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.13), residues: 3546 helix: -0.04 (0.19), residues: 828 sheet: 0.12 (0.19), residues: 738 loop : -3.94 (0.11), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.024 0.002 PHE J 185 TYR 0.012 0.001 TYR N 100 ARG 0.002 0.000 ARG L 166 *********************** 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 866 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 745 time to evaluate : 2.547 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 45 GLN cc_start: 0.7706 (tt0) cc_final: 0.7428 (mt0) REVERT: A 84 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8509 (mp10) REVERT: A 132 ASP cc_start: 0.8414 (t0) cc_final: 0.7971 (t0) REVERT: A 147 ASP cc_start: 0.8845 (m-30) cc_final: 0.8506 (m-30) REVERT: B 154 ASP cc_start: 0.7871 (t0) cc_final: 0.7424 (t0) REVERT: C 105 ASP cc_start: 0.9297 (t0) cc_final: 0.9019 (t0) REVERT: D 53 ASN cc_start: 0.8552 (p0) cc_final: 0.7939 (p0) REVERT: D 103 ASN cc_start: 0.7526 (t0) cc_final: 0.6926 (p0) REVERT: D 105 ASP cc_start: 0.9235 (t0) cc_final: 0.8916 (t0) REVERT: E 41 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7378 (mt-10) REVERT: E 154 ASP cc_start: 0.8494 (t70) cc_final: 0.8277 (t0) REVERT: F 32 GLN cc_start: 0.7984 (pt0) cc_final: 0.7630 (pt0) REVERT: F 53 ASN cc_start: 0.8411 (p0) cc_final: 0.8066 (p0) REVERT: F 104 GLN cc_start: 0.8509 (pp30) cc_final: 0.7756 (pp30) REVERT: F 132 ASP cc_start: 0.7925 (t0) cc_final: 0.7523 (t0) REVERT: F 134 ASP cc_start: 0.8365 (p0) cc_final: 0.7817 (p0) REVERT: F 147 ASP cc_start: 0.9040 (m-30) cc_final: 0.8679 (m-30) REVERT: G 30 PHE cc_start: 0.7631 (t80) cc_final: 0.6906 (t80) REVERT: G 132 ASP cc_start: 0.7935 (t0) cc_final: 0.7541 (t0) REVERT: G 154 ASP cc_start: 0.8915 (t0) cc_final: 0.8643 (t0) REVERT: G 198 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8643 (mp) REVERT: H 53 ASN cc_start: 0.8591 (p0) cc_final: 0.8338 (p0) REVERT: H 105 ASP cc_start: 0.9163 (t0) cc_final: 0.8792 (t0) REVERT: H 154 ASP cc_start: 0.8077 (t0) cc_final: 0.7751 (t0) REVERT: I 53 ASN cc_start: 0.8751 (p0) cc_final: 0.8328 (p0) REVERT: I 92 ASN cc_start: 0.7825 (t0) cc_final: 0.7622 (t0) REVERT: I 139 ASP cc_start: 0.6782 (t0) cc_final: 0.6499 (t0) REVERT: J 104 GLN cc_start: 0.8109 (pp30) cc_final: 0.7049 (pp30) REVERT: J 134 ASP cc_start: 0.8475 (p0) cc_final: 0.8080 (p0) REVERT: L 53 ASN cc_start: 0.7730 (p0) cc_final: 0.7437 (p0) REVERT: L 132 ASP cc_start: 0.7917 (t0) cc_final: 0.7342 (t0) REVERT: L 135 ASP cc_start: 0.8833 (p0) cc_final: 0.8528 (p0) REVERT: L 147 ASP cc_start: 0.9160 (m-30) cc_final: 0.8933 (m-30) REVERT: M 53 ASN cc_start: 0.8963 (p0) cc_final: 0.8642 (p0) REVERT: M 132 ASP cc_start: 0.7899 (t0) cc_final: 0.7286 (t0) REVERT: M 134 ASP cc_start: 0.9060 (p0) cc_final: 0.8570 (p0) REVERT: M 147 ASP cc_start: 0.9398 (m-30) cc_final: 0.9092 (m-30) REVERT: N 33 GLN cc_start: 0.7710 (tm-30) cc_final: 0.7476 (tm-30) REVERT: N 65 LYS cc_start: 0.9002 (pttt) cc_final: 0.8656 (pttt) REVERT: N 66 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8161 (mp) REVERT: N 132 ASP cc_start: 0.8064 (t0) cc_final: 0.7655 (t0) REVERT: N 154 ASP cc_start: 0.8565 (t0) cc_final: 0.8283 (t0) REVERT: O 13 MET cc_start: 0.7713 (mtp) cc_final: 0.7285 (mtp) REVERT: O 132 ASP cc_start: 0.8051 (t0) cc_final: 0.7730 (t0) REVERT: O 135 ASP cc_start: 0.8785 (p0) cc_final: 0.8272 (p0) REVERT: O 147 ASP cc_start: 0.8744 (m-30) cc_final: 0.8153 (m-30) REVERT: P 84 GLN cc_start: 0.8825 (mp10) cc_final: 0.8107 (mp10) REVERT: Q 10 PHE cc_start: 0.7236 (t80) cc_final: 0.6949 (t80) REVERT: Q 13 MET cc_start: 0.7996 (mtp) cc_final: 0.7635 (mtp) REVERT: Q 132 ASP cc_start: 0.7327 (t0) cc_final: 0.7086 (t0) REVERT: Q 135 ASP cc_start: 0.8607 (p0) cc_final: 0.8318 (p0) REVERT: R 32 GLN cc_start: 0.8202 (pt0) cc_final: 0.7985 (pt0) REVERT: R 103 ASN cc_start: 0.7660 (t0) cc_final: 0.7389 (t0) REVERT: R 104 GLN cc_start: 0.8423 (pp30) cc_final: 0.7351 (pp30) REVERT: R 132 ASP cc_start: 0.8425 (t0) cc_final: 0.8066 (t0) REVERT: R 134 ASP cc_start: 0.8356 (p0) cc_final: 0.7762 (p0) REVERT: R 140 ASN cc_start: 0.8304 (p0) cc_final: 0.7878 (t0) REVERT: R 147 ASP cc_start: 0.9100 (m-30) cc_final: 0.8831 (m-30) REVERT: R 177 PHE cc_start: 0.8153 (p90) cc_final: 0.7668 (p90) outliers start: 121 outliers final: 93 residues processed: 821 average time/residue: 0.2935 time to fit residues: 405.3007 Evaluate side-chains 812 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 716 time to evaluate : 2.855 ------------------------------------------------------------------------------- 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 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 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 165 GLU 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 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 51 LEU Chi-restraints excluded: chain F residue 67 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 155 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 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 155 VAL 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 51 LEU 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 196 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 198 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 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 O residue 33 GLN Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 67 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 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 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 165 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 8.9990 chunk 297 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 330 optimal weight: 9.9990 chunk 274 optimal weight: 10.0000 chunk 153 optimal weight: 50.0000 chunk 27 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 GLN L 126 GLN M 26 ASN ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 26 ASN ** P 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 126 GLN R 33 GLN R 126 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 25848 Z= 0.385 Angle : 0.772 10.827 35244 Z= 0.422 Chirality : 0.055 0.324 4464 Planarity : 0.004 0.055 4554 Dihedral : 5.865 25.042 3672 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.77 % Favored : 82.23 % Rotamer: Outliers : 5.45 % Allowed : 17.96 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.13), residues: 3546 helix: 0.30 (0.19), residues: 792 sheet: -0.20 (0.18), residues: 738 loop : -4.03 (0.11), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.003 PHE A 185 TYR 0.012 0.001 TYR N 100 ARG 0.002 0.000 ARG L 166 *********************** 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 857 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 705 time to evaluate : 2.463 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: 0.9007 (OUTLIER) cc_final: 0.8687 (tt) REVERT: A 84 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8621 (mp10) REVERT: A 132 ASP cc_start: 0.8596 (t0) cc_final: 0.8016 (t0) REVERT: A 147 ASP cc_start: 0.8885 (m-30) cc_final: 0.8585 (m-30) REVERT: B 154 ASP cc_start: 0.8092 (t0) cc_final: 0.7701 (t0) REVERT: C 66 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8476 (mt) REVERT: C 165 GLU cc_start: 0.7252 (pt0) cc_final: 0.7022 (pt0) REVERT: D 53 ASN cc_start: 0.8615 (p0) cc_final: 0.7918 (p0) REVERT: D 103 ASN cc_start: 0.7546 (t0) cc_final: 0.7085 (p0) REVERT: D 105 ASP cc_start: 0.9308 (t0) cc_final: 0.9006 (t0) REVERT: E 41 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7496 (mt-10) REVERT: F 32 GLN cc_start: 0.7924 (pt0) cc_final: 0.7604 (pt0) REVERT: F 53 ASN cc_start: 0.8613 (p0) cc_final: 0.8271 (p0) REVERT: F 104 GLN cc_start: 0.8483 (pp30) cc_final: 0.7640 (pp30) REVERT: F 132 ASP cc_start: 0.7924 (t0) cc_final: 0.7503 (t0) REVERT: F 134 ASP cc_start: 0.8609 (p0) cc_final: 0.8094 (p0) REVERT: F 147 ASP cc_start: 0.9062 (m-30) cc_final: 0.8729 (m-30) REVERT: G 84 GLN cc_start: 0.9134 (mt0) cc_final: 0.8780 (mt0) REVERT: G 132 ASP cc_start: 0.8046 (t0) cc_final: 0.7562 (t0) REVERT: G 198 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8866 (mp) REVERT: H 53 ASN cc_start: 0.8707 (p0) cc_final: 0.8376 (p0) REVERT: H 105 ASP cc_start: 0.9312 (t0) cc_final: 0.9095 (t0) REVERT: H 132 ASP cc_start: 0.8202 (t0) cc_final: 0.7831 (t0) REVERT: H 154 ASP cc_start: 0.8216 (t0) cc_final: 0.7832 (t0) REVERT: I 53 ASN cc_start: 0.8815 (p0) cc_final: 0.8539 (p0) REVERT: I 139 ASP cc_start: 0.6269 (t0) cc_final: 0.5951 (t0) REVERT: I 154 ASP cc_start: 0.7662 (t70) cc_final: 0.7320 (t0) REVERT: J 34 LYS cc_start: 0.8621 (tttp) cc_final: 0.8280 (ttmm) REVERT: J 134 ASP cc_start: 0.8561 (p0) cc_final: 0.8205 (p0) REVERT: K 11 ILE cc_start: 0.7965 (mt) cc_final: 0.7666 (mt) REVERT: K 53 ASN cc_start: 0.8689 (p0) cc_final: 0.8445 (p0) REVERT: K 132 ASP cc_start: 0.8333 (t0) cc_final: 0.8125 (t0) REVERT: L 33 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.6906 (pp30) REVERT: L 53 ASN cc_start: 0.7814 (p0) cc_final: 0.7473 (p0) REVERT: L 132 ASP cc_start: 0.8064 (t0) cc_final: 0.7514 (t0) REVERT: L 135 ASP cc_start: 0.8719 (p0) cc_final: 0.8451 (p0) REVERT: L 154 ASP cc_start: 0.8619 (t0) cc_final: 0.8325 (t0) REVERT: M 53 ASN cc_start: 0.8870 (p0) cc_final: 0.8492 (p0) REVERT: M 132 ASP cc_start: 0.7936 (t0) cc_final: 0.7452 (t0) REVERT: M 134 ASP cc_start: 0.8938 (p0) cc_final: 0.8360 (p0) REVERT: M 145 LYS cc_start: 0.8223 (mttt) cc_final: 0.8008 (mttt) REVERT: N 33 GLN cc_start: 0.7694 (tm-30) cc_final: 0.7418 (tm-30) REVERT: N 65 LYS cc_start: 0.9056 (pttt) cc_final: 0.8718 (ptmt) REVERT: N 66 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8342 (mp) REVERT: N 132 ASP cc_start: 0.8100 (t0) cc_final: 0.7688 (t0) REVERT: O 10 PHE cc_start: 0.7100 (t80) cc_final: 0.6690 (t80) REVERT: O 135 ASP cc_start: 0.8857 (p0) cc_final: 0.8276 (p0) REVERT: O 177 PHE cc_start: 0.7969 (p90) cc_final: 0.7581 (p90) REVERT: P 84 GLN cc_start: 0.8874 (mp10) cc_final: 0.8451 (mp10) REVERT: Q 13 MET cc_start: 0.8134 (mtp) cc_final: 0.7713 (mtp) REVERT: Q 135 ASP cc_start: 0.8558 (p0) cc_final: 0.8267 (p0) REVERT: R 74 ASN cc_start: 0.8831 (t0) cc_final: 0.8466 (t0) REVERT: R 103 ASN cc_start: 0.7447 (t0) cc_final: 0.7244 (t0) REVERT: R 104 GLN cc_start: 0.8340 (pp30) cc_final: 0.7124 (pp30) REVERT: R 132 ASP cc_start: 0.8515 (t0) cc_final: 0.8297 (t0) REVERT: R 134 ASP cc_start: 0.8276 (p0) cc_final: 0.7522 (p0) REVERT: R 177 PHE cc_start: 0.8174 (p90) cc_final: 0.7700 (p90) outliers start: 152 outliers final: 122 residues processed: 793 average time/residue: 0.3038 time to fit residues: 400.9760 Evaluate side-chains 825 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 697 time to evaluate : 2.698 ------------------------------------------------------------------------------- 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 41 GLU 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 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 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 85 THR 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 85 THR Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 GLU 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 46 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 112 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 51 LEU Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 170 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 177 PHE 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 97 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 155 VAL 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 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 165 GLU 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 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 85 THR Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 198 LEU 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 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 O residue 33 GLN Chi-restraints excluded: chain O residue 46 VAL 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 62 SER Chi-restraints excluded: chain P residue 88 MET Chi-restraints excluded: chain P residue 97 VAL 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 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 33 GLN Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 67 LEU Chi-restraints excluded: chain R residue 124 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 20.0000 chunk 37 optimal weight: 0.0010 chunk 188 optimal weight: 9.9990 chunk 241 optimal weight: 7.9990 chunk 187 optimal weight: 7.9990 chunk 278 optimal weight: 6.9990 chunk 184 optimal weight: 20.0000 chunk 329 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 200 optimal weight: 8.9990 chunk 152 optimal weight: 50.0000 overall best weight: 5.5994 ------------------------------------------------------------------------------- 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** ** N 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 33 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25848 Z= 0.283 Angle : 0.723 10.325 35244 Z= 0.396 Chirality : 0.054 0.287 4464 Planarity : 0.004 0.051 4554 Dihedral : 5.720 25.571 3672 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.23 % Favored : 84.77 % Rotamer: Outliers : 5.30 % Allowed : 19.82 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.13), residues: 3546 helix: 0.25 (0.19), residues: 828 sheet: -0.16 (0.19), residues: 738 loop : -4.06 (0.11), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.041 0.002 PHE N 185 TYR 0.012 0.001 TYR N 100 ARG 0.002 0.000 ARG L 166 *********************** 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 845 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 697 time to evaluate : 2.541 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 24 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8676 (tt) REVERT: A 84 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8585 (mp10) REVERT: A 132 ASP cc_start: 0.8583 (t0) cc_final: 0.7931 (t0) REVERT: A 147 ASP cc_start: 0.8873 (m-30) cc_final: 0.8580 (m-30) REVERT: A 198 LEU cc_start: 0.8839 (mp) cc_final: 0.8626 (mt) REVERT: B 154 ASP cc_start: 0.8065 (t0) cc_final: 0.7836 (t0) REVERT: C 66 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8466 (mt) REVERT: D 53 ASN cc_start: 0.8675 (p0) cc_final: 0.8032 (p0) REVERT: D 103 ASN cc_start: 0.7564 (t0) cc_final: 0.7100 (p0) REVERT: D 105 ASP cc_start: 0.9296 (t0) cc_final: 0.8985 (t0) REVERT: E 41 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7646 (mt-10) REVERT: F 32 GLN cc_start: 0.7921 (pt0) cc_final: 0.7594 (pt0) REVERT: F 53 ASN cc_start: 0.8594 (p0) cc_final: 0.8255 (p0) REVERT: F 104 GLN cc_start: 0.8555 (pp30) cc_final: 0.7708 (pp30) REVERT: F 132 ASP cc_start: 0.8035 (t0) cc_final: 0.7565 (t0) REVERT: F 134 ASP cc_start: 0.8531 (p0) cc_final: 0.7924 (p0) REVERT: F 147 ASP cc_start: 0.9061 (m-30) cc_final: 0.8725 (m-30) REVERT: G 84 GLN cc_start: 0.9025 (mt0) cc_final: 0.8786 (mt0) REVERT: G 132 ASP cc_start: 0.7895 (t0) cc_final: 0.7508 (t0) REVERT: G 177 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7834 (p90) REVERT: G 198 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8783 (mp) REVERT: H 53 ASN cc_start: 0.8667 (p0) cc_final: 0.8332 (p0) REVERT: H 105 ASP cc_start: 0.9247 (t0) cc_final: 0.9030 (t0) REVERT: H 132 ASP cc_start: 0.8152 (t0) cc_final: 0.7772 (t0) REVERT: H 154 ASP cc_start: 0.8151 (t0) cc_final: 0.7830 (t0) REVERT: I 53 ASN cc_start: 0.8787 (p0) cc_final: 0.8527 (p0) REVERT: I 65 LYS cc_start: 0.8734 (pttm) cc_final: 0.8418 (ptpt) REVERT: I 139 ASP cc_start: 0.6243 (t0) cc_final: 0.5955 (t0) REVERT: J 134 ASP cc_start: 0.8603 (p0) cc_final: 0.8219 (p0) REVERT: K 11 ILE cc_start: 0.7943 (mt) cc_final: 0.7664 (mt) REVERT: K 94 LYS cc_start: 0.7794 (mttt) cc_final: 0.7554 (mttt) REVERT: K 132 ASP cc_start: 0.8348 (t0) cc_final: 0.8147 (t0) REVERT: L 33 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6891 (pp30) REVERT: L 53 ASN cc_start: 0.7801 (p0) cc_final: 0.7451 (p0) REVERT: L 132 ASP cc_start: 0.7927 (t0) cc_final: 0.7390 (t0) REVERT: L 135 ASP cc_start: 0.8725 (p0) cc_final: 0.8429 (p0) REVERT: L 154 ASP cc_start: 0.8577 (t0) cc_final: 0.8234 (t0) REVERT: M 53 ASN cc_start: 0.8844 (p0) cc_final: 0.8458 (p0) REVERT: M 132 ASP cc_start: 0.7910 (t0) cc_final: 0.7428 (t0) REVERT: M 134 ASP cc_start: 0.8885 (p0) cc_final: 0.8327 (p0) REVERT: M 145 LYS cc_start: 0.8158 (mttt) cc_final: 0.7911 (mttt) REVERT: N 65 LYS cc_start: 0.8968 (pttt) cc_final: 0.8650 (ptmt) REVERT: N 66 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8253 (mp) REVERT: N 132 ASP cc_start: 0.8107 (t0) cc_final: 0.7632 (t0) REVERT: N 154 ASP cc_start: 0.8651 (t0) cc_final: 0.8346 (t0) REVERT: N 184 SER cc_start: 0.8943 (t) cc_final: 0.8696 (m) REVERT: O 131 GLN cc_start: 0.8143 (tt0) cc_final: 0.7826 (tt0) REVERT: O 147 ASP cc_start: 0.8316 (m-30) cc_final: 0.8099 (m-30) REVERT: O 177 PHE cc_start: 0.7952 (p90) cc_final: 0.7613 (p90) REVERT: P 55 ILE cc_start: 0.8951 (mt) cc_final: 0.8721 (mp) REVERT: P 84 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8497 (mp10) REVERT: P 184 SER cc_start: 0.8842 (t) cc_final: 0.8086 (p) REVERT: Q 13 MET cc_start: 0.8112 (mtp) cc_final: 0.7737 (mtp) REVERT: R 74 ASN cc_start: 0.8816 (t0) cc_final: 0.8476 (t0) REVERT: R 103 ASN cc_start: 0.7463 (t0) cc_final: 0.7237 (t0) REVERT: R 104 GLN cc_start: 0.8361 (pp30) cc_final: 0.7223 (pp30) REVERT: R 132 ASP cc_start: 0.8417 (t0) cc_final: 0.8048 (t0) REVERT: R 134 ASP cc_start: 0.8292 (p0) cc_final: 0.7695 (p0) REVERT: R 177 PHE cc_start: 0.8274 (p90) cc_final: 0.7861 (p90) outliers start: 148 outliers final: 128 residues processed: 789 average time/residue: 0.2936 time to fit residues: 387.2374 Evaluate side-chains 824 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 688 time to evaluate : 2.697 ------------------------------------------------------------------------------- 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 41 GLU Chi-restraints excluded: chain A residue 45 GLN 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 112 SER Chi-restraints excluded: chain A residue 195 LEU 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 129 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 177 PHE 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 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 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 140 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 GLU 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 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 31 LEU Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 74 ASN 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 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 G residue 174 GLN Chi-restraints excluded: chain G residue 177 PHE 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 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 131 GLN 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 177 PHE 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 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 124 THR Chi-restraints excluded: chain K residue 139 ASP 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 85 THR Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 198 LEU 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 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 33 GLN Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 67 LEU 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 62 SER Chi-restraints excluded: chain P residue 84 GLN 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 34 LYS 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 140 ASN Chi-restraints excluded: chain R residue 152 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 64 optimal weight: 0.0870 chunk 63 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- 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** E 131 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 ASN M 140 ASN N 84 GLN ** N 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 131 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3758 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= 0.218 Angle : 0.683 10.066 35244 Z= 0.373 Chirality : 0.053 0.276 4464 Planarity : 0.004 0.055 4554 Dihedral : 5.402 23.946 3672 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.96 % Favored : 84.04 % Rotamer: Outliers : 4.95 % Allowed : 20.75 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.13), residues: 3546 helix: 0.46 (0.19), residues: 828 sheet: -0.04 (0.19), residues: 738 loop : -3.98 (0.11), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.036 0.002 PHE N 185 TYR 0.011 0.001 TYR N 100 ARG 0.001 0.000 ARG L 166 *********************** 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 852 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 714 time to evaluate : 2.735 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: 0.9026 (OUTLIER) cc_final: 0.8681 (tt) REVERT: A 84 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8629 (mp10) REVERT: A 132 ASP cc_start: 0.8539 (t0) cc_final: 0.8087 (t0) REVERT: A 147 ASP cc_start: 0.8871 (m-30) cc_final: 0.8490 (m-30) REVERT: B 154 ASP cc_start: 0.8054 (t0) cc_final: 0.7833 (t0) REVERT: C 55 ILE cc_start: 0.9147 (mt) cc_final: 0.8903 (mp) REVERT: C 66 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8496 (mt) REVERT: D 53 ASN cc_start: 0.8669 (p0) cc_final: 0.8099 (p0) REVERT: D 103 ASN cc_start: 0.7519 (t0) cc_final: 0.7118 (p0) REVERT: D 105 ASP cc_start: 0.9312 (t0) cc_final: 0.9005 (t0) REVERT: E 41 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7665 (mt-10) REVERT: F 32 GLN cc_start: 0.7993 (pt0) cc_final: 0.7704 (pt0) REVERT: F 53 ASN cc_start: 0.8484 (p0) cc_final: 0.8175 (p0) REVERT: F 104 GLN cc_start: 0.8556 (pp30) cc_final: 0.7744 (pp30) REVERT: F 132 ASP cc_start: 0.7943 (t0) cc_final: 0.7603 (t0) REVERT: F 134 ASP cc_start: 0.8455 (p0) cc_final: 0.8005 (p0) REVERT: F 147 ASP cc_start: 0.9064 (m-30) cc_final: 0.8823 (m-30) REVERT: G 84 GLN cc_start: 0.9051 (mt0) cc_final: 0.8787 (mt0) REVERT: G 132 ASP cc_start: 0.7833 (t0) cc_final: 0.7499 (t0) REVERT: G 177 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7846 (p90) REVERT: G 198 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8769 (mp) REVERT: H 53 ASN cc_start: 0.8601 (p0) cc_final: 0.8350 (p0) REVERT: H 132 ASP cc_start: 0.8099 (t0) cc_final: 0.7780 (t0) REVERT: H 154 ASP cc_start: 0.8068 (t0) cc_final: 0.7798 (t0) REVERT: I 53 ASN cc_start: 0.8762 (p0) cc_final: 0.8495 (p0) REVERT: I 139 ASP cc_start: 0.6571 (t0) cc_final: 0.6261 (t0) REVERT: J 30 PHE cc_start: 0.7565 (t80) cc_final: 0.6945 (t80) REVERT: J 34 LYS cc_start: 0.8589 (tttp) cc_final: 0.8187 (ttmm) REVERT: J 104 GLN cc_start: 0.8103 (pp30) cc_final: 0.7073 (pp30) REVERT: J 134 ASP cc_start: 0.8575 (p0) cc_final: 0.8176 (p0) REVERT: K 53 ASN cc_start: 0.8608 (p0) cc_final: 0.8380 (p0) REVERT: K 94 LYS cc_start: 0.7832 (mttt) cc_final: 0.7594 (mttt) REVERT: L 33 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6620 (pp30) REVERT: L 53 ASN cc_start: 0.7792 (p0) cc_final: 0.7454 (p0) REVERT: L 132 ASP cc_start: 0.7903 (t0) cc_final: 0.7371 (t0) REVERT: L 135 ASP cc_start: 0.8733 (p0) cc_final: 0.8421 (p0) REVERT: M 53 ASN cc_start: 0.8799 (p0) cc_final: 0.8428 (p0) REVERT: M 132 ASP cc_start: 0.7874 (t0) cc_final: 0.7276 (t0) REVERT: M 134 ASP cc_start: 0.8822 (p0) cc_final: 0.8270 (p0) REVERT: M 145 LYS cc_start: 0.8112 (mttt) cc_final: 0.7831 (mttt) REVERT: M 147 ASP cc_start: 0.9375 (m-30) cc_final: 0.9149 (m-30) REVERT: N 65 LYS cc_start: 0.8935 (pttt) cc_final: 0.8588 (ptmt) REVERT: N 66 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8244 (mp) REVERT: N 84 GLN cc_start: 0.8497 (mt0) cc_final: 0.8227 (mt0) REVERT: N 104 GLN cc_start: 0.8581 (pp30) cc_final: 0.8155 (pp30) REVERT: N 132 ASP cc_start: 0.8151 (t0) cc_final: 0.7651 (t0) REVERT: N 154 ASP cc_start: 0.8574 (t0) cc_final: 0.8329 (t0) REVERT: P 84 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8498 (mp10) REVERT: P 184 SER cc_start: 0.8841 (t) cc_final: 0.8097 (p) REVERT: Q 10 PHE cc_start: 0.7301 (t80) cc_final: 0.6984 (t80) REVERT: Q 13 MET cc_start: 0.8068 (mtp) cc_final: 0.7710 (mtp) REVERT: R 66 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8151 (mp) REVERT: R 74 ASN cc_start: 0.8781 (t0) cc_final: 0.8483 (t0) REVERT: R 103 ASN cc_start: 0.7471 (t0) cc_final: 0.7221 (t0) REVERT: R 104 GLN cc_start: 0.8386 (pp30) cc_final: 0.7256 (pp30) REVERT: R 132 ASP cc_start: 0.8415 (t0) cc_final: 0.8074 (t0) REVERT: R 134 ASP cc_start: 0.8295 (p0) cc_final: 0.7706 (p0) REVERT: R 177 PHE cc_start: 0.8452 (p90) cc_final: 0.7898 (p90) outliers start: 138 outliers final: 113 residues processed: 806 average time/residue: 0.2966 time to fit residues: 400.6670 Evaluate side-chains 826 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 704 time to evaluate : 2.572 ------------------------------------------------------------------------------- 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 45 GLN 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 174 GLN Chi-restraints excluded: chain A residue 195 LEU 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 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 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 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 140 ASN 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 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 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 51 LEU Chi-restraints excluded: chain F residue 74 ASN 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 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 G residue 177 PHE 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 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 131 GLN Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 165 GLU Chi-restraints excluded: chain I residue 183 ILE 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 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 124 THR Chi-restraints excluded: chain K residue 139 ASP 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 L residue 198 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 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 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 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 62 SER Chi-restraints excluded: chain P residue 84 GLN 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 34 LYS Chi-restraints excluded: chain Q residue 45 GLN Chi-restraints excluded: chain Q residue 50 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 140 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 9.9990 chunk 315 optimal weight: 9.9990 chunk 288 optimal weight: 6.9990 chunk 307 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 chunk 133 optimal weight: 50.0000 chunk 241 optimal weight: 7.9990 chunk 94 optimal weight: 0.0370 chunk 277 optimal weight: 6.9990 chunk 290 optimal weight: 9.9990 chunk 306 optimal weight: 10.0000 overall best weight: 6.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN J 53 ASN ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 131 GLN R 92 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25848 Z= 0.317 Angle : 0.752 11.499 35244 Z= 0.412 Chirality : 0.055 0.269 4464 Planarity : 0.004 0.058 4554 Dihedral : 5.713 24.821 3672 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 17.26 % Favored : 82.71 % Rotamer: Outliers : 5.63 % Allowed : 20.97 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.13), residues: 3546 helix: 0.51 (0.20), residues: 810 sheet: -0.16 (0.18), residues: 738 loop : -3.95 (0.11), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.041 0.002 PHE N 185 TYR 0.011 0.001 TYR N 100 ARG 0.002 0.000 ARG A 166 *********************** 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 855 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 698 time to evaluate : 2.597 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 24 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8641 (tt) REVERT: A 84 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8577 (mp10) REVERT: A 86 LYS cc_start: 0.8362 (mmtt) cc_final: 0.7942 (mmtt) REVERT: A 132 ASP cc_start: 0.8622 (t0) cc_final: 0.8007 (t0) REVERT: A 147 ASP cc_start: 0.8791 (m-30) cc_final: 0.8532 (m-30) REVERT: B 154 ASP cc_start: 0.8163 (t0) cc_final: 0.7921 (t0) REVERT: C 66 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8509 (mt) REVERT: D 53 ASN cc_start: 0.8757 (p0) cc_final: 0.8094 (p0) REVERT: D 103 ASN cc_start: 0.7685 (t0) cc_final: 0.7211 (p0) REVERT: D 166 ARG cc_start: 0.7392 (mtt90) cc_final: 0.7072 (mtt90) REVERT: E 41 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7653 (mt-10) REVERT: F 10 PHE cc_start: 0.7388 (t80) cc_final: 0.7087 (t80) REVERT: F 32 GLN cc_start: 0.7917 (pt0) cc_final: 0.7605 (pt0) REVERT: F 53 ASN cc_start: 0.8526 (p0) cc_final: 0.8134 (p0) REVERT: F 104 GLN cc_start: 0.8631 (pp30) cc_final: 0.7786 (pp30) REVERT: F 132 ASP cc_start: 0.7909 (t0) cc_final: 0.7510 (t0) REVERT: F 134 ASP cc_start: 0.8545 (p0) cc_final: 0.8000 (p0) REVERT: F 147 ASP cc_start: 0.9073 (m-30) cc_final: 0.8747 (m-30) REVERT: F 162 GLU cc_start: 0.5422 (pm20) cc_final: 0.4862 (pm20) REVERT: G 84 GLN cc_start: 0.9133 (mt0) cc_final: 0.8870 (mt0) REVERT: G 132 ASP cc_start: 0.7987 (t0) cc_final: 0.7588 (t0) REVERT: G 177 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7859 (p90) REVERT: G 198 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8888 (mp) REVERT: H 53 ASN cc_start: 0.8667 (p0) cc_final: 0.8342 (p0) REVERT: H 132 ASP cc_start: 0.8156 (t0) cc_final: 0.7857 (t0) REVERT: H 154 ASP cc_start: 0.8120 (t0) cc_final: 0.7788 (t0) REVERT: I 53 ASN cc_start: 0.8791 (p0) cc_final: 0.8509 (p0) REVERT: I 65 LYS cc_start: 0.8730 (pttm) cc_final: 0.8441 (ptpt) REVERT: I 139 ASP cc_start: 0.6598 (t0) cc_final: 0.6307 (t0) REVERT: J 30 PHE cc_start: 0.7739 (t80) cc_final: 0.7059 (t80) REVERT: J 34 LYS cc_start: 0.8611 (tttp) cc_final: 0.8206 (ttmm) REVERT: J 104 GLN cc_start: 0.8097 (pp30) cc_final: 0.7070 (pp30) REVERT: J 134 ASP cc_start: 0.8601 (p0) cc_final: 0.8191 (p0) REVERT: K 53 ASN cc_start: 0.8679 (p0) cc_final: 0.8477 (p0) REVERT: K 84 GLN cc_start: 0.9084 (mp10) cc_final: 0.8801 (mp10) REVERT: K 132 ASP cc_start: 0.8452 (t0) cc_final: 0.8206 (t0) REVERT: L 33 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.6875 (pp30) REVERT: L 53 ASN cc_start: 0.7867 (p0) cc_final: 0.7490 (p0) REVERT: L 132 ASP cc_start: 0.7952 (t0) cc_final: 0.7416 (t0) REVERT: L 135 ASP cc_start: 0.8719 (p0) cc_final: 0.8377 (p0) REVERT: L 154 ASP cc_start: 0.8551 (t0) cc_final: 0.8249 (t0) REVERT: M 132 ASP cc_start: 0.7789 (t0) cc_final: 0.7268 (t0) REVERT: M 134 ASP cc_start: 0.8808 (p0) cc_final: 0.8239 (p0) REVERT: M 145 LYS cc_start: 0.8127 (mttt) cc_final: 0.7832 (mttt) REVERT: N 65 LYS cc_start: 0.8937 (pttt) cc_final: 0.8586 (ptmt) REVERT: N 66 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8279 (mp) REVERT: N 132 ASP cc_start: 0.8074 (t0) cc_final: 0.7681 (t0) REVERT: N 154 ASP cc_start: 0.8633 (t0) cc_final: 0.8309 (t0) REVERT: O 10 PHE cc_start: 0.7071 (t80) cc_final: 0.6548 (t80) REVERT: O 145 LYS cc_start: 0.9105 (ttpp) cc_final: 0.8673 (tmtt) REVERT: O 177 PHE cc_start: 0.7938 (p90) cc_final: 0.7586 (p90) REVERT: P 55 ILE cc_start: 0.9017 (mt) cc_final: 0.8807 (mp) REVERT: P 84 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8514 (mp10) REVERT: P 184 SER cc_start: 0.8932 (t) cc_final: 0.8266 (p) REVERT: Q 13 MET cc_start: 0.8103 (mtp) cc_final: 0.7743 (mtp) REVERT: R 66 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8168 (mp) REVERT: R 74 ASN cc_start: 0.8811 (t0) cc_final: 0.8483 (t0) REVERT: R 104 GLN cc_start: 0.8358 (pp30) cc_final: 0.7262 (pp30) REVERT: R 132 ASP cc_start: 0.8560 (t0) cc_final: 0.8118 (t0) REVERT: R 134 ASP cc_start: 0.8226 (p0) cc_final: 0.7621 (p0) REVERT: R 177 PHE cc_start: 0.8472 (p90) cc_final: 0.7935 (p90) outliers start: 157 outliers final: 129 residues processed: 794 average time/residue: 0.3069 time to fit residues: 406.7681 Evaluate side-chains 830 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 692 time to evaluate : 2.795 ------------------------------------------------------------------------------- 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 26 ASN Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 45 GLN 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 195 LEU 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 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 66 LEU Chi-restraints excluded: chain C residue 85 THR 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 85 THR Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 GLU 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 173 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 6 THR 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 74 ASN 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 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 177 PHE 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 155 VAL 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 131 GLN 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 183 ILE 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 53 ASN Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 165 GLU Chi-restraints excluded: chain J residue 195 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 124 THR Chi-restraints excluded: chain K residue 139 ASP 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 84 GLN Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 198 LEU 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 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 6 THR 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 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 84 GLN 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 34 LYS 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 140 ASN Chi-restraints excluded: chain R residue 152 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 20.0000 chunk 324 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 225 optimal weight: 0.9990 chunk 340 optimal weight: 10.0000 chunk 313 optimal weight: 8.9990 chunk 271 optimal weight: 30.0000 chunk 28 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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** E 131 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN K 33 GLN M 140 ASN N 84 GLN ** N 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 131 GLN R 92 ASN R 174 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25848 Z= 0.279 Angle : 0.738 11.222 35244 Z= 0.404 Chirality : 0.055 0.275 4464 Planarity : 0.004 0.057 4554 Dihedral : 5.669 23.904 3672 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.50 % Favored : 83.50 % Rotamer: Outliers : 5.05 % Allowed : 21.79 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.13), residues: 3546 helix: 0.50 (0.19), residues: 828 sheet: -0.17 (0.18), residues: 738 loop : -4.03 (0.11), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.040 0.002 PHE J 185 TYR 0.011 0.001 TYR N 100 ARG 0.002 0.000 ARG A 166 ********************** 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 844 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 703 time to evaluate : 2.563 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: 0.9154 (OUTLIER) cc_final: 0.8577 (mp10) REVERT: A 86 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8126 (mmtt) REVERT: A 98 LEU cc_start: 0.9369 (mt) cc_final: 0.9155 (mp) REVERT: A 132 ASP cc_start: 0.8612 (t0) cc_final: 0.7983 (t0) REVERT: A 147 ASP cc_start: 0.8788 (m-30) cc_final: 0.8528 (m-30) REVERT: B 154 ASP cc_start: 0.8139 (t0) cc_final: 0.7867 (t0) REVERT: C 66 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8501 (mt) REVERT: D 53 ASN cc_start: 0.8737 (p0) cc_final: 0.8086 (p0) REVERT: D 103 ASN cc_start: 0.7691 (t0) cc_final: 0.7213 (p0) REVERT: D 166 ARG cc_start: 0.7382 (mtt90) cc_final: 0.7100 (mtt90) REVERT: E 41 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7648 (mt-10) REVERT: F 10 PHE cc_start: 0.7372 (t80) cc_final: 0.7115 (t80) REVERT: F 13 MET cc_start: 0.7486 (mtt) cc_final: 0.7188 (mtp) REVERT: F 32 GLN cc_start: 0.7890 (pt0) cc_final: 0.7591 (pt0) REVERT: F 53 ASN cc_start: 0.8519 (p0) cc_final: 0.8176 (p0) REVERT: F 104 GLN cc_start: 0.8621 (pp30) cc_final: 0.7776 (pp30) REVERT: F 132 ASP cc_start: 0.7999 (t0) cc_final: 0.7613 (t0) REVERT: F 134 ASP cc_start: 0.8508 (p0) cc_final: 0.7957 (p0) REVERT: F 147 ASP cc_start: 0.9061 (m-30) cc_final: 0.8747 (m-30) REVERT: F 162 GLU cc_start: 0.5402 (pm20) cc_final: 0.4868 (pm20) REVERT: G 84 GLN cc_start: 0.9109 (mt0) cc_final: 0.8874 (mt0) REVERT: G 132 ASP cc_start: 0.7963 (t0) cc_final: 0.7580 (t0) REVERT: G 177 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7849 (p90) REVERT: G 198 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8839 (mp) REVERT: H 53 ASN cc_start: 0.8645 (p0) cc_final: 0.8323 (p0) REVERT: H 132 ASP cc_start: 0.8178 (t0) cc_final: 0.7952 (t0) REVERT: H 154 ASP cc_start: 0.8084 (t0) cc_final: 0.7771 (t0) REVERT: H 191 TYR cc_start: 0.8552 (m-80) cc_final: 0.8341 (m-80) REVERT: I 53 ASN cc_start: 0.8778 (p0) cc_final: 0.8495 (p0) REVERT: I 139 ASP cc_start: 0.6495 (t0) cc_final: 0.6219 (t0) REVERT: J 30 PHE cc_start: 0.7767 (t80) cc_final: 0.7082 (t80) REVERT: J 34 LYS cc_start: 0.8596 (tttp) cc_final: 0.8212 (ttmm) REVERT: J 104 GLN cc_start: 0.8083 (pp30) cc_final: 0.7071 (pp30) REVERT: J 134 ASP cc_start: 0.8583 (p0) cc_final: 0.8167 (p0) REVERT: K 53 ASN cc_start: 0.8666 (p0) cc_final: 0.8463 (p0) REVERT: K 84 GLN cc_start: 0.9094 (mp10) cc_final: 0.8808 (mp10) REVERT: K 132 ASP cc_start: 0.8426 (t0) cc_final: 0.8185 (t0) REVERT: L 33 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6806 (pp30) REVERT: L 53 ASN cc_start: 0.7841 (p0) cc_final: 0.7465 (p0) REVERT: L 132 ASP cc_start: 0.7939 (t0) cc_final: 0.7401 (t0) REVERT: L 135 ASP cc_start: 0.8725 (p0) cc_final: 0.8390 (p0) REVERT: L 154 ASP cc_start: 0.8525 (t0) cc_final: 0.8213 (t0) REVERT: M 53 ASN cc_start: 0.8782 (p0) cc_final: 0.8370 (p0) REVERT: M 132 ASP cc_start: 0.7674 (t0) cc_final: 0.7317 (t0) REVERT: M 134 ASP cc_start: 0.8764 (p0) cc_final: 0.8190 (p0) REVERT: M 154 ASP cc_start: 0.8265 (t70) cc_final: 0.7719 (t0) REVERT: N 65 LYS cc_start: 0.8939 (pttt) cc_final: 0.8585 (ptmt) REVERT: N 66 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8251 (mp) REVERT: N 132 ASP cc_start: 0.8091 (t0) cc_final: 0.7622 (t0) REVERT: N 154 ASP cc_start: 0.8594 (t0) cc_final: 0.8300 (t0) REVERT: O 145 LYS cc_start: 0.9118 (ttpp) cc_final: 0.8658 (tmtt) REVERT: O 177 PHE cc_start: 0.7923 (p90) cc_final: 0.7583 (p90) REVERT: O 195 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6630 (mm) REVERT: P 55 ILE cc_start: 0.9001 (mt) cc_final: 0.8790 (mp) REVERT: P 84 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8445 (mp10) REVERT: P 184 SER cc_start: 0.9009 (t) cc_final: 0.8358 (p) REVERT: Q 13 MET cc_start: 0.8074 (mtp) cc_final: 0.7755 (mtp) REVERT: Q 86 LYS cc_start: 0.7718 (mttm) cc_final: 0.7502 (mmtm) REVERT: R 66 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8141 (mp) REVERT: R 74 ASN cc_start: 0.8807 (t0) cc_final: 0.8478 (t0) REVERT: R 104 GLN cc_start: 0.8297 (pp30) cc_final: 0.7279 (pp30) REVERT: R 132 ASP cc_start: 0.8518 (t0) cc_final: 0.8095 (t0) REVERT: R 134 ASP cc_start: 0.8316 (p0) cc_final: 0.7736 (p0) outliers start: 141 outliers final: 126 residues processed: 790 average time/residue: 0.2890 time to fit residues: 380.8652 Evaluate side-chains 826 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 691 time to evaluate : 2.797 ------------------------------------------------------------------------------- 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 41 GLU Chi-restraints excluded: chain A residue 45 GLN 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 195 LEU 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 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 66 LEU Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 177 PHE 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 85 THR Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 GLU 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 173 VAL Chi-restraints excluded: chain E residue 190 SER Chi-restraints excluded: chain F residue 6 THR 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 74 ASN 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 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 177 PHE 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 155 VAL 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 131 GLN 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 183 ILE 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 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 124 THR Chi-restraints excluded: chain K residue 139 ASP 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 L residue 198 LEU 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 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 6 THR 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 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 84 GLN 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 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 34 LYS 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 92 ASN Chi-restraints excluded: chain R residue 140 ASN Chi-restraints excluded: chain R residue 152 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 4.9990 chunk 289 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 250 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 271 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 279 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN J 26 ASN K 33 GLN ** M 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 ASN ** N 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 174 GLN ** P 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 131 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.159656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.120801 restraints weight = 33972.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.124019 restraints weight = 23531.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.125312 restraints weight = 18329.513| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 25848 Z= 0.367 Angle : 0.788 11.838 35244 Z= 0.432 Chirality : 0.056 0.291 4464 Planarity : 0.004 0.059 4554 Dihedral : 5.884 25.114 3672 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 17.94 % Favored : 82.04 % Rotamer: Outliers : 5.30 % Allowed : 21.68 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.13), residues: 3546 helix: 0.50 (0.20), residues: 810 sheet: -0.32 (0.18), residues: 738 loop : -3.99 (0.11), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.044 0.003 PHE A 185 TYR 0.012 0.001 TYR I 70 ARG 0.002 0.000 ARG A 166 =============================================================================== Job complete usr+sys time: 6504.68 seconds wall clock time: 115 minutes 48.77 seconds (6948.77 seconds total)